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Genome Mapping and Genomics in Fishes and Aquatic Animals(2008). Edited by T.D. Kocher and C. Kole. 8 chapters, 180 pp. Springer-Verlag, Berlin. Link to Springer.com

Molecular Systematics of Fishes (1997). Edited by T.D. Kocher and C.A. Stepien. 17 chapters, 314 pp. Academic Press, San Diego. Link to Amazon.com



165. Zheng Q, Xiao H, Shi H, Wang T, Sun L, Tao W, Kocher TD, Li M, Wang D. Loss of Cyp11c1 causes delayed spermatogenesis due to absence of 11-ketotestosterone. J Endocrinol. 2020 Jan 1. pii: JOE-19-0438.R1. doi: 10.1530/JOE-19-0438. [Epub ahead of print](PDF)


164. Tao W, Shi H, Yang J, Diakite H, Kocher TD, Wang D. Homozygous mutation of foxh1 arrests oogenesis causing infertility in female Nile tilapia. Biol Reprod. Dec 14. pii: ioz225. doi: 10.1093/biolre/ioz225. [Epub ahead of print](PDF)

163. Clark FE, Kocher TD. Changing sex for selfish gain: B chromosomes of Lake Malawi cichlid fish. Sci Reports 9:20213.(PDF)

162. Kocher TD. Sex chromosomes and cichlid evolution. Buntbarsche Bulletin 300: 8-17. (PDF)

161. Carleton KL, Escobar-Camacho D, Kocher TD. Visual adaptation could aid sympatric speciation in a deep crater lake. Molecular Ecology (in press). (PDF)

160. Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Mol Ecol Resour. (PDF)

159. Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 8:1-20. (PDF)

158. Gammerdinger WJ, Conte MA, Sandkam BA, Penman DJ, Kocher TD. Characterization of sex chromosomes in three deeply diverged species of Pseudocrenilabrinae (Teleostei: Cichlidae). Hydrobiologia 832: 397-408. (PDF)


157. Clark F, Conte MA, Kocher TD. Genomic characterization of a B chromosome in Lake Malawi cichlid fishes. Genes 9:610.

156. Gammerdinger WJ, Kocher TD. Unusual diversity of sex chromosomes in African cichlid fishes. Genes 9:480.

155. Gammerdinger WJ, Conte MA, Sandkam BA, Penman DJ, Kocher TD. Characterization of sex chromosomes in three deeply diverged species of Pseudocrenilabrinae (Teleostei: Cichlidae). Hydrobiologia doi.org/10.1007/s10750-018-3778-6.

154. Gammerdinger WJ, Kocher TD. Understanding student perceptions and practices for pre-lecture content reading in the genetics classroom. J Microbiol Biol Educ 19(2). doi: 10.1128/jmbe.v19i2.1371.

153. Gammerdinger WJ, Conte MA, Sandkam BA, Ziegelbecker A, Koblmüller S, Kocher TD. Novel sex chromosomes in 3 cichlid fishes from Lake Tanganyika. J Hered 109(5):489-500.

152. Tao W, Chen J, Tan D, Yang J, Sun L, Wei J, Conte MA, Kocher TD, Wang D. Transcriptome display during tilapia sex determination and differentiation as revealed by RNA-Seq analysis. BMC Genomics 19(1):363. (PDF)


151. Conte MA, Gammerdinger WJ, Bartie KL, Penman DJ, Kocher TD. A high quality assembly of the Nile tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 18(1):341 (PDF)

150. Roberts RB, Moore EC, Kocher TD. An allelic series at pax7a underlies color polymorphism diversity in Lake Malawi cichlid fish. Molecular Ecology 26(10):2625-2639.

149. Clark FE, Conte MA, Ferreira-Bravo IA, Poletto AB, Martins C, Kocher TD. Dynamic sequence evolution of a sex-associated B chromosome in Lake Malawi cichlid fish. Journal of Heredity 108:53-62.


148. Gammerdinger WJ, Conte MA, Baroiller J-F, D’Cotta H, Kocher TD. Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron. BMC Genomics 17:808. (PDF)

147. Tao W, Sun L, Shi H, Cheng Y, Jiang D, Fu B, Conte MA, Gammerdinger WJ, Kocher TD, Wang D. Integrated analysis of miRNA and mRNA expression profiles in tilapia gonads at an early stage of sex differentiation. BMC Genomics 17:328. (PDF)

146. Valente G, Kocher T, Eickbush T, Simoes RP, Marins C. Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus. Mol Genet Genomics 291:1-7.


