Species Flock Research Articles

Spawning aggregation and segregation of Labeobarbus spp. (Pisces: Cyprinidae) in the Megech and Dirma River mouths, Lake Tana, Ethiopia

Spawning aggregation and segregation of Labeobarbus species congregating at the mouths of Megech and Dirma Rivers were studied using catch data collected from December 2003 to November 2004. Fish were collected monthly from November to June and twice in July. However, during the main rainy season (August to October 2004), samples were collected weekly at both river mouths. Polyfilament gillnets with mesh sizes: 6, 8, 10 and 12cm were set overnight. A total of 4280 Labeobarbus specimens were collected. Six Labeobarbus species (L. intermedius, L. megastoma, L. tsanensis, L. truttiformis, L. brevicephalus and L. surkis) formed spawning aggregations in the river mouths during the peak of the rainy season (August to October). Although there was overlap of spawning aggregations between these six Labeobarbus species weekly catch data indicated temporal segregation among all species, except L. intermedius. Four species (L. intermedius, L. megastoma, L. truttiformis and L. tsanensis) were significantly higher in abundance at Megech River than at Dirma River during the peak aggregation months. Labeobarbus surkis, never reported in other previous studies, was found to aggregate at both river mouths. However, three species (L. acutirostris, L. macrophtalmus and L. platydorsus) formed spawning aggregation in other tributaries were rare in the present study. Closing commercial gillnet fishing in both river mouths during the peak aggregation months (August to October) is highly recommended to conserve the already declining endemic Labeobarbus species flock of Lake Tana. Dam constructions for irrigation in Megech River upstream will impede spawning migration of Labeobarbus species.

On the Age and Origin of Lake Ejagham, Cameroon, and Its Endemic Fishes

AbstractLake Ejagham is a small, shallow lake in Cameroon, West Africa, which supports five endemic species of cichlid fishes in two distinct lineages. Genetic evidence suggests a relatively young age for the species flocks, but supporting geologic evidence has thus far been unavailable. Here we present diatom, geochemical, mineralogical, and radiocarbon data from two sediment cores that provide new insights into the age and origin of Lake Ejagham and its endemic fishes. Radiocarbon ages at the base of the longer core indicate that the lake formed approximately 9 ka ago, and the diatom record of the shorter core suggests that hydroclimate variability during the last 3 millennia was similar to that of other lakes in Cameroon and Ghana. These findings establish a maximum age of ca. 9 cal ka BP for the lake and its endemic species and suggest that repeated cichlid speciation in two distinct lineages occurred rapidly within the lake. Local geology and West African paleoclimate records argue against a volcanic, chemical, or climatic origin for Lake Ejagham. Although not conclusive, the morphometry of the lake and possible signs of impact-induced effects on quartz grains are instead more suggestive of a bolide impact.

Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America.

Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in cichlids have focussed largely on the African rift lake species flocks, Neotropical cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats.

Speciation in the genus Cloacina (Nematoda: Strongylida): species flocks and intra-host speciation.

Sequences of the first and second internal transcribed spacers (ITS1 + ITS2) of nuclear ribosomal DNA were employed to determine whether the congeneric assemblages of species of the strongyloid nematode genus Cloacina, found in the forestomachs of individual species of kangaroos and wallabies (Marsupialia: Macropodidae), considered to represent species flocks, were monophyletic. Nematode assemblages examined in the black-striped wallaby, Macropus (Notamacropus) dorsalis, the wallaroos, Macropus (Osphranter) antilopinus/robustus, rock wallabies, Petrogale spp., the quokka, Setonix brachyurus, and the swamp wallaby, Wallabia bicolor, were not monophyletic and appeared to have arisen by host colonization. However, a number of instances of within-host speciation were detected, suggesting that a variety of methods of speciation have contributed to the evolution of the complex assemblages of species present in this genus.

