We present a comprehensive phylogenetic analysis of the Utaka, an informal taxonomic group of cichlid species from Lake Malawi. We analyse both nuclear and mtDNA data from five Utaka species representing two (Copadichromis and Mchenga) of the three genera within Utaka. Within three of the five analysed species we find two very divergent mtDNA lineages. These lineages are widespread and occur sympatrically in conspecific individuals in different areas throughout the lake. In a broader taxonomic context including representatives of the main groups within the Lake Malawi cichlid fauna, we find that one of these lineages clusters within the non-Mbuna mtDNA clade, while the other forms a separate clade stemming from the base of the Malawian cichlid radiation. This second mtDNA lineage was only found in Utaka individuals, mostly within Copadichromis sp. “virginalis kajose” specimens. The nuclear genes analysed, on the other hand, did not show traces of divergence within each species. We suggest that the discrepancy between the mtDNA and the nuclear DNA signatures is best explained by a past hybridisation event by which the mtDNA of another species introgressed into the ancestral Copadichromis sp. “virginalis kajose” gene pool. 1. Introduction The Lake Malawi cichlid fauna comprises over 800 species [1] offering a spectacular example of adaptive radiation with virtually all niches in the lake being filled by members of this family [2, 3]. With a few exceptions, all Lake Malawi cichlids form a monophyletic group as supported by mitochondrial [4–6] and nuclear ([7–9] but see [10]) markers as well as allozymes [11, 12]. The phylogenetic reconstruction of Lake Malawi cichlid fauna has recovered six main mitochondrial DNA (mtDNA) lineages [5, 6, 10, 13]. Two of these lineages correspond to the Rhamphochromis and Diplotaxodon genera. A third lineage contains the nonendemic riverine Astatotilapia calliptera. The remaining cichlid fauna has been traditionally divided into two groups: one containing predominantly the rock-dwelling species commonly called Mbuna and the second containing the remaining Lake Malawi cichlids. However, phylogenetic reconstructions have shown that both groups are artificial [5, 10, 13, 14]. Several Lethrinops, Aulonocara, and Alticorpus species (ecologically and morphologically typically assigned to the non-Mbuna) cluster within the Mbuna clade. Furthermore, the non-Mbuna genus Copadichromis has been shown to have representatives belonging to both the non-Mbuna clade, as well as to a separate lineage. The genus Copadichromis, together with
References
[1]
J. Snoeks, “Material and methods,” in The Cichlid Diversity of Lake Malawi/Nyasa/Niassa: Identification, Distribution and Taxonomy, J. Snoeks, Ed., pp. 12–19, Cichlid Press, El Paso, Tex, USA, 2004.
[2]
G. Fryer and T. D. Iles, The Cichlid Fishes of the Great Lakes of Africa: Their Biology and Evolution, TFH Publications, UK, Edinburgh, 1972.
[3]
D. H. Eccles and E. Trewavas, Malawian Cichlid Fishes: The Classification of Some Haplochromine Genera, Lake Fish Movies, Herten, Germany, 1989.
[4]
A. Meyer, T. D. Kocher, P. Basasibwaki, and A. C. Wilson, “Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences,” Nature, vol. 347, no. 6293, pp. 550–553, 1990.
[5]
P. Moran, I. Kornfield, and P. N. Reinthal, “Molecular systematics and radiation of the haplochromine cichlids (Teleostei: Perciformes) of Lake Malawi,” Copeia, no. 2, pp. 274–288, 1994.
[6]
P. W. Shaw, G. F. Turner, M. R. Idid, R. L. Robinson, and G. R. Carvalho, “Genetic population structure indicates sympatric speciation of Lake Malawi pelagic cichlids,” Proceedings of the Royal Society B, vol. 267, no. 1459, pp. 2273–2280, 2000.
[7]
R. C. Albertson, J. A. Markert, P. D. Danley, and T. D. Kocher, “Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 9, pp. 5107–5110, 1999.
[8]
C. J. Allender, O. Seehausen, M. E. Knight, G. F. Turner, and N. Maclean, “Divergent selection during speciation of Lake Malawi cichlid fishes inferred from parallel radiations in nuptial coloration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 2, pp. 14074–14079, 2003.
