Roger Bills

Nuclear markers reveal unexpected genetic variation and a Congolese-Nilotic origin of the Lake Victoria cichlid species flock

Phylogenetic analyses based on mitochondrial (mt) DNA have indicated that the cichlid species flock of the Lake Victoria region is derived from a single ancestral species found in East African rivers, closely related to the ancestor of the Lake Malawi cichlid species flock. The Lake Victoria flock contains ten times less mtDNA variation than the Lake Malawi radiation, consistent with current estimates of the ages of the lakes. We present results of a phylogenetic investigation using nuclear (amplified fragment length polymorphism) markers and a wider coverage of riverine haplochromines. We demonstrate that the Lake Victoria–Edward flock is derived from the morphologically and ecologically diverse cichlid genus Thoracochromis from the Congo and Nile, rather than from the phenotypically conservative East African Astatotilapia. This implies that the ability to express much of the morphological diversity found in the species flock may by far pre–date the origin of the flock. Our data indicate that the nuclear diversity of the Lake Victoria–Edward species flock is similar to that of the Lake Malawi flock, indicating that the genetic diversity is considerably older than the 15 000 years that have passed since the lake began to refill. Most of this variation is manifested in trans–species polymorphisms, indicating very recent cladogenesis from a genetically very diverse founder stock. Our data do not confirm strict monophyly of either of the species flocks, but raise the possibility that these flocks have arisen from hybrid swarms.

An extant cichlid fish radiation emerged in an extinct Pleistocene lake

The haplochromine cichlid fish of the East African Great Lakes represent some of the fastest and most species-rich adaptive radiations known, but rivers in most of Africa accommodate only a few morphologically similar species of haplochromine cichlid fish. This has been explained by the wealth of ecological opportunity in large lakes compared with rivers. It is therefore surprising that the rivers of southern Africa harbour many, ecologically diverse haplochromines. Here we present genetic, morphological and biogeographical evidence suggesting that these riverine cichlids are products of a recent adaptive radiation in a large lake that dried up in the Holocene. Haplochromine species richness peaks steeply in an area for which geological data reveal the historical existence of Lake palaeo-Makgadikgadi. The centre of this extinct lake is now a saltpan north of the Kalahari Desert, but it once hosted a rapidly evolving fish species radiation, comparable in morphological diversity to that in the extant African Great Lakes. Importantly, this lake seeded all major river systems of southern Africa with ecologically diverse cichlids. This discovery reveals how local evolutionary processes operating during a short window of ecological opportunity can have a major and lasting effect on biodiversity on a continental scale.

Continental diversification of an African catfish radiation (Mochokidae: Synodontis).

Despite African rivers containing high species diversity, continental-scale studies investigating the mechanisms generating biological diversity of African riverine faunas are limited compared with lacustrine systems. To investigate the build-up of diversity in a tropical aquatic continental radiation, we test different models of lineage diversification and reconstruct the biogeographic history in a species-rich siluriform genus, Synodontis (~130 species), with a broad distribution across all major tropical African drainage basins. The resulting robust species-level phylogeny (~60% complete, based on a multigene data set) exhibits a near constant rate of lineage accumulation throughout the mid-Cenozoic to recent, irrespective of missing species and despite the changing environmental conditions that were prevalent during this time period. This pattern contrasts with the findings for species-level diversification of large clades that commonly show an early burst of cladogenesis followed by declining rates through time. The identification of distinct biogeographic clades demonstrates a correlation between river hydrology and cladogenesis, although there is evidence of recent repeat dispersal into the southern range of the focal group. We conclude that diverse freshwater fish radiations with tropical continental distributions represent important organisms to test hypotheses of diversification and investigate the effects of palaeo-landscapes and climates on present day biodiversity.

Lacustrine radiations in African Synodontis catfish

Synodontis catfish are a species‐rich, tropical pan‐African genus that predominately occur in fluviatile environments, but which also form a small radiation within Lake Tanganyika (LT). Here we estimate Synodontis relationships, based on mitochondrial and nuclear DNA, greatly expanding previous sampling. Data were analysed using different methods of phylogenetic inference: Bayesian (also testing compositional heterogeneity), likelihood and parsimony, in order to investigate biogeographic history and the extent of intralacustrine speciation within this group. Bayesian‐