Nuclear and mitochondrial phylogeny of Rossella (Hexactinellida: Lyssacinosida, Rossellidae): a species and a species flock in the Southern Ocean

Hexactinellida (glass sponges) are abundant and important components of Antarctic benthic communities. However, the relationships and systematics within the common genus Rossella Carter, 1872 (Lyssacinosida: Rossellidae), are unclear and in need of revision. The species content of this genus has changed dramatically over the years depending on the criteria used by the taxonomic authority consulted. Rossella was formerly regarded as a putatively monophyletic group distributed in the Southern Ocean and the North Atlantic. However, molecular phylogenetic analyses have shown that Rossella is restricted to the Southern Ocean, where it shows a circum-Antarctic and subantarctic distribution. Herein, we provide a molecular phylogenetic analysis of the genus Rossella, based on mitochondrial (16S rDNA and COI) and nuclear (28S rDNA) markers. We corroborate the monophyly of Rossella and provide evidence supporting the existence of one species, namely Rossella antarctica Carter, 1872 and a species flock including specimens determined as Rossella racovitzae Topsent, 1901, Rossella nuda Topsent, 1901, Rossella fibulata Schulze and Kirkpatrick 1910, and Rossella levis (Kirkpatrick 1907).

Parasite escape through trophic specialization in a species flock.

Adaptive radiation occurs when species diversify rapidly to occupy an array of ecological niches. As opportunities for parasite infection and transmission may greatly vary among these niches, adaptive radiation is expected to be associated with a turnover of the parasite community. As major agents of natural and sexual selection, parasites may play a central role in host diversification. The study of parasite turnover may thus be of general relevance and could significantly improve our understanding of adaptive radiation. In this study, we examined the parasite faunas of eleven species belonging to the tribe Tropheini, one of several adaptive radiations of cichlid fishes in Lake Tanganyika. The most parsimonious ancestral foraging strategy among the Tropheini is relatively unselective substrate browsing of aufwuchs. Several lineages evolved more specialized foraging strategies, such as selective combing of microscopic diatoms or picking of macro-invertebrates. We found that representatives of these specialized lineages bear reduced infection with food-web-transmitted acanthocephalan helminths, but not with parasites with a direct life cycle. Possibly, the evolution of selective foraging strategies entailed reduced ingestion of intermediate invertebrate hosts of acanthocephalans. We conclude that some species belonging to the Tropheini virtually escape acanthocephalan infection as a by-product of trophic specialization.

Phylogenomic analysis of Lake Malawi cichlid fishes: Further evidence that the three-stage model of diversification does not fit

Adaptive radiations could often occur in discrete stages. For instance, the species flock of ∼1000 species of Lake Malawi cichlid fishes might have only diverged once between rocky and sandy environments during the initial stage of their diversification. All further diversification within the rock-dwelling (mbuna) or sand-dwelling (utaka) cichlids would have occurred during a subsequent second stage of extensive trophic evolution that was followed by a third stage of sexual trait divergence. We provide an improved phylogenetic framework for Malawi cichlids to test this three-stage hypothesis based on newly reconstructed phylogenetic relationships among 32 taxonomically disparate Malawi cichlids species. Using several reconstruction methods and 1037 ultra-conserved element (UCE) markers, we recovered a molecular phylogeny that confidently resolved relationships among most of the Malawi lineages sampled when a bifurcating framework was enforced. These bifurcating reconstructions also indicated that the sand-dwelling species Cyathochromis obliquidens was well-nested within the primarily rock-dwelling radiation known as the mbuna. In contrast to predictions from the three-stage model of vertebrate diversification, the recovered phylogeny reveals an initial colonization of rocky reefs, followed by substantial diversification of rock-dwelling lineages, and then at least one instance of subsequent evolution back into sandy habitats. This repeated evolution into major habitat types provides further evidence that the three-stage model of Malawi cichlid diversification has numerous exceptions.

Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation.

East African cichlids display extensive variation in sex determination systems. The species Astatotilapia calliptera is one of the few cichlids that reside both in Lake Malawi and in surrounding waterways. A. calliptera is of interest in evolutionary studies as a putative immediate outgroup species for the Lake Malawi species flock and possibly as a prototype ancestor-like species for the radiation. Here, we use linkage mapping to test association of sex in A. calliptera with loci that have been previously associated with genetic sex determination in East African cichlid species. We identify a male heterogametic XY system segregating at linkage group (LG) 7 in an A. calliptera line that originated from Lake Malawi, at a locus previously shown to act as an XY sex determination system in multiple species of Lake Malawi cichlids. Significant association of genetic markers and sex produce a broad genetic interval of approximately 26 megabases (Mb) using the Nile tilapia genome to orient markers; however, we note that the marker with the strongest association with sex is near a gene that acts as a master sex determiner in other fish species. We demonstrate that alleles of the marker are perfectly associated with sex in Metriaclima mbenjii, a species from the rock-dwelling clade of Lake Malawi. While we do not rule out the possibility of other sex determination loci in A. calliptera, this study provides a foundation for fine mapping of the cichlid sex determination gene on LG7 and evolutionary context regarding the origin and persistence of the LG7 XY across diverse, rapidly evolving lineages.