[9]
M. R. Kidd, C. E. Kidd, and T. D. Kocher, “Axes of differentiation in the bower-building cichlids of Lake Malawi,” Molecular Ecology, vol. 15, no. 2, pp. 459–478, 2006.
[10]
D. A. Joyce, D. H. Lunt, M. J. Genner, G. F. Turner, R. Bills, and O. Seehausen, “Repeated colonization and hybridization in Lake Malawi cichlids,” Current Biology, vol. 21, no. 3, pp. R108–R109, 2011.
[11]
I. L. Kornfield, “Evidence for rapid speciation in African cichlid fishes,” Experientia, vol. 34, no. 3, pp. 335–336, 1978.
[12]
I. L. Kornfield, K. R. McKaye, and T. D. Kocher, “Evidence for the immigration hypothesis in the endemic cichlid fauna of Lake Tanganyika,” Isozyme Bulletin, vol. 18, p. 76, 1985.
[13]
G. F. Turner, R. L. Robinson, P. W. Shaw, and G. R. Carvalho, “Identification and biology of Diplotaxodon, Rhamphochromis and Pallidochromis,” in The Cichlid Diversity of Lake Malawi/Nyasa/Niassa: Identification, Distribution and Taxonomy, J. Snoeks, Ed., Cichlid Press, El Paso, Tex, USA, 2004.
[14]
M. J. Genner and G. F. Turner, “Ancient hybridization and phenotypic novelty within Lake Malawi’s cichlid fish radiation,” Molecular Biology and Evolution, vol. 29, pp. 195–206, 2012.
[15]
L. Rüber, A. Meyer, C. Sturmbauer, and E. Verheyen, “Population structure in two sympatric species of the Lake Tanganyika cichlid tribe Eretmodini: evidence for introgression,” Molecular Ecology, vol. 10, no. 5, pp. 1207–1225, 2001.
[16]
M. C. Mims, C. D. Hulsey, B. M. Fitzpatrick, and J. T. Streelman, “Geography disentangles introgression from ancestral polymorphism in Lake Malawi cichlids,” Molecular Ecology, vol. 19, no. 5, pp. 940–951, 2010.
[17]
O. Seehausen, “Hybridization and adaptive radiation,” Trends in Ecology and Evolution, vol. 19, no. 4, pp. 198–207, 2004.
[18]
L. H. Rieseberg, M. A. Archer, and R. K. Wayne, “Transgressive segregation, adaptation and speciation,” Heredity, vol. 83, no. 4, pp. 363–372, 1999.
[19]
M. Barrier, B. G. Baldwin, R. H. Robichaux, and M. D. Purugganan, “Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications,” Molecular Biology and Evolution, vol. 16, no. 8, pp. 1105–1113, 1999.
[20]
S. M. Aljanabi and I. Martinez, “Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques,” Nucleic Acids Research, vol. 25, no. 22, pp. 4692–4693, 1997.
[21]
W. Salzburger, A. Meyer, S. Baric, E. Verheyen, and C. Sturmbauer, “Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas,” Systematic Biology, vol. 51, no. 1, pp. 113–135, 2002.
[22]
W. J. Lee, J. Conroy, W. H. Howell, and T. D. Kocher, “Structure and evolution of teleost mitochondrial control regions,” Journal of Molecular Evolution, vol. 41, no. 1, pp. 54–66, 1995.
[23]
M. J. H. Van Oppen, C. Rico, J. C. Deutsch, G. F. Turner, and G. M. Hewitt, “Isolation and characterization of microsatellite loci in the cichlid fish Pseudotropheus zebra,” Molecular Ecology, vol. 6, no. 4, pp. 185–186, 1997.
[24]
K. A. Kellogg, J. A. Markert, J. R. Stauffer, and T. D. Kocher, “Microsatellite variation demonstrates multiple paternity in lekking cichlid fishes from Lake Malawi, Africa,” Proceedings of the Royal Society B, vol. 260, no. 1357, pp. 79–84, 1995.
[25]
R. Zardoya, D. M. Vollmer, C. Craddock, J. T. Streelman, S. Karl, and A. Meyer, “Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes),” Proceedings of the Royal Society B, vol. 263, no. 1376, pp. 1589–1598, 1996.
