Ansseuw, D., J. A. M. Raeymaekers, P. Busslen, E. Verheyen & J. Snokes, 2011. Low genetic and morphometric intraspecific divergence in peripheral Copadichromis populations (Perciformes: Cichlidae) in the Lake Malawi basin. International Journal of Evolutionary Biology 2011: 835946.
Google Scholar
Arnason, E., 2004. Mitochondrial cytochrome b variation in the high-fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy. Genetics 166: 1871–1885.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bandelt, J. J., P. Forster & A. Rohl, 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48.
Article
CAS
PubMed
Google Scholar
Bayona, J. D. R., 1991a. Some aspects of the biology of Kuhe, Boulengerochromis microlepis, in the Kigoma region, eastern coast of Lake Tanganyika. African Study Monographs 12: 63–74.
Google Scholar
Bayona, J. D. R., 1991b. Species composition and some observations on the littoral fishes based on beach-seining in the Kigoma region, eastern coast of Lake Tanganyika. African Study Monographs 12: 75–86.
Google Scholar
Büscher, H., 2009. Beobachtungen zum Brutverhalten von Boulengerochromis microlepis. DCG-Informationen 40: 280–286.
Google Scholar
Christie, M. R., D. W. Johnson, C. D. Stallings & M. A. Hixon, 2010. Self-recruitment and sweepstakes reproduction amid extensive gene flow in a coral-reef fish. Molecular Ecology 19: 1042–1057.
Article
PubMed
Google Scholar
Cohen, A. S., K. E. Lezzar, J. J. Tiercelin & M. Soreghan, 1997. New paleogeographic and lake-level reconstructions of Lake Tanganyika: implications for tectonic, climatic and biological evolution in a rift lake. Basin Research 7: 107–132.
Article
Google Scholar
Coulter, G. W., 1991. Lake Tanganyika and Its Life. Oxford University Press, Oxford.
Google Scholar
Crapon de Crapona, M.-D., 1986. Are ‘preferences’ and ‘tolerances’ in cichlid mate choice important for speciation? Journal of Fish Biology 29(Supplement A): 151–158.
Article
Google Scholar
Drummond, A. J. & A. Rambaut, 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
Article
PubMed Central
PubMed
Google Scholar
Duftner, N., S. Koblmüller & C. Sturmbauer, 2005. Evolutionary relationships of the Limnochromini, a tribe of benthic deepwater cichlid fish endemic to Lake Tanganyika, East Africa. Journal of Molecular Evolution 60: 277–289.
Article
CAS
PubMed
Google Scholar
Duftner, N., K. M. Sefc, S. Koblmüller, B. Nevado, E. Verheyen, H. Phiri & C. Sturmbauer, 2006. Distinct population structure in a phenotypically homogeneous rock-dwelling cichlid fish from Lake Tanganyika. Molecular Ecology 15: 2381–2396.
Article
CAS
PubMed
Google Scholar
Duftner, N., K. M. Sefc, S. Koblmüller, W. Salzburger, M. Taborsky & C. Sturmbauer, 2007. Parallel evolution of facial stripe patterns in the Neolamprologus brichardi/pulcher species complex endemic to Lake Tanganyika. Molecular Phylogenetics and Evolution 45: 706–715.
Article
PubMed
Google Scholar
Dunz, A. R. & U. K. Schliewen, 2013. Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”. Molecular Phylogenetics and Evolution 68: 64–80.
Article
PubMed
Google Scholar
Dupanloup, I., S. Schneider & L. Excoffier, 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology 11: 2571–2581.
Article
CAS
PubMed
Google Scholar
Excoffier, L. & H. E. Lischer, 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetic analyses under Linux and Windows. Molecular Ecology Resources 10: 564–567.
Article
PubMed
Google Scholar
Fohrman, K., 1994. Bred in the aquarium: Boulengerochromis microlepis. Cichlids Yearbook 4: 22–23.
Google Scholar
Friedman, M., B. P. Keck, Dornburg, R. I. Eytan, C. H. Martin, C. D. Hulsey, P. C. Wainwright & T. J. Near, 2013. Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proceedings of the Royal Society B: Biological Sciences 280: 20131733.