Molecular species delimitation methods provide new insight into taxonomy of the endemic gammarid species flock from the ancient Lake Ohrid

Evidence for cryptic diversity has been accumulated for many animal groups. In reply, effective tools for ordering this diversity by detecting and delimiting new species have been developed. Although molecular methods of species delimitation become fast means to order information upon hidden diversity, cryptic species discoveries are rarely followed by formal species descriptions and implementation of DNA data in species diagnoses, enhancing rather than reducing the taxonomic impediment. DNA-based diagnostic characters may serve as the backbone for a taxonomic description of cryptic species. In this article, we verify an established taxonomy of an ancient lake endemic species flock, through confrontation of the morphological taxonomy and molecular species delimitation methods. The endemic Gammarus species flock inhabiting Lake Ohrid was tested with several distance- and phylogeny-based delimitation methods using the mitochondrial cytochrome oxidase subunit I and 16S ribosomal RNA genes. We described three new species, including the Gammarus sywulaisp. nov., on the basis of morphological and molecular characters and two cryptic species, Gammarus cryptoparechiniformissp. nov. and Gammarus cryptosalemaaisp. nov., diagnosed exclusively on the basis of molecular characters. A simple taxonomic key is provided for provisional morphological identification of the Lake Ohrid Gammarus species.

Rapid and Parallel Adaptive Evolution of the Visual System of Neotropical Midas Cichlid Fishes.

Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only a few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted toward shorter wavelengths compared with the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution.

A Plio–Pleistocene Caspiocypris species flock (Candoninae, Ostracoda) from the Palaeolake Tiberino (Umbria, central Italy)

The Tiberino Basin is a wide Plio–Pleistocene intermountain basin located in central Apennine (central Italy). Its sedimentary infill is made of a thick succession of Pliocene–early Quaternary continental deposits, the oldest of which can be referred to the Fosso Bianco Formation, composed of grey clays deposited in a huge (at least 500 km2) and relatively deep (not less than 50 m) lake, the Palaeolake Tiberino. We analyse the lacustrine ostracod assemblages from the Fosso Bianco Formation and provide descriptions of five new species included in the subfamily Candoninae (Caspiocypris basilicii sp. nov., Caspiocypris perusia sp. nov., Caspiocypris posteroacuta sp. nov., Caspiocypris tiberina sp. nov. and Caspiocypris tuderis sp. nov.)) and one new species included in the subfamily Limnocytherinae (Paralimnocythere umbra sp. nov.)). The five species of Caspiocypris seem to represent a species flock, i.e. Caspiocypris includes a group of closely related species characterized by monophyly, endemism and speciosity, confirming the ‘ancient lake’ nature of the Palaeolake Tiberino during the Piacenzian–Gelasian. The ostracod assemblage points to a relatively deep-water and low energy lacustrine environment marked by a high level of endemism.http://zoobank.org/urn:lsid:zoobank.org:pub:BDF228DA-7866-4E9D-B691-6E63C6C182A2

Molecular evolution of the Lake Baikal endemic caddisflies (Trichoptera)

Phylogenetic relationships of the nine Lake Baikal endemic caddisfly species with the representatives of the genus Apatania (Apataniidae) were reconstructed on the basis on nucleotide sequences of the mitochondrial COI gene. The results of Bayesian analysis pointed to the relationships of the endemics with the North American Apatania incerta (Banks, 1897) and A. sorex (Ross, 1941). The divergence of the genetic lineages of the Baikalian and Nearctic apataniids occurred in the Late Oligocene–Early Miocene. On the dendrogram, endemic species formed two monophyletic clades corresponding to the tribes Thamastini and Baicalinini. It was also found that the genus Protobaicalina was polyphyletic, while the genus Baicalina was a species flock. Our analysis showed that the nearest common ancestor of the studied Baikal caddisfly species existed about 21 Mya, while the modern species composition of endemic fauna dates back to Pliocene–Pleistocene age (2.5–0.7 million years).