[26]
A. Parker and I. Kornfield, “Polygynandry in Pseudotropheus zebra, a cichlid fish from Lake Malawi,” Environmental Biology of Fishes, vol. 47, no. 4, pp. 345–352, 1996.
[27]
J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994.
[28]
N. Galtier, M. Gouy, and C. Gautier, “SEA VIEW and PHYLO_ WIN: Two graphic tools for sequence alignment and molecular phytogeny,” Computer Applications in the Biosciences, vol. 12, no. 6, pp. 543–548, 1996.
[29]
D. Posada, “Collapse: Describing haplotypes from sequence alignments,” 2004, http://darwin.uvigo.es/software/collapse.html.
[30]
D. Posada and K. A. Crandall, “MODELTEST: Testing the model of DNA substitution,” Bioinformatics, vol. 14, no. 9, pp. 817–818, 1998.
[31]
S. Guindon and O. Gascuel, “A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696–704, 2003.
[32]
M. Clement, D. Posada, and K. A. Crandall, “TCS: A computer program to estimate gene genealogies,” Molecular Ecology, vol. 9, no. 10, pp. 1657–1659, 2000.
[33]
F. Ronquist and J. P. Huelsenbeck, “MrBayes 3: Bayesian phylogenetic inference under mixed models,” Bioinformatics, vol. 19, no. 12, pp. 1572–1574, 2003.
[34]
H. Shimodaira and M. Hasegawa, “Multiple comparisons of log-likelihoods with applications to phylogenetic inference,” Molecular Biology and Evolution, vol. 16, no. 8, pp. 1114–1116, 1999.
[35]
M. Raymond and F. Rousset, “GENEPOP Version 1.2: Populations genetics software for exact tests and ecumenicism,” Journal of Heredity, vol. 86, pp. 248–249, 1995.
[36]
J. K. Pritchard, M. Stephens, and P. Donnelly, “Inference of population structure using multilocus genotype data,” Genetics, vol. 155, no. 2, pp. 945–959, 2000.
[37]
D. Falush, M. Stephens, and J. K. Pritchard, “Inference of population structure using multilocus genotype data: Dominant markers and null alleles,” Molecular Ecology Notes, vol. 7, no. 4, pp. 574–578, 2007.
[38]
G. Evanno, S. Regnaut, and J. Goudet, “Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study,” Molecular Ecology, vol. 14, no. 8, pp. 2611–2620, 2005.
[39]
D. A. Earl and B. M. von Holdt, “STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method,” Conservation Genetics Resources. In press.
[40]
P. F. Smith, A. Konings, and I. Kornfield, “Hybrid origin of a cichlid population in Lake Malawi: implications for genetic variation and species diversity,” Molecular Ecology, vol. 12, no. 9, pp. 2497–2504, 2003.
[41]
J. T. Streelman, S. L. Gmyrek, M. R. Kidd et al., “Hybridization and contemporary evolution in an introduced cichlid fish from Lake Malawi National Park,” Molecular Ecology, vol. 13, no. 8, pp. 2471–2479, 2004.
[42]
R. C. Albertson and T. D. Kocher, “Genetic architecture sets limits on transgressive segregation in hybrid cichlid fishes,” Evolution, vol. 59, no. 3, pp. 686–690, 2005.
[43]
Y. H. E. Loh, L. S. Katz, M. C. Mims, T. D. Kocher, S. V. Yi, and J. T. Streelman, “Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids,” Genome Biology, vol. 9, no. 7, article R113, 2008.
[44]
D. Garant, S. E. Forde, and A. P. Hendry, “The multifarious effects of dispersal and gene flow on contemporary adaptation,” Functional Ecology, vol. 21, no. 3, pp. 434–443, 2007.
[45]
P. A. Larsen, M. R. Marchán-Rivadeneira, and R. J. Baker, “Natural hybridization generates mammalian lineage with species characteristics,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 25, pp. 11447–11452, 2010.
[46]
W. Salzburger, S. Baric, and C. Sturmbauer, “Speciation via introgressive hybridization in East African cichlids?” Molecular Ecology, vol. 11, no. 3, pp. 619–625, 2002.
