@misc{stenzel1949successional10,
    author = "Stenzel, H. B",
    title = "Successional speciation in paleontology - the case of the oysters of the sellaeformis stock",
    year = "1949",
    howpublished = "Evolution, v. 3, p. 34-50",
    note = "talkorigins\_source = {true}; raw\_reference = {Stenzel, H. B., 1949, Successional speciation in paleontology - the case of the oysters of the sellaeformis stock: Evolution, v. 3, p. 34-50.}"
}

@book{dobzhansky1951genetics3,
    author = "Dobzhansky, T",
    title = "Genetics and the Origin of Species [3rd ed.]",
    year = "1951",
    publisher = "New York, Columbia University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., 1951, Genetics and the Origin of Species [3rd ed.]: New York, Columbia University Press.}"
}

@article{greenwood1951evolution,
    author = "GREENWOOD, P. H.",
    title = "Evolution of the African Cichlid Fishes: the Haplochromis Species-Flock in Lake Victoria",
    year = "1951",
    journal = "Nature",
    url = "https://doi.org/10.1038/167019a0",
    doi = "10.1038/167019a0",
    number = "4236",
    pages = "19-20",
    volume = "167"
}

@misc{cain1963animal1,
    author = "Cain, A. J",
    title = "Animal Species and Their Evolution [2nd ed.]",
    year = "1963",
    howpublished = "London, Hutchinson",
    note = "talkorigins\_source = {true}; raw\_reference = {Cain, A. J., 1963, Animal Species and Their Evolution [2nd ed.]: London, Hutchinson.}"
}

@techreport{greenwood1965the6,
    author = "Greenwood, P. H",
    title = "The cichlid fishes of Lake Nabugabo, Uganda",
    year = "1965",
    howpublished = "British Museum of Natural History Bulletin (Zoology), v. 12, p. 315-357",
    note = "talkorigins\_source = {true}; raw\_reference = {Greenwood, P. H., 1965, The cichlid fishes of Lake Nabugabo, Uganda: British Museum of Natural History Bulletin (Zoology), v. 12, p. 315-357.}"
}

@misc{erhlich1969differentiations4,
    author = "Erhlich, P. R. and Raven, P. H",
    title = "Differentiations in populations",
    year = "1969",
    howpublished = "Science, v. 165, p. 1228-1231",
    note = "talkorigins\_source = {true}; raw\_reference = {Erhlich, P. R., and Raven, P. H., 1969, Differentiations in populations: Science, v. 165, p. 1228-1231.}"
}

@techreport{greenwood1974the7,
    author = "Greenwood, P. H",
    title = "The cichlid fishes of Lake Victoria, East Africa",
    year = "1974",
    howpublished = "the biology and evolution of a species stock: Bulletin of the British Museum (Natural History), v. Zoology, Suppl. 6",
    note = "talkorigins\_source = {true}; raw\_reference = {Greenwood, P. H., 1974, The cichlid fishes of Lake Victoria, East Africa: the biology and evolution of a species stock: Bulletin of the British Museum (Natural History), v. Zoology, Suppl. 6.}"
}

@article{gingerich1976paleontology5,
    author = "Gingerich, P. D",
    title = "Paleontology and phylogeny",
    year = "1976",
    journal = "patterns of evolution of the species level in early Tertiary mammals: American Journal of Science, v. 276, p. 1-28",
    note = "talkorigins\_source = {true}; raw\_reference = {Gingerich, P. D., 1976, Paleontology and phylogeny: patterns of evolution of the species level in early Tertiary mammals: American Journal of Science, v. 276, p. 1-28.}"
}

@misc{stebbins1977patterns9,
    author = "Stebbins, G. L",
    title = "Patterns of Speciation, in Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W., eds., Evolution",
    year = "1977",
    howpublished = "San Francisco, W.H. Freeman and Co., p. 195-232",
    note = "talkorigins\_source = {true}; raw\_reference = {Stebbins, G. L., 1977, Patterns of Speciation, in Dobzhansky, T., Ayala, F. J., Stebbins, G. L., and Valentine, J. W., eds., Evolution: San Francisco, W.H. Freeman and Co., p. 195-232.}"
}

@misc{white1977modes11,
    author = "White, M. J. D",
    title = "Modes of Speciation",
    year = "1977",
    howpublished = "San Francisco, Ca., Freeman",
    note = "talkorigins\_source = {true}; raw\_reference = {White, M. J. D., 1977, Modes of Speciation: San Francisco, Ca., Freeman.}"
}