Article
PubMed Central
PubMed
Google Scholar
Fryer, G. & T. D. Iles, 1972. The Cichlid Fishes of the Great Lakes of Africa. T.H.F., Neptune.
Google Scholar
Fu, Y. X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915–925.
PubMed Central
CAS
PubMed
Google Scholar
Genner, M. J., O. Seehausen, D. H. Lunt, S. A. Joyce, P. W. Shaw, G. R. Carvalho & G. F. Turner, 2007. Age of cichlids: new dates for ancient lake fish radiations. Molecular Biology and Evolution 24: 1268–1282.
Article
Google Scholar
Genner, M. J., P. Nichols, P. W. Shaw, G. R. Carvalho, R. L. Robinson & G. F. Turner, 2008. Genetic homogeneity among breeding grounds and nursery areas of an exploited Lake Malawi cichlid fish. Freshwater Biology 53: 1823–1831.
Article
Google Scholar
Genner, M. J., M. E. Knight, M. P. Haeseler & G. F. Turner, 2010a. Establishment and expansion of Lake Malawi rock fish populations after a dramatic Late Pleistocene lake level rise. Molecular Ecology 19: 170–182.
Article
PubMed
Google Scholar
Genner, M. J., P. Nichols, P. W. Shaw, G. R. Carvalho, R. L. Robinson & G. F. Turner, 2010b. Population structure on breeding grounds of Lake Malawi’s ‘twilight zone’ cichlid fishes. Journal of Biogeography 37: 258–269.
Article
Google Scholar
Grant, W. S. & B. W. Bowen, 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. Journal of Heredity 89: 415–426.
Article
Google Scholar
Hedgecock, D., 1994. Does variance in reproductive success limit effective population size of marine organisms? In Beaumont, A. (ed.), Genetics and Evolution of Aquatic Organisms. Chapman & Hall, London: 122–134.
Google Scholar
Hedgecock, D. & A. I. Pudovkin, 2011. Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bulletin of Marine Science 87: 971–1002.
Article
Google Scholar
Hedrick, P., 2005. Large variance in reproductive success and the N
e/N ratio. Evolution 59: 1596–1599.
Article
PubMed
Google Scholar
Hoban, S. M., M. Mezzavilla, O. E. Gaggiotti, A. Benazzo, C. van Oosterhout & G. Bertorelle, 2013. High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study. BMC Bioinformatics 14: 309.
Article
PubMed Central
PubMed
Google Scholar
Kawabata, M. & N. Y. K. Mihigo, 1982. Littoral fish fauna near Uvira, northwestern end of Lake Tanganyika. African Study Monographs 2: 133–143.
Google Scholar
Klett, V. & A. Meyer, 2002. What, if anything, is a Tilapia? Mitochondrial ND2 phylogeny of tilapiines and the evolution of parental care systems in the African cichlid fishes. Molecular Biology and Evolution 19: 865–883.
Article
CAS
PubMed
Google Scholar
Koblmüller, S., N. Duftner, C. Katongo, H. Phiri & C. Sturmbauer, 2005. Ancient divergence in bathypelagic Lake Tanganyika deepwater cichlids: mitochondrial phylogeny of the tribe Bathybatini. Journal of Molecular Evolution 60: 297–314.
Article
PubMed
Google Scholar
Koblmüller, S., K. M. Sefc, N. Duftner, M. Warum & C. Sturmbauer, 2007. Genetic population structure as indirect measure of dispersal ability in a Lake Tanganyika cichlid. Genetica 130: 121–131.
Article
PubMed
Google Scholar
Koblmüller, S., K. M. Sefc & C. Sturmbauer, 2008. The Lake Tanganyika cichlid species assemblage: recent advances in molecular phylogenetics. Hydrobiologia 615: 5–20.
Article
Google Scholar
Koblmüller, S., N. Duftner, K. M. Sefc, U. Aigner, M. Rogetzer & C. Sturmbauer, 2009. Phylogeographic structure and gene flow in the scale-eating cichlid Perissodus microlepis (Teleostei, Perciformes, Cichlidae) in southern Lake Tanganyika. Zoologica Scripta 38: 257–268.