Are there species flocks in freshwater diatoms? A review of past reports and a look to the future

We review the literature on species flocks in diatoms. Past descriptions of species flocks in diatoms are of few species and do not demonstrate monophyly of the taxa explicitly. The genus Tetralunata, with 19 taxa described from Lake Toba, Indonesia, may be the best example to date of species flocks in freshwater diatoms. Other examples for this group are evaluated, from ancient lakes, river drainages and islands, to more geologically short-lived areas and habitats. Other examples may reside in the Rift Valley lakes of East Africa, Amazonia, lakes Baikal, and Ohrid, and some islands such as New Caledonia, Sulawesi, and Madagascar. It would appear that the phenomenon is not expressed in Hawaii, which has endemic, but very few, species. It is interesting to note that nearly all of the examples of species flocks of extant diatoms are of those groups that possess a raphe system. The role of molecular studies to study species flocks is discussed. Other features not traditionally examined to recognize species-level distinctions (physiology, ecology) which may be useful in the future to help identify species flocks in freshwater diatoms.

Transcriptome-based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection.

Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two nonendemic outgroups, we report a revised phylogeny of this species flock and analyse evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armour and reduction in appendages and sensory organs, evolved in several lineages in parallel. Radiation of Baikal amphipods has been characterized by short phylogenetic branches and frequent episodes of positive selection which tended to be more frequent in the early phase of the second invasion of amphipods into Baikal when the most intensive diversification occurred. Notably, signatures of positive selection are frequent in genes encoding mitochondrial membrane proteins with electron transfer chain and ATP synthesis functionality. In particular, subunits of both the membrane and substrate-level ATP synthases show evidence of positive selection in the plankton species Macrohectopus branickii, possibly indicating adaptation to active plankton lifestyle and to survival under conditions of low temperature and high hydrostatic pressures known to affect membranes functioning. Other functional categories represented among genes likely to be under positive selection include Ca-binding muscle-related proteins, possibly indicating adaptation to Ca-deficient low mineralization Baikal waters.

Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation.

Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype‐environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large‐scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi.

Urbanized White Ibises (Eudocimus albus) as Carriers of Salmonella enterica of Significance to Public Health and Wildlife.

Worldwide, Salmonella spp. is a significant cause of disease for both humans and wildlife, with wild birds adapted to urban environments having different opportunities for pathogen exposure, infection, and transmission compared to their natural conspecifics. Food provisioning by people may influence these factors, especially when high-density mixed species flocks aggregate. White Ibises (Eudocimus albus), an iconic Everglades species in decline in Florida, are becoming increasingly common in urbanized areas of south Florida where most are hand-fed. We examined the prevalence of Salmonella shedding by ibises to determine the role of landscape characteristics where ibis forage and their behavior, on shedding rates. We also compared Salmonella isolated from ibises to human isolates to better understand non-foodborne human salmonellosis. From 2010–2013, 13% (n = 261) adult/subadult ibises and 35% (n = 72) nestlings sampled were shedding Salmonella. The prevalence of Salmonella shedding by ibises significantly decreased as the percent of Palustrine emergent wetlands and herbaceous grasslands increased, and increased as the proportion of open-developed land types (e.g. parks, lawns, golf courses) increased, suggesting that natural ecosystem land cover types supported birds with a lower prevalence of infection. A high diversity of Salmonella serotypes (n = 24) and strain types (43 PFGE types) were shed by ibises, of which 33% of the serotypes ranked in the top 20 of high significance for people in the years of the study. Importantly, 44% of the Salmonella Pulsed-Field Gel Electrophoresis patterns for ibis isolates (n = 43) matched profiles in the CDC PulseNet USA database. Of these, 20% came from Florida in the same three years we sampled ibis. Importantly, there was a negative relationship between the amount of Palustrine emergent wetland and the number of Salmonella isolates from ibises that matched human cases in the PulseNet database (p = 0.056). Together, our results indicate that ibises are good indicators of salmonellae strains circulating in their environment and they have both the potential and opportunity to transmit salmonellae to people. Finally, they may act as salmonellae carriers to natural environments where other more highly-susceptible groups (nestlings) may be detrimentally affected.

Experimental Evidence Shows the Importance of Behavioural Plasticity and Body Size under Competition in Waterfowl.