145. Li M, Sun Y, Zhao J, Shi H, Zeng S, Ye K, Jiang D, Zhou L, Sun L, Tao W, Nagahama Y, Kocher TD, Wang D. A tandem duplicate of anti-Müllerian hormone with a missense SNP on the Y chromosome is essential for male sex determination in Nile tilapia, Oreochromis niloticus. PLoS Genet 11:e1005678. (PDF)

144. Conte MA, Kocher TD. An improved genome reference for the African cichlid, Metriaclima zebra. BMC Genomics 16:724.(PDF)


143. Gammerdinger WJ, Conte MA, Acquah EA, Roberts RB, Kocher TD. Structure and Decay of a Proto-Y Region in Tilapia, Oreochromis niloticus. BMC Genomics. (PDF)

142. Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A,Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann, HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SC, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F. The genomic substrate for adaptive radiation in African cichlid fish. Nature 513:375-381. (PDF)

141. Valente GT, Conte MA, Fantinatti BEA, Cabral-de-Mello DC, Carvalho RF, Vicari MR, Kocher TD, Martins C. Origin and evolution of B chromosomes in the cichlid fish Astatotilapia latifasciata based on integrated genomic analyses. Molecular Biology and Evolution 31(8): 2061-2072. (PDF)


140. OQuin CT, Drilea AC, Conte MA, Kocher TD. Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra. BMC Genomics 14:287. (PDF)

139. Nikaido M, Suzuki H, Toyoda A, Fujiyama A, Hagino-Yamagishi K, Kocher TD, Carleton K, Okada N. Lineage-specific expansion of vomeronasal type 2 receptor-like (OlfC) genes in cichlids may contribute to diversification of amino acid detection systems. Genome Biol. Evol. 5:711-22. (PDF)

138. Loh, Y-H E, Bezault, E, Muenzel FM, Roberts RB, Swofford R, Barluenga M, Kidd CE, Howe AE, Di Palma F, Lindblad-Toh K, Hey J, Seehausen O, Salzburger W, Kocher TD, Streelman JT. Origins of shared genetic variation in African cichlids. Mol. Biol. Evol. 30:906-917. (PDF)

137. Shirak A, Palti Y, Bern O, Kocher TD, Gootwine E, Seroussi E, Hulata G, Ron M, Avtalion RR. A deleterious effect associated with UNH159 is attenuated in twin embryos of an inbred line of blue tilapia Oreochromis aureus. J. Fish Biology 82:42-53. (PDF)


136. Mazzuchelli J, Kocher TD, Yang F, Martins C. Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish. BMC Genomics 13:463. (PDF)

135. Guyon R, Rakotomanga M, Azzouzi N, Coutanceau JP, Bonillo C, D'Cotta H, Pepey E, Soler L, Rodier-Goud M, D'Hont A, Conte MA, van Bers NE, Penman DJ, Hitte C, Crooijmans RP, Kocher TD, Ozouf-Costaz C, Baroiller JF, Galibert F. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. BMC Genomics 13:222. (PDF)

134. OQuin CT, Drilea AC, Roberts RB, Kocher TD. A small number of genes underlie male pigmentation traits in Lake Malawi cichlids. JEZ Part B: Molecular and Developmental Evolution 318:199-208. (PDF)


133. Fujimura K, Conte MA, Kocher TD. Circular DNA intermediate in the duplication of Nile tilapia vasa genes. PLoS One 6:e29477. (PDF)

132. Fujimura K, Kocher TD. Tol2-mediated transgenesis in tilapia (Oreochromis niloticus). Aquaculture 319: 342-346. (PDF)

131. Roberts RB, Hu Y, Albertson RC, Kocher TD. Craniofacial divergence and ongoing adaptation via the hedgehog pathway. Proc. Natl. Acad. Sci. USA 108:13194-13199. (PDF)

130. Mazzuchelli J, Yang F, Kocher TD, Martins C. Comparative cytogenetic mapping of Sox2 and Sox14 in cichlid fishes and inferences on the genomic organization of both genes in vertebrates. Chromosome Research 19:657-667. (PDF)

129. Lee BY, Coutanceau JP, Ozouf-Costaz C, D'Cotta H, Baroiller JF, Kocher TD. Genetic and physical mapping of sex-linked AFLP markers in Nile tilapia (Oreochromis niloticus). Mar Biotechnol (NY) 13:557-562. (PDF)


128. Poletto AB, Ferreira IA, Cabral-de-Mello DC, Nakajima RT, Mazzuchelli J, Ribeiro HB, Venere, PC, Nirchio M, Kocher TD, Martins C.  2010.  Chromosome differentiation patterns during cichlid fish evolution.  BMC Genetics 11: 50. (PDF)

127. Lee BY, Howe AE, Conte MA, D’Cotta H, Pepey E, Baroiller J-F, di Palma F, Carleton KL, Kocher TD. An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags. BMC Genomics 11: 278. (PDF)