Article
Google Scholar
Koblmüller, S., W. Salzburger, B. Obermüller, E. Eigner, C. Sturmbauer & K. M. Sefc, 2011. Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations. Molecular Ecology 20: 2272–2290.
Article
PubMed
Google Scholar
Koch, M., S. Koblmüller, K. M. Sefc, N. Duftner, C. Katongo & C. Sturmbauer, 2007. Evolutionary history of the endemic Lake Tanganyika cichlid fish Tylochromis polylepis: a recent intruder to a mature adaptive radiation. Journal of Zoological Systematics and Evolutionary Research 45: 64–71.
Konings, A., 1998. Tanganyika Cichlids in Their Natural Habitat. Cichlid Press, El Paso.
Google Scholar
Kuwamura, T., 1986. Substratum spawning and biparental guarding of the Tanganyikan cichlid Boulengerochromis microlepis, with notes on its life history. Physiology and Ecology Japan 23: 31–43.
Google Scholar
Lee, W.-J., J. Conroy, W. H. Howell & T. D. Kocher, 1995. Structure and evolution of the teleost mitochondrial control region. Journal of Molecular Evolution 41: 54–66.
Article
CAS
PubMed
Google Scholar
Li, G. & D. Hedgecock, 1998. Genetic heterogeneity, detected by PCR-SSCP, among samples of larval Pacific oysters (Crassostrea gigas) supports the hypothesis of large variance in reproductive success. Canadian Journal of Fisheries and Aquatic Sciences 55: 1025–1033.
Article
CAS
Google Scholar
Librado, P. & J. Rozas, 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.
Article
CAS
PubMed
Google Scholar
Liem, K. F., 1973. Evolutionary strategies and morphological innovations: cichlid pharyngeal jaws. Systematic Zoology 22: 425–441.
Article
Google Scholar
Markert, J. A., M. E. Arnegard, P. D. Danley & T. D. Kocher, 1999. Biogeography and population genetics of the Lake Malawi cichlid Melanochromis auratus: habitat transience, philopatry and speciation. Molecular Ecology 8: 1013–1026.
Article
Google Scholar
Matthes, H., 1961. Boulengerochromis microlepis, a Lake Tanganyika fish of economic importance. Bulletin Aquatic Biology 3: 1–15.
Google Scholar
Mayr, E., 1963. Animal Species and Evolution. Harvard University Press, Cambridge.
Book
Google Scholar
McGlue, M. M., K. E. Lezzar, A. S. Cohen, J. M. Russell, J. J. Tiercelin, A. A. Felton, E. Mbede & H. H. Nkotagu, 2008. Seismic records of late Pleistocene aridity in Lake Tanganyika, tropical East Africa. Journal of Palaeolimnology 40: 635–653.
Article
Google Scholar
Meyer, A., L. L. Knowles & E. Verheyen, 1996. Widespread geographic distribution of mitochondrial haplotypes in rock-dwelling cichlid fishes from Lake Tanganyika. Molecular Ecology 5: 341–350.
Article
CAS
PubMed
Google Scholar
Minin, V. N., E. W. Bloomquist & M. A. Suchard, 2008. Smooth skyride through a rough sykline: Bayesian coalescent based inference of population dynamics. Molecular Biology and Evolution 25: 1459–1471.
Article
PubMed Central
CAS
PubMed
Google Scholar
Muschick, M., A. Indermaur & W. Salzburger, 2012. Convergent evolution within an adaptive radiation of cichlid fishes. Current Biology 22: 2362–2368.
Article
CAS
PubMed
Google Scholar
Nevado, B., S. Koblmüller, C. Sturmbauer, J. Snoeks, J. Usano-Alemany & E. Verheyen, 2009. Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish. Molecular Ecology 18: 4240–4255.
Article
CAS
PubMed
Google Scholar
Nevado, B., S. Mautner, C. Sturmbauer & E. Verheyen, 2013. Water-level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species. Molecular Ecology 22: 2933–3948.
Nishida, M., 1997. Phylogenetic relationships and evolution of Tanganyika cichlids. In Kawanabe, H., M. Hori & M. Nagoshi (eds), Fish Communities in Lake Tanganyika. Kyoto University Press, Kyoto: 1–23.