When differently sized species feed on the same resources, interference competition may occur, which may negatively affect their food intake rate. It is expected that competition between species also alters behaviour and feeding patch selection. To assess these changes in behaviour and patch selection, we applied an experimental approach using captive birds of three differently sized Anatidae species: wigeon (Anas penelope) (~600 g), swan goose (Anser cygnoides) (~2700 g) and bean goose (Anser fabalis) (~3200 g). We quantified the functional response for each species and then recorded their behaviour and patch selection with and without potential competitors, using different species combinations. Our results showed that all three species acquired the highest nitrogen intake at relatively tall swards (6, 9 cm) when foraging in single species flocks in the functional response experiment. Goose species were offered foraging patches differing in sward height with and without competitors, and we tested for the effect of competition on foraging behaviour. The mean percentage of time spent feeding and being vigilant did not change under competition for all species. However, all species utilized strategies that increased their peck rate on patches across different sward heights, resulting in the same instantaneous and nitrogen intake rate. Our results suggest that variation in peck rate over different swards height permits Anatidae herbivores to compensate for the loss of intake under competition, illustrating the importance of behavioural plasticity in heterogeneous environments when competing with other species for resources.

A Revision of the Pseudotropheus elongatus species group (Teleostei: Cichlidae) With Description of a New Genus and Seven New Species

Lake Malaŵi is known for its endemic haplochromine species flock, most notably the rock-dwelling cichlids known as mbuna. The group of mbuna referred to as the Pseudotropheus elongatus species group is currently comprised of Metriaclima spp., Tropheops spp., Cynotilapia spp., and Pseudotropheus spp. In this study, Chindongo, a new genus with the type species C. bellicosus, is described for additional species in this group. Chindongo is distinguished from other mbuna genera by 1) the presence of bicuspid teeth in the anterior portion of the outer row of both upper and lower jaw; 2) a moderately to steeply sloped vomer with a narrow rostral tip which makes an angle of between 53° and 68° with the parasphenoid; 3) a small mouth with the lower jaw slightly shorter than the upper; 4) a broad anterior dentigerous area on both premaxilla and dentary with three or more rows of teeth (usually 5-6 rows); 5) a flank melanin pattern consisting of vertical bars without horizontal elements at any stage of development. Chindongo bellicosus is distinguished by its color pattern and shallower body from the other species which we have transferred to Chindongo. We also describe six new elongate mbuna species and place them into three available genera, they include: Metriaclima flavicauda, M. usisyae, Tropheops kumwera, T. biriwera, T. kamtambo, and Cynotilapia chilundu.

Use of urban areas by two emblematic and threatened birds in the central Andes of Colombia

The Turquoise Dacnis ( Dacnis hartlaubi ) and the Cerulean Warbler ( Setophaga cerulea ) are categorized as “vulnerable” at global scale. Habitat loss and degradation following rapid agricultural expansion and urban development are the main causes of their declines. In this note we present the first documented records of these species in urban green areas in South America. Our observations were undertaken between 2007–2014 during surveys of the avifauna of Armenia City in the central Andes of Colombia. We recorded Turquoise Dacnis on 19 occasions and Cerulean Warbler on 10. Most records were solitary males foraging in Cecropia angustifolia and Inga ornata trees, and some were associated with mixed species flocks. Both species used forest patches, parks and areas with scattered trees. Our observations suggest that cities may provide passage and/or wintering areas for these threatened species.

Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes.

Adaptive radiation is thought to be responsible for the evolution of a great portion of the past and present diversity of life. Instances of adaptive radiation, characterized by the rapid emergence of an array of species as a consequence to their adaptation to distinct ecological niches, are important study systems in evolutionary biology. However, because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression. This led us to formulate three hypotheses of introgression between different lineages of Tanganyika cichlids: the ancestor of Boulengerochromini (or of Boulengerochromini and Bathybatini) received genomic material from the derived H-lineage; the common ancestor of Cyprichromini and Perissodini experienced, in turn, introgression from Boulengerochromini and/or Bathybatini; and the Lake Tanganyika Haplochromini and closely related riverine lineages received genetic material from Cyphotilapiini. We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree, in which the Lamprologini were placed as sister lineage to the H-lineage (including the Eretmodini), and we identify a series of rapid splitting events at the base of the H-lineage. Divergence ages estimated with the multispecies coalescent model were substantially younger than age estimates based on concatenation, and agree with the geological history of the Great Lakes of East Africa. Finally, we formally tested the three hypotheses of introgression using a likelihood framework, and find strong support for introgression between some of the cichlid tribes of Lake Tanganyika.