[47]
S. Koblmüller, N. Duftner, K. M. Sefc et al., “Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika—the result of repeated introgressive hybridization,” BMC Evolutionary Biology, vol. 7, article 7, 2007.
[48]
S. Koblmüller, B. Egger, C. Sturmbauer, and K. M. Sefc, “Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini,” Molecular Phylogenetics and Evolution, vol. 55, no. 1, pp. 318–334, 2010.
[49]
B. Nevado, S. Koblmüller, C. Sturmbauer, J. Snoeks, J. Usano-Alemany, and E. Verheyen, “Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish,” Molecular Ecology, vol. 18, no. 20, pp. 4240–4255, 2009.
[50]
J. R. Stauffer, N. J. Bowers, T. D. Kocher, and K. R. McKaye, “Evidence of hybridisation between Cyanotilapia afra and Pseudotropheus zebra (Teleostei: Cichlidae) following an intralacustrine translocation in Lake Malawi,” Copeia, vol. 1996, no. 1, pp. 203–208, 1996.
[51]
P. F. Smith, A. Konings, and I. Kornfield, “Hybrid origin of a cichlid population in Lake Malawi: Implications for genetic variation and species diversity,” Molecular Ecology, vol. 12, no. 9, pp. 2497–2504, 2003.
[52]
I. Van Der Sluijs, J. J. M. Van Alphen, and O. Seehausen, “Preference polymorphism for coloration but no speciation in a population of Lake Victoria cichlids,” Behavioral Ecology, vol. 19, no. 1, pp. 177–183, 2008.
[53]
M. E. Maan, O. Seehausen, and J. J. M. Van Alphen, “Female mating preferences and male coloration covary with water transparency in a Lake Victoria cichlid fish,” Biological Journal of the Linnean Society, vol. 99, no. 2, pp. 398–406, 2010.
[54]
I. E. Samonte, Y. Satta, A. Sato, H. Tichy, N. Takahata, and J. Klein, “Gene flow between species of Lake Victoria haplochromine fishes,” Molecular Biology and Evolution, vol. 24, no. 9, pp. 2069–2080, 2007.
[55]
O. Seehausen, G. Takimoto, D. Roy, and J. Jokela, “Speciation reversal and biodiversity dynamics with hybridization in changing environments,” Molecular Ecology, vol. 17, no. 1, pp. 30–44, 2008.
[56]
S. Nagl, H. Tichy, W. E. Mayer, N. Takezaki, N. Takahata, and J. Klein, “The origin and age of haplochromine fihes in Lake Victoria, East Africa,” Proceedings of the Royal Society of London B, vol. 267, pp. 1049–1061, 2000.
[57]
A. Sato, N. Takezaki, H. Tichy, F. Figueroa, W. E. Mayer, and J. Klein, “Origin and speciation of haplochromine fishes in East African crater lakes investigated by the analysis of their mtDNA, Mhc genes, and SINEs,” Molecular Biology and Evolution, vol. 20, no. 9, pp. 1448–1462, 2003.
[58]
O. Seehausen, “Hybridization and adaptive radiation,” Trends in Ecology and Evolution, vol. 19, no. 4, pp. 198–207, 2004.
[59]
U. K. Schliewen and B. Klee, “Reticulate sympatric speciation in Cameroonian crater lake cichlids,” Frontiers in Zoology, vol. 1, article 5, 2004.
[60]
J. Schwarzer, B. Misof, and U. K. Schliewen, “Speciation within genomic networks: a case study based on Steatocranus cichlids of the lower Congo rapids,” Journal of Evolutionary Biology, vol. 25, pp. 138–148, 2012.
[61]
D. E. Pearse and K. A. Crandall, “Beyond FST: Analysis of population genetic data for conservation,” Conservation Genetics, vol. 5, no. 5, pp. 585–602, 2004.
[62]
D. Anseeuw, G. E. Maes, P. Busselen, D. Knapen, J. Snoeks, and E. Verheyen, “Subtle population structure and male-biased dispersal in two Copadichromis species (Teleostei, Cichlidae) from Lake Malawi, East Africa,” Hydrobiologia, vol. 615, no. 1, pp. 69–79, 2008.
