HAPLOCHROMIS

Repeated trans-watershed hybridization
among haplochromine cichlids
(Cichlidae) was triggered by Neogene
landscape evolution
Julia Schwarzer, Ernst Roelof Swartz, Emmanuel Vreven,Jos Snoeks, Fenton Peter David Cotterill, Bernhard Misof and Ulrich Kurt Schliewen
Bavarian State Collection of Zoology, Munchhausenstrasse 21, 81247 Munchen, Germany
2
Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
3
South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown 6140, South Africa
4
Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren, Belgium
5
Laboratory of Biodiversity and Evolutionary Genomics, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
6
Africa Earth Observatory Network AEON
, Geoecodynamics Research Hub, University of Stellenbosch,
Private Bag X1, Matieland 7602, South Africa
The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explo-
sive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine
lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from
extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo
and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox
of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands
of kilometres apart and across major African watersheds, whereas some neighbouring species carry dras-
tically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of
hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African
rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochro-
mine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature
species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only
on a spatially restricted scale, but massively over almost the whole range of the haplochromine distri-
bution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic
vertebrate group

Mol Ecol. 2013 Jun;22(11):2848-63. doi: 10.1111/mec.12083. Epub 2012 Nov 5.
Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes.
Keller I1, Wagner CE, Greuter L, Mwaiko S, Selz OM, Sivasundar A, Wittwer S, Seehausen O.
Author information
Abstract

Adaptive radiations are an important source of biodiversity and are often characterized by many speciation events in very short succession. It has been proposed that the high speciation rates in these radiations may be fuelled by novel genetic combinations produced in episodes of hybridization among the young species. The role of such hybridization events in the evolutionary history of a group can be investigated by comparing the genealogical relationships inferred from different subsets of loci, but such studies have thus far often been hampered by shallow genetic divergences, especially in young adaptive radiations, and the lack of genome-scale molecular data. Here, we use a genome-wide sampling of SNPs identified within restriction site-associated DNA (RAD) tags to investigate the genomic consistency of patterns of shared ancestry and adaptive divergence among five sympatric cichlid species of two genera, Pundamilia and Mbipia, which form part of the massive adaptive radiation of cichlids in the East African Lake Victoria. Species pairs differ along several axes: male nuptial colouration, feeding ecology, depth distribution, as well as the morphological traits that distinguish the two genera and more subtle morphological differences. Using outlier scan approaches, we identify signals of divergent selection between all species pairs with a number of loci showing parallel patterns in replicated contrasts either between genera or between male colour types. We then create SNP subsets that we expect to be characterized to different extents by selection history and neutral processes and describe phylogenetic and population genetic patterns across these subsets. These analyses reveal very different evolutionary histories for different regions of the genome. To explain these results, we propose at least two intergeneric hybridization events (between Mbipia spp. and Pundamilia spp.) in the evolutionary history of these five species that would have lead to the evolution of novel trait combinations and new species.

© 2012 John Wiley & Sons Ltd.