@misc{malmgren1984species8,
    author = "Malmgren, B. A. and Berggren, W. A. and Lohmann, G. P",
    title = "Species formation through punctuated gradualism in planktonic foraminifera",
    year = "1984",
    howpublished = "Science, p. 317- 319",
    note = "talkorigins\_source = {true}; raw\_reference = {Malmgren, B. A., Berggren, W. A., and Lohmann, G. P., 1984, Species formation through punctuated gradualism in planktonic foraminifera: Science, p. 317- 319.}"
}

@misc{cronin1985speciation2,
    author = "Cronin, T. M",
    title = "Speciation and stasis in marine ostracoda; climatic modulation of evolution",
    year = "1985",
    howpublished = "Science, v. 227, p. 60-63",
    note = "talkorigins\_source = {true}; raw\_reference = {Cronin, T. M., 1985, Speciation and stasis in marine ostracoda; climatic modulation of evolution: Science, v. 227, p. 60-63.}"
}

@article{barluenga2004the,
    author = "BARLUENGA, MARTA and MEYER, AXEL",
    title = "The Midas cichlid species complex: incipient sympatric speciation in Nicaraguan cichlid fishes?",
    year = "2004",
    journal = "Molecular Ecology",
    abstract = "Sympatric speciation is a contentious concept, although theoretical models as well as empirical evidence support its relevance in evolutionary biology. The Midas cichlid species complex (Amphilophus citrinellus, labiatus, zaliosus) from several crater lakes in Nicaragua fits several of the key characteristics of a sympatric speciation model. In particular, in A. citrinellus (i) strong assortative mating on the basis of colour polymorphism and (ii) ecological differentiation based on morphological polymorphisms involving the feeding apparatus and body shape might both be mechanisms of incipient speciation. Seven microsatellite markers and mtDNA control region sequences [836 base pairs (bp)] were used to study the population genetic structure of 519 specimens of Midas cichlid populations from the two Great Lakes Managua and Nicaragua, and three crater lakes in Nicaragua, Central America. The three named species of the species complex occupy different ecological niches, are morphologically distinct and can be distinguished genetically. We uncovered allopatric genetic differentiation of populations of A. citrinellus from different lakes and distant locations within Lake Managua and, more interestingly, incipient genetic differentiation of several sympatric populations based on colouration (in A. citrinellus and A. labiatus) but not on the morphology of the pharyngeal jaws (in A. citrinellus). Sexual selection and assortative mating might be the driven forces of diversification within named species. The Midas cichlid species complex in Nicaragua is an excellent model system for the study of the incipient stages of adaptation, speciation and the formation of species flocks.",
    url = "https://doi.org/10.1111/j.1365-294x.2004.02211.x",
    doi = "10.1111/j.1365-294x.2004.02211.x",
    number = "7",
    pages = "2061-2076",
    volume = "13"
}

@article{fryer2006evolution,
    author = "Fryer, Geoffrey",
    title = "Evolution in ancient lakes: radiation of Tanganyikan atyid prawns and speciation of pelagic cichlid fishes in Lake Malawi",
    year = "2006",
    journal = "Hydrobiologia",
    url = "https://doi.org/10.1007/s10750-006-0322-x",
    doi = "10.1007/s10750-006-0322-x",
    number = "S1",
    pages = "131-142",
    volume = "568"
}

@article{fryer2008evolution,
    author = "Fryer, Geoffrey",
    title = "Evolution in ancient lakes: radiation of Tanganyikan atyid prawns and speciation of pelagic cichlid fishes in Lake Malawi",
    year = "2008",
    journal = "Hydrobiologia",
    url = "https://doi.org/10.1007/s10750-007-9155-5",
    doi = "10.1007/s10750-007-9155-5",
    number = "1",
    pages = "425-426",
    volume = "596"
}

@article{gante2016genomics,
    author = "Gante, Hugo F. and Matschiner, Michael and Malmstrøm, Martin and Jakobsen, Kjetill S. and Jentoft, Sissel and Salzburger, Walter",
    title = "Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika",
    year = "2016",
    journal = "Molecular Ecology",
    abstract = "How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation‐related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the Neolamprologus savoryi ‐complex (the ‘Princess cichlids’) from Lake Tanganyika. We present a time‐calibrated species tree based on whole‐genome sequences and provide strong evidence for incomplete lineage sorting in the early phases of diversification and multiple introgression events affecting different stages. Importantly, we find that the Neolamprologus chromosomes show centre‐to‐periphery biases in nucleotide diversity, sequence divergence, GC content, incomplete lineage sorting and rates of introgression, which are likely modulated by recombination density and linked selection. The detection of heterogeneous genomic landscapes has strong implications on the genomic mechanisms involved in speciation. Collinear chromosomal regions can be protected from gene flow and harbour incompatibility genes if they reside in lowly recombining regions, and coupling can evolve between nonphysically linked genomic regions (chromosome centres in particular). Simultaneously, higher recombination towards chromosome peripheries makes these more dynamic, evolvable regions where adaptation polymorphisms have a fertile ground. Hence, differences in genome architecture could explain the levels of taxonomic and phenotypic diversity seen in taxa with collinear genomes and might have contributed to the spectacular cichlid diversity observed today.",
    url = "https://doi.org/10.1111/mec.13767",
    doi = "10.1111/mec.13767",
    number = "24",
    pages = "6143-6161",
    volume = "25"
}