Google Scholar
Pereyra, R., M. I. Taylor, G. F. Turner & C. Rico, 2004. Variation in habitat preferences and population structure among three species of the Lake Malawi cichlid genus Protomelas. Moelcular Ecology 13: 2691–2697.
Article
CAS
Google Scholar
Poll, M., 1956. Poissons Cichlidae. Exploration hydrobiologique du Lac Tanganika (1946–1947): Résultates scientifiques, 3, fasc. 5B, Brussels, Belgium.
Polzin, T. & S. V. Daneschmand, 2003. On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters 31: 12–20.
Article
Google Scholar
Posada, D., 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253–1256.
Article
CAS
PubMed
Google Scholar
Rambaut, A. & A. J. Drummond, 2009. Tracer v1.5. http://beast.bio.ed.ac.uk/Tracer. Accessed December 2013.
Ramos-Onsins, S. E. & J. Rozas, 2002. Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19: 2092–2100.
Article
CAS
PubMed
Google Scholar
Rico, C. & G. F. Turner, 2002. Extreme microallopatric divergence in a cichlid species from Lake Malawi. Molecular Ecology 11: 1585–1590.
Article
CAS
PubMed
Google Scholar
Salzburger, W., 2009. The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes. Molecular Ecology 18: 169–185.
Article
PubMed
Google Scholar
Salzburger, W., A. Meyer, S. Baric, E. Verheyen & C. Sturmbauer, 2002. Phylogeny of the Lake Tanganyika cichlid species flock and ist relationships to Central- and East African haplochromine cichlid fish faunas. Systematic Biology 51: 113–135.
Article
PubMed
Google Scholar
Sanderson, M. J. & M. J. Donoghue, 1994. Shifts in diversification rate with the origin of angiosperms. Science 264: 1590–1593.
Article
CAS
PubMed
Google Scholar
Sargsyan, O. & J. Wakeley, 2008. A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms. Theoretical Population Biology 74: 104–114.
Article
PubMed
Google Scholar
Scholz, C. A., T. C. Johnson, A. S. Cohen, J. W. King, J. A. Peck, J. T. Overpeck, M. R. Talbot, E. T. Brown, L. Kalindafe, P. Y. O. Amoako, R. P. Lyons, T. M. Shanahan, I. S. Castaneda, C. W. Heil, S. L. Forman, L. R. McHargue, K. R. Beuning, J. Gomez & J. Pierson, 2007. East African megadroughts between 135 and 75 thousand years ago and bearing on early-modern human origins. Proceedings of the National Academy of Sciences of the United States of America 104: 16416–16421.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schwarzer, J., B. Misof, D. Tautz & U. K. Schliewen, 2009. The root of the East African cichlid radiations. BMC Evolutionary Biology 9: 186.
Article
PubMed Central
PubMed
Google Scholar
Seehausen, O., F. Witte, E. F. Katunzi, J. Smits & N. Bouton, 1997. Patterns of the remnant cichlid fauna in southern Lake Tanganyika. Conservation Biology 11: 890–904.
Article
Google Scholar
Sefc, K. M., S. Baric, W. Salzburger & C. Sturmbauer, 2007. Species-specific population structure in rock-specialized sympatric cichlid species in Lake Tanganyika, East Africa. Journal of Molecular Evolution 64: 33–49.
Article
CAS
PubMed
Google Scholar
Shaw, P. W., G. F. Turner, M. R. Idid, R. L. Robinson & G. R. Carvalho, 2000. Genetic population structure indicates sympatric speciation of Lake Malawi pelagic cichlids. Proceedings of the Royal Society London Series B: Biological Sciences 267: 2273–2280.
Article
CAS
Google Scholar
Sturmbauer, C., 1998. Explosive speciation in cichlid fishes of the African Great Lakes: a dynamic model of adaptive radiation. Journal of Fish Biology 53(Supplement A): 18–36.
Article
Google Scholar
Sturmbauer, C., S. Baric, W. Salzburger, L. Rüber & E. Verheyen, 2001. Lake level fluctuations synchronize genetic divergence of cichlid fishes in African lakes. Molecular Biology and Evolution 18: 144–154.
Article
CAS
PubMed
Google Scholar
Sturmbauer, C., C. Fuchs, G. Harb, E. Damm, N. Duftner, M. Maderbacher, M. Koch & S. Koblmüller, 2008. Abundance, distribution, and territory areas of rock-dwelling Lake Tanganyika cichlid fish species. Hydrobiologia 615: 57–68.
Article
Google Scholar
Sturmbauer, C., M. Husemann & P. Danley, 2011. Explosive speciation and adaptive radiation of East African cichlid fishes. In Zachos, F. E. & J. C. Habel (eds), Distribution and Protection of Conservation Priority Areas. Springer, Berlin: 333–362.
Google Scholar
Tajima, F., 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
Takahashi, T., 2003. Systematics of Tanganyikan cichlid fishes (Teleostei: Perciformes). Ichthyological Research 50: 367–382.
Article
Google Scholar
Takahashi, T., K. Watanabe, H. Munehara, L. Rüber & M. Hori, 2009. Evidence for divergent natural selection of a Lake Tanganyika cichlid inferred from repeated radiations in body size. Molecular Ecology 18: 3110–3119.
Article
CAS
PubMed
Google Scholar
Tamura, K., D. Peterson, G. Stecher, M. Nei & S. Kumar, 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739.
Article
PubMed Central
CAS
PubMed
Google Scholar
Taylor, M. I. & E. Verheyen, 2001. Microsatellite data reveals weak population substructuring in Copadichromis sp. “virginalis kajose”, a demersal cichlid from Lake Malawi, Africa. Journal of Fish Biology 59: 593–604.
Google Scholar
Taylor, M. I., L. Rüber & E. Verheyen, 2001. Microsatellites reveal high levels of population substructuring in the species-poor eretmodine cichlid lineage from Lake Tanganyika. Proceedings of the Royal Society London Series B: Biological Sciences 268: 803–808.
Article
CAS
Google Scholar
Turelli, M., N. H. Barton & J. A. Coyne, 2001. Theory and speciation. Trends in Ecology and Evolution 16: 330–343.
Article
PubMed
Google Scholar
Turner, G. F., 1996. Offshore Cichlids of Lake Malawi. Cichlid Press, Lauenau.
Google Scholar
Turner, G. F., R. L. Robinson, B. P. Ngatunga, P. W. Shaw & G. R. Carvalho, 2002. Pelagic cichlid fishes of Lake Malawi/Nyasa: biology, management and conservation. In Cowx, I. G. (ed.), Management and Ecology of Lake and Reservoir Fisheries. Blackwell, Oxford: 353–366.
Google Scholar
Van Oppen, M. J. H., G. F. Turner, C. Rico, J. C. Deutsch, K. M. Ibrahim, R. L. Robinson & G. M. Hewitt, 1997. Unusually fine-scale genetic structuring found in rapidly speciating Malawi cichlid fishes. Proceedings of the Royal Society London Series B: Biological Sciences 264: 1803–1812.
Article
Google Scholar
Van Steenberge, M., M. P. M. Vanhove, F. C. Breman & J. Snoeks, 2014. Complex geographical variation patterns in Tropheus duboisi Marlier, 1959 (Perciformes, Cichlidae) from Lake Tanganyika. Hydrobiologia. doi:10.1007/s10750-013-1692-5.
Google Scholar
Wagner, C. E. & A. R. McCune, 2009. Contrasting patterns of spatial genetic structure in sympatric rock-dwelling cichlid fishes. Evolution 63: 1312–1326.
Article
PubMed
Google Scholar
Wagner, C. E., L. J. Harmon & O. Seehausen, 2012. Ecological opportunity and sexual selection together predict adaptive radiation. Nature 487: 366–369.
Article
CAS
PubMed
Google Scholar
Walsh, P. S., D. W. Metzger & R. Higuchi, 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10: 506–518.
CAS
PubMed
Google Scholar
Wright, S., 1978. Evolution and the Genetic of Populations 4. Variability Within and Among Natural Populations. University of Chicago Press, Chicago, IL.
Google Scholar