126. Ferreira IA, Poletto AB, Kocher TD, Mota-Velasco J, Penman DJ, Martins C. Chromosome evolution in African cichlid fish: contributions from the physical mapping of repeated DNAs. Cytogenetic and Genome Research 129: 314-322. (PDF)

125. Shirak A, Grabherr, Di Palma F, Lindblad-Toh K, Hulata G, Ron M, Kocher TD, Seroussi E. Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker. Marine Biotechnology (in press, DOI: 10.1007/s10126-009-9236-8). (PDF)

124. Ser J, Roberts RB, Kocher TD. Multiple interacting loci control sex determination in Lake Malawi cichlid fishes. Evolution 64: 486-501. (PDF)


123. Roberts RB, Ser J, Kocher TD. Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlids. Science 326: 998-1001. Access article free!


122. Cnaani A, Kocher TD. Sex-linked markers and microsatellite locus duplication in the cichlid species Oreochromis tanganicae. Biology Letters 4: 700-703. (PDF)

121. Loh, Y-H E, Katz, LS, Mims MC, Kocher TD, Yi S, Streelman JT. Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids. Genome Biology 9: R113. (PDF)

120. Shirak, A, Golik M, Lee, B-Y, Howe AE, Kocher TD, Hulata G, Ron M, Seroussi E. Copy number variation of lipocalin family genes for male-specific proteins in tilapia and its association with gender. Heredity 101: 405-415. (PDF)

119. Cnaani A, Lee BY, Zilberman N, Ozouf-Costaz C, Hulata F, Ron M, D’Hont A, Baroiller, J-F, D’Cotta H, Penman DJ, Tomasino E, Coutanceau J-P, Pepey E, Shirak A, Kocher TD. Genetics of sex determination in tilapiine species. Sexual Development 2: 43-54. (PDF)


118. Cnaani A, Lee BY, Ozouf-Costaz C, Kocher TD. Mapping of Sox2 and Sox14 in tilapia (Oreochromis spp.). Sexual Development 1: 207-210. (PDF)

117. Streelman JT, Albertson RC, Kocher TD. Variation in body size and trophic morphology within and among genetically differentiated populations of the cichlid fish, Metriaclima zebra, from Lake Malawi. Freshwater Biology 52: 525-538. (PDF)

116. Lee BY, Kocher TD. . Comparative genomics and positional cloning. Pp. 325-337 in J. Liu (ed.) Aquaculture Genome Technologies. Blackwell. (PDF)

115. Lee B-Y, Kocher TD. Exclusion of Wilms Tumor (WT1_2) and ovarian aromatase (CYP19A1) as candidates for sex determining genes in Nile tilapia (Oreochromis niloticus) Animal Genetics 38: 85 (PDF)

114. DiPalma F, Kidd C, Borowsky R, Kocher TD. Construction of bacterial artificial chromosome libraries for two model fish species: the Lake Malawi cichlid (Metriaclima zebra), and the blind cavefish (Astyanax mexicanus) Zebrafish 4: 41-47. (PDF)


113. Schliewen UK, Kocher TD, McKaye KR, Seehausen O, Tautz D. Evolutionary Biology: evidence for sympatric speciation? Nature 444: E12-3. (PDF)

112. Shirak A, Seroussi E, Cnaani A, Howe AE, Domokhovsky R, Zilberman N, Kocher TD, Hulata G, Ron M. Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within QTL regions for sex determination. Genetics 174(3): 1573-1581. (PDF)

111. Albertson RC, Kocher TD. Genetic and developmental basis of adaptive variation in the cichlid feeding apparatus. Heredity 97: 211-221. (PDF)

110. Kidd MR, Kidd CE, Kocher TD. Axes of differentiaion in the bower building cichlids of Lake Malawi. Molecular Ecology 15: 459-478. (PDF)

109. Kidd MR, Danley PD, Kocher TD. A direct assay of female choice in cichlid fishes: all the eggs in one basket. Journal of Fish Biology 68:373-384. (PDF)

108. Carleton KL, Spady TC, Kocher TD. Visual communication in East African cichlid fishes: diversity in a phylogenetic context. Pp. 485-515 in Communication in Fishes, F Ladich, SP Collin, P Moller and BG Kapoor, eds. Science Publishers Inc., Enfield NH.


107. Kocher TD. 2005. Fish models for studying adaptive evolution and speciation (Special Feature - Roundtable Discussion). Zebrafish 2(3): 147-156. (PDF)

106. Albertson RC, Streelman JT, Kocher TD, Yelick PC. Integration and evolution of the cichlid mandible: the molecular basis of alternate feeding strategies. Proc. Natl. Acad. Sci. USA 102:16287-16292. (PDF)

105. Katagiri T, Kidd C. Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD. A BAC-based physical map of the Nile tilapia genome. BMC Genomics 6:89. (PDF)

104. Kocher TD. Ghost of speciation past (News and Views). Nature 435: 29-30. (PDF)

103. Curole JP, Kocher TD. Evolution of a unique mitotype-specific protein-coding extennsion of the cytochrome c oxidase II gene in freshwater mussels (Bivalvia: Unionoida). J. Mol. Evol. 61(3):381-9. (PDF)

102. Spady TC, Seehausen O, Loew ER, Jordan RC, Kocher TD, Carleton KL. Adaptive molecular evolution in the opsin genes of rapidly speciating cichlid species. Molecular Biology and Evolution 22: 1412-1422. (PDF)

101. Lee BY, Lee WJ, Streelman JT, Carleton KL, Howe AE, Hulata G, Slettan A, Stern JE, Terai Y, Kocher TD. A second generation genetic linkage map of tilapia (Oreochromis spp.) Genetics 170: 237-244. (PDF)

100. Albertson RC, Kocher TD. Genetic architecture sets limits on transgressive segregation in hybrid cichlid fishes. Evolution 59: 686-690. (PDF)


99. Streelman JT, Gmyrek SL, Kidd MR, Kidd C, Robinson RL, Hert E, Ambali AJ, Kocher TD. Hybridization and contemporary evolution in an introduced cichlid fish from Lake Malawi National Park. Molecular Ecology 13:2471-2479. (PDF)

98. Kocher TD. Adaptive evolution and explosive speciation: the cichlid fish model. Nature Reviews Genetics 5: 288-298. (PDF)

97. Lee B-Y, Hulata G, Kocher TD. Two unlinked loci controlling the sex of blue tilapia (Oreochromis aureus). Heredity 92(6): 543-549. (PDF)


96. Cnaani A, Lee B-Y, Ron M, Hulata G, Kocher TD, and Seroussi E. Linkage mapping of major histocompatibilty complex class I loci in tilapia (Oreochromis spp.). Animal Genetics 34:390-391. (PDF)

95. Streelman JT, Albertson RC and Kocher TD. Genome mapping of the orange blotch color pattern in cichlid fishes. Molecular Ecology 12: 2465-2471. (Abstract) (PDF)

94. Streelman JT, Webb JF, Albertson RC and Kocher TD. The cusp of evolution and development: A model of cichlid tooth shape diversity. Evolution and Development 5: 600-608. (PDF)

93. Lee B-Y, Penman, DJ and Kocher TD. Identification of a sex-determining region in Nile tilapia (Oreochromis niloticus) using bulked segregant analysis. Animal Genetics 34(5): 379-383. (PDF)

92. Kocher TD. Evolutionary biology: Fractious phylogenies (News and Views). Nature 423: 489 - 491. (PDF)

91. Albertson RC, Streelman JT and Kocher TD. Genetic basis of adaptive shape differences in the cichlid head. J. Heredity 94(4):291-301. (Abstract) (PDF)

90. Albertson RC, Streelman JT and Kocher TD. Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. Proc. Natl. Acad. Sci. USA 100: 5252-5257. (Abstract) (PDF) (Commentary)

89. Carleton KL and Kocher TD. Evolutionary Genetics: Rose-colored goggles. (Commentary). Heredity 90:116-7. (Abstract) (PDF)


88. Rosel, P.E. and T.D. Kocher. DNA-based identification of larval cod in stomach contents of predatory fishes. J. Exp. Marine Biology and Ecology 267: 75-88. (Abstract) (PDF)

87. Kocher TD, Albertson RC, Carleton KL and Streelman JT. The genetic basis of biodiversity: genomic studies of cichlid fishes. pp. 35-44 in Aquatic Genomics: Steps Toward a Great Future, N. Shimizu, T. Aoki, I. Hirono and F. Takashima, Editors. Springer, Tokyo. (PDF)

86. Diller KC, Gilbert WA and Kocher TD. Selective sweeps in the human genome: a starting point for identifying genetic differences between modern humans and chimpanzees. Mol Biol Evol 19:2342-5. (Abstract) (PDF)

85. McKaye KR, Stauffer JR Jr, Van Den Berghe EP, Vivas R, Lopez Perez LJ, McCrary JK, Waid R, Konings A, Lee WJ and Kocher TD. 2002. Behavioral, Morphological and Genetic Evidence of Divergence of the Midas Cichlid Species Complex in Two Nicaraguan Crater Lakes. Cuadernos de la Investigacion de la UCA, volume 12; p 19-47. (PDF)

84. Curole JP and Kocher TD Ancient sex-specific extension of the cytochrome c oxidase II gene in bivalves and the fidelity of doubly-uniparental inheritance. Molecular Biology and Evolution 19(8):1323-8. (Abstract) (PDF)

83. Carleton, KL, Streelman JT, Lee BY, Garnhart N, Kidd M, and Kocher TD. Rapid isolation of CA microsatellites from the tilapia genome. Animal Genetics 33(2):140-4. (Abstract) (PDF)

82. Streelman, JT and Kocher TD. Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia. Physiological Genomics 9(1):1-4. (Abstract) (PDF)

81. Cnaani A, Ron M, Lee BY, Hulata G, Kocher TD, and Seroussi E. Mapping the transferrin gene in tilapia. Animal Genetics 33(1):78-80. (Abstract) (PDF)


80. Albertson RC and Kocher TD. Assessing morphological differences in an adaptive trait: a landmark-based morphometric approach. Journal of Experimental Zoology 289(6):385-403. (Abstract) (PDF)

79. Carleton KL and Kocher TD. Cone opsin genes of African cichlid fishes: tuning spectral sensitivity by differential gene expression. Molecular Biology and Evolution 18(8):1540-50. (Abstract) (PDF)

78. Danley PD and Kocher TD. Speciation in rapidly diverging systems: lessons from Lake Malawi. Molecular Ecology 10:1075-1086.(Abstract) (PDF)

77. Schliewen U, Rassmann K, Markmann M, Markert J, Kocher T and Tautz D. Genetic and ecological divergence of a monophyletic cichlid species pair under fully sympatric conditions in Lake Ejagham, Cameroon. Molecular Ecology 10(6):1471-1488. (Abstract) (PDF)


76. Danley PD, Markert JA, Arnegard ME, and Kocher TD. Divergence with gene flow in the rock-dwelling cichlids of Lake Malawi. Evolution 54(5):1725-37. (Abstract) (PDF)

75. Koh HS, Lee WJ and Kocher TD. The genetic relationships of two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis. Heredity 85(1):30-6. (Abstract) (PDF)

74. Streelman JT and Kocher TD. From phenotype to genotype. Evolution and Development 2:166-173. (Abstract) (PDF)

73. Carleton KL, Harosi FI, and Kocher TD. Visual pigments of African cichlid fishes: Evidence for ultraviolet vision from microspectrophotometry and DNA sequences. Vision Research 40: 879-890. (Abstract) (PDF)

72. Carter PA, Mitton JB, Kocher TD and Coelho JR. Maintenance of the alcohol dehydrogenase polymorphism in tiger salamanders, II. Differences in biochemical function among allozymes. Functional Ecology 14: 70-76. (PDF)


71. Rosel PE, France SC, Wang JY and Kocher TD. Genetic structure of harbour porpoise, Phocoena phocoena populations in northwest Atlantic based on mitochondrial and nuclear markers. Molecular Ecology 8:S41-S54. (Abstract) (PDF)

70. Curole JP and Kocher TD. Mitogenomics: digging deeper with complete mitochondrial genomes. Trends in Ecology and Evolution 14: 394-398. (Abstract) (PDF)

69. Albertson RC, Markert JA, Danley PD and Kocher TD. Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa. Proceedings of the National Academy of Sciences USA 96(9): 5107-5110.(Abstract) (PDF)

68. Arnegard ME, Markert JA, Danley PD, Stauffer JR Jr., Ambali AJ and Kocher TD. Population structure and colour variation of the cichlid fish Labeotropheus fuelleborni Ahl along a recently formed achipelago of rocky habitat patches in southern Lake Malawi. Proceedings Royal Society London B 266: 119-130. (PDF)

67. Markert, JA, Arnegard ME, Danley PD and Kocher TD. Biogeography and population genetics of the Lake Malawi cichlid Melanochromis auratus: habitat transience, philopatry and speciation. Mol. Ecol. 8(6): 1013-1026.(Abstract) (PDF)


66. Kellogg KA, Markert JA, Stauffer JR Jr. and Kocher TD. Intraspecific brood mixing and reduced polyandry in a maternal mouth-brooding cichlid. Behavioral Ecology 9(3): 309-312. (PDF)

65. Lee WJ and Kocher TD. Microsatellite mapping of the prolactin locus in the tilapia genome. Animal Genetics 29:68. (Abstract) (PDF)

64. Kocher TD, Lee WJ, Sobolewska H, Penman D and McAndrew B. A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus). Genetics 148:1225-1232. (Abstract) (PDF)


63. Litvaitis MK, Litvaitis JA, Lee WJ, and Kocher TD. Variation in the mitochondrial DNA of the Sylvilagus complex occupying the northeastern United States. Canadian Journal of Zoology 75:595-605. (PDF)

62. Stepien CA and Kocher TD. Molecules and morphology in studies of fish evolution. Pp. 1-11 in Molecular Systematics of Fishes, TD Kocher and CA Stepien (editors). Academic Press. (PDF)

61. Kocher TD and Carleton KL. Base substitution in fish mtDNA: patterns and rates. Pp. 13-24 in Molecular Systematics of Fishes, TD Kocher and CA Stepien (editors). Academic Press. (PDF)

60. Kocher, T.D. Linkage mapping of fishes using DNA markers. Proceedings of the First International Conference on Population Genetics and Aquaculture in Africa. CRO-ORSTOM, Abidjan, Ivory Coast.

59. Kocher, T.D. Status of linkage mapping in tilapia. Proceedings of the Aquaculture Species Genome Mapping Workshop, May 18-19, 1997, A. Alvarez-Warren and T.D. Kocher (eds). USDA Northeast Regional Aquaculture Center, University of Massachusetts, Dartmouth, MA.

58. Kocher, T.D. Introduction to the genetics of tilapia. pp. 61-64 in Fitzsimmons, K. (ed.), Tilapia Aquaculture: Proceedings from the Fourth International Symposium on Tilapia in Aquaculture. Northeast Regional Agricultural Engineering Service, Ithaca, NY.


57. France SC and Kocher TD. DNA sequencing of formalin-fixed crustaceans from archival research collections. Molecular Marine Biology and Biotechnology 5:304-313. (Abstract) (PDF)

56. France SC and Kocher TD. Geographic and bathymetric patterns of mitochondrial 16S rRNA sequence divergence among deep-sea amphipods, Eurythenes gryllus. Marine Biology 126:633-643. (PDF)

55. Litvaitis MK, Curini-Galletti MC, Martens PM, and Kocher TD. A reappraisal of the systematics of the Moncelididae (Platyhelminthes, Proseriata):inferences from rDNA sequences. Molecular Phylogenetics and Evolution 6(1):150-156. (Abstract) (PDF)

54. Perna NT and Kocher TD. Mitochondrial DNA: Molecular fossils in the nucleus. Current Biology 6: 128-129. (Abstract) (PDF)

53. France SC, Rosel PE, Agenbroad JE, Mullineaux LS and Kocher TD. DNA sequence variation of mitochondrial large-subunit rRNA provides support for a two subclass organization of the Anthozoa (Cnidaria). Molecular Marine Biology and Biotechnology 5(1): 15-28. (Abstract) (PDF)

52. Lee WJ, and Kocher TD. Microsatellite DNA markers for genetic mapping in the tilapia, Oreochromis niloticus. Journal of Fish Biology 49: 169-171. (PDF)

51. Bucklin A and Kocher TD. Source regions for recruitment of Calanus finmarchicus to Georges Bank: Evidence from molecular population genetic analysis of mtDNA. Deep-Sea Research II, 43:1665-1681. (PDF)


50. Rich SM, Caporale DA, Telford SR 3rd, Kocher TD, Hartl DL and Spielman A. Distribution of the Ixodes ricinus-like ticks of eastern North America. Proceedings of the National Academy of Sciences, USA 92(4): 6284-6288.. (Abstract) (PDF)

49. Stauffer JR Jr, Bowers NJ, Kocher TD and McKaye KR. Hybridization between Cynotilapia afra and Pseudotropheus zebra (Teleostei: Cichlidae) following an intralacustrine introduction in Lake Malawi, Africa. Copeia 1996: 203-208. (PDF)

48. Miller, H.G., T.D. Kocher and B. Loy. 1995. New MADS box domains in Asparagus officinalis L. Sex. Plant. Reprod. 8:318-320. (PDF)

47. Caporale DA, Rich SM, Spielman A, Telford SR 3rd and Kocher TD. Discriminating between Ixodes ticks by means of mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 4:361-365. (Abstract) (PDF)

46. Kocher TD, Conroy JA, McKaye KR, Stauffer JR and Lockwood SF. Evolution of the ND2 gene in East African cichlids. Molecular Phylogenetics and Evolution 4:420-432. (Abstract) (PDF)

45. Medeiros-Bergen D, Olson RR, Conroy JA and Kocher TD. Distribution of holothurian larvae determined with species-specific genetic probes. Limnology and Oceanography 40:1225-1236. (PDF)

44. Kellogg KA, Markert JA, Stauffer JR Jr and Kocher TD. Microsatellite variation demonstrates multiple paternity in lekking cichlid fishes from Lake Malawi, Africa. Proceedings Royal Society London Series B. 260:79-84. (PDF)

43. Perna NT and Kocher TD. Patterns of nucleotide composition at four-fold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution 41:353-358. (Abstract) (PDF)

42. Stauffer JR Jr, Bowers NJ, McKaye KR and Kocher TD. Evolutionary significant units among cichlid fishes: the role of behavioral studies. American Fisheries Society Symposia 17: 227-244. (PDF)

41. Lee WJ, Conroy J, Howell WH and Kocher TD. Structure and evolution of fish mitochondrial control regions. Journal of Molecular Evolution 41:54-66. (Abstract) (PDF)

40. Lee WJ and Kocher TD. Complete sequence of the sea lamprey (Petromyzon marinus) mitochondrial genome: a unique gene order and significance for the inference of early vertebrate phylogeny. Genetics 139:873-887. (Abstract) (PDF)

39. Perna NT and Kocher TD. Unequal base frequencies and the estimation of substitution rates. Molecular Biology and Evolution 12:359-361. (PDF)

38. Glasner JD, Kocher TD and Collins JJ. Caenorhabditis elegans contains genes encoding two new members of the Zn-containing alcohol dehydrogenase family. Journal of Molecular Evolution 41:46-53. (Abstract) (PDF)

37. Bucklin A, Frost BW, Miller CB and Kocher TD. Molecular systematics of six Calanus and three Metridia species (Calanoida; Copepoda). Marine Biology 121:655-664. (PDF)


36. Litvaitis MK, Nunn G, Thomas WK, and Kocher TD. A molecular approach for the identification of meiofaunal turbellarians (Platyhelminthes, Turbellaria). Marine Biology 120: 437-442. (PDF)

35. Caporale DA, Kocher TD, Smith RP, Rand PW, and Lacombe EH. OspB sequence variation of Borrelia burgdorferi along the coast of Maine. Pp. 175-180 in Lyme Borreliosis. J.S. Axford and D.H.E. Rees (eds). Plenum Press, NY. (PDF)

34. Bowers N, Stauffer JR, and Kocher TD. Intra- and interspecific mitochondrial DNA sequence variation within two species of rock-dwelling cichlids (Teleostei: Cichlidae) from Lake Malawi, Africa. Molecular Phylogenetics and Evolution 3:75-82. (Abstract) (PDF)

33. Caporale DA and Kocher TD. Sequence variation in the outer surface protein genes of Borrelia burgdorferi. Molecular Biology and Evolution 11:51-64. (Abstract) (PDF)


32. Xiong B and Kocher TD. Phylogeny of sibling species of Simulium venustum and S. vercundum complexes (Diptera: Simuliidae) based on sequences of the mitochondrial large ribosomal RNA gene. Molecular Phylogenetics and Evolution 2: 293-303. (Abstract) (PDF)

31. Thomas WK and Kocher TD. Sequencing of PCR-amplified DNAs. Methods in Enzymology 224:391-399. (Abstract) (PDF)

30. Kornegay JR, Kocher TD, Williams LA, and Wilson AC. Pathways of lysozyme evolution inferred from the sequences of cytochrome b in birds. Journal of Molecular Evolution 37:367-379. (Abstract) (PDF)

29. Hasegawa M, DiRienzo A, Kocher TD and Wilson AC. Toward a more accurate time scale for the human mitochondrial DNA tree. Journal of Molecular Evolution 37:347-354. (Abstract) (PDF)

28. Kocher TD, Conroy JA, McKaye KR and Stauffer JR. Similar morphologies of cichlids in lakes Tanganyika and Malawi are due to convergence. Molecular Phylogenetics and Evolution 2:158-165. (Abstract) (PDF)

27. Xiong B and Kocher TD. Intraspecific variation in sibling species of Simulium venustum and S. verecundum complexes (Diptera: Simulidae) revealed by the sequence of the mitochondrial large ribosomal RNA gene. Canadian Journal of Zoology 71:1202-1206. (PDF)


26. Bucklin A, Frost BW, Kocher TD. DNA sequence variation of the mitochondrial 16S rRNA in Calanus (Copepoda; Calanoida): intra- and interspecific patterns. Molecular Marine Biology and Biotechnology 1:397-407. (PDF)

25. Kocher TD. PCR, direct sequencing, and the comparative approach. PCR Methods and Applications 1:217-221. (Abstract) (PDF)


24. Runstadler JA and Kocher TD. A new antennapedia-class gene from the zebrafish. Nucleic Acids Research 19:5434. (Abstract) (PDF)

23. Olson RR, Runstadler JR, and Kocher TD. Whose larvae? Nature 351:357-358. (Abstract) (PDF)

22. Meyer A, Kocher TD and Wilson AC. African fishes. Nature 350:467-468. (PDF)

21. Kocher TD. The joy of systematics. Nature 349:290. (Book review). (PDF)

20. Xiong B and Kocher TD. Comparison of mitochondrial DNA sequences of seven morphospecies of black flies (Diptera: Simulidae). Genome 34:306-311. (Abstract) (PDF)

19. Irwin DM, Kocher TD and Wilson AC. Evolution of the cytochrome b gene of mammals. Journal of Molecular Evolution 32:128-144. (Abstract) (PDF)

18. Shields, G.F. and T.D. Kocher. Phylogenetic relationships of North American Ursids based on analysis of mitochondrial DNA. Evolution 45:218-221. (PDF)

17. Kocher TD and Wilson AC. Sequence evolution of mitochondrial DNA in humans and chimpanzees: control region and a protein-coding region. pp. 391-413 in Evolution of Life: Fossils, molecules, and culture, S. Osawa and T. Honjo (editors), Springer-Verlag, Tokyo. (PDF)

16. Kocher TD and Wilson AC. DNA amplification by the polymerase chain reaction. pp. 187-209 in Essential Molecular Biology, Volume 2. T.A. Brown (ed.) Oxford University Press. (PDF)


15. Meyer A, Kocher TD, Basaibwaki P and Wilson AC. Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347:550-553. (Abstract) (PDF)

14. Simon C, Paabo S, Kocher TD and Wilson AC. Evolution of mitochondrial ribosomal RNA in insects as shown by the polymerase chain reaction. in Molecular Evolution, M. Clegg and S. Clark (eds.). UCLA Symposia on Molecular and Cellular Biology, New Series 122:235-244. (PDF)


13. Vigilant L, Pennington R, Harpending H, Kocher TD and Wilson AC. Mitochondrial DNA sequences in single hairs from a Southern African population. Proceedings of the National Academy of Sciences, USA 86:9350-9354. (Abstract) (PDF)

12. Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX and Wilson AC. Dynamics of mitochondrial DNA sequence evolution in animals. Proceedings of the National Academy of Sciences, USA 86:6196-6200. (Abstract) (PDF)

11. Kocher TD and White TJ. Evolutionary Analysis. pp. 137-147 in PCR Technology: Principles and Applications for DNA Amplification, H. Erlich (ed.). Stockton Press, New York. (PDF)

10. Wilson AC, Zimmer EA, Prager EM and Kocher TD. Restriction mapping in the molecular systematics of mammals: a retrospective salute. pp.407-419 in B. Fernholm and K. Bremer (eds.) The Hierarchy of Life: Molecules and Morphology in Phylogenetic Analysis. Elsevier Press, Amsterdam. (PDF)


9. Jones TR, Collins JP, Kocher TD and Mitton JB. Systematic status and distribution of Ambystoma tigrinum stebbinsi Lowe (Amphibia: Caudata). Copeia 1988:621-635. (PDF)


8. Mitton JB, Carey C and Kocher TD. The relation of enzyme heterozygosity to standard and active oxygen consumption and body size of tiger salamanders, Ambystoma tigrinum. Physiological Zoology 59:574-582. (PDF)

7. Kocher TD and Sage RD. Equilibrium and multilocus analyses of the hybrid zone between leopard frogs (Rana pipiens complex) in central Texas. Evolution 40:21-33. (PDF)


6. Kornfield I, McKaye K and Kocher T. Evidence for the immigration hypothesis in the endemic cichlid fauna of Lake Tanganyika. Isozyme Bulletin 18:76. (PDF)


5. Louda SM, McKaye KR, Kocher TD and Stackhouse CJ. Activity, dispersion, and size of Lanistes nyassanus and L. solidus (Gastropoda, Ampullariidae) over the depth gradient at Cape Maclear, Lake Malawi, Africa. The Veliger 26:145-152. (PDF)

4. McKaye KR, Kocher T, Reinthal P, Harrison R and Kornfield I. Genetic evidence of allopatric and sympatric differentiation among color morphs of a Lake Malawi cichlid fish. Evolution 38:215-219. (PDF)


3. Kocher TD and McKaye KR. Territorial defense of heterospecific cichlids by Cyrtocara moorii in Lake Malawi, Africa. Copeia 1983:544-547. (PDF)

2. McKaye KR and Kocher T. Head ramming behavior by three paedophagous cichlids in Lake Malawi, Africa. Animal Behavior 31:206-210. (PDF)


1. McKaye KR, Kocher T, Reinthal P, Harrison R and Kornfield I. A sympatric sibling species complex of Petrotilapia trewavas (Cichlidae) from Lake Malawi analyzed by enzyme electrophoresis. Zoological Journal of the Linnean Society 76:91-96. (PDF)



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