@article{doi101038s41467018054799,
    author = "Irisarri, Iker and Singh, Pooja and Koblmüller, Stephan and Torres-Dowdall, Julián and Henning, Frederico and Franchini, Paolo and Fischer, Christoph and Lemmon, Alan R and Lemmon, Emily Moriarty and Thallinger, Gerhard G and Sturmbauer, Christian and Meyer, Axel",
    title = "Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes.",
    year = "2018",
    journal = "Nature communications",
    abstract = "Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC6082878/",
    doi = "10.1038/s41467-018-05479-9",
    pmcid = "PMC6082878",
    pmid = "30089797"
}

@article{weber2021speciation,
    author = "Weber, Alexandra A.-T. and Rajkov, Jelena and Smailus, Kolja and Egger, Bernd and Salzburger, Walter",
    title = "Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes",
    year = "2021",
    journal = "Science Advances",
    abstract = "African cichlid fishes reveal the dynamics of speciation and the predictability of evolution.",
    url = "https://doi.org/10.1126/sciadv.abg5391",
    doi = "10.1126/sciadv.abg5391",
    number = "45",
    volume = "7"
}

@article{olave2022early,
    author = "Olave, Melisa and Nater, Alexander and Kautt, Andreas F. and Meyer, Axel",
    title = "Early stages of sympatric homoploid hybrid speciation in crater lake cichlid fishes",
    year = "2022",
    journal = "Nature Communications",
    abstract = "Homoploid hybrid speciation (i.e., hybrid speciation without a change in ploidy) has traditionally been considered to be rare in animals. Only few accepted empirical examples of homoploid hybrid speciation in nature exist, and in only one previous case (insects) was it convincingly shown that this process occurred in complete sympatry. Here, we report an instance of sympatric homoploid hybrid speciation in Midas cichlid fishes in Crater Lake Xiloá, Nicaragua. The hybrid lineage, albeit at an early stage of speciation, has genomically and phenotypically diverged from both of its two parental species. Together with a distinct stable isotope signature this suggests that this hybrid lineages occupies a different trophic niche compared to the other sympatric Midas cichlid species in Crater Lake Xiloá.",
    url = "https://doi.org/10.1038/s41467-022-33319-4",
    doi = "10.1038/s41467-022-33319-4",
    number = "1",
    volume = "13"
}

@article{doi101038s4155902502819z,
    author = "Nichols, Annika L A and Shafer, Maxwell E R and Indermaur, Adrian and Rüegg, Attila and Gonzalez-Dominguez, Rita and Malinsky, Milan and Sommer-Trembo, Carolin and Fritschi, Laura and Mesich, Amelia and Abdalla-Wyse, Ayasha and Salzburger, Walter and Schier, Alexander F",
    title = "Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes.",
    year = "2025",
    journal = "Nature ecology \& evolution",
    abstract = "The partitioning of ecological niches is a fundamental component of species diversification in adaptive radiations. However, it is currently unknown if and how such bursts of organismal diversity are influenced by temporal niche partitioning, wherein species avoid competition by being active or sleeping during different time windows. Here we address this question through profiling temporal activity patterns in the exceptionally diverse fauna of cichlid fishes from the African Lake Tanganyika. By integrating week-long longitudinal behavioural recordings of over 500 individuals from 60 species with eco-morphological and genomic information, we provide two lines of evidence that temporal niche partitioning occurs in this massive adaptive radiation. First, Tanganyikan cichlids exhibit all known circadian temporal activity patterns (diurnal, nocturnal, crepuscular and cathemeral) and display substantial interspecific variation in daily amounts of locomotion. Second, many species with similar habitat and diet niches occupy distinct temporal niches. Moreover, our results suggest that shifts between diurnal and nocturnal activity patterns are facilitated by a crepuscular intermediate state. Genome-wide association studies indicate that the genetics underlying activity patterns is complex, with different clades associated with different combinations of variants. The identified variants were not associated with core circadian clock genes but with genes implicated in synapse function. These observations indicate that temporal niche partitioning may have contributed to adaptive radiation in cichlids and that many genes are associated with the diversity and evolution of temporal activity patterns.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12507676/",
    doi = "10.1038/s41559-025-02819-z",
    pmcid = "PMC12507676",
    pmid = "40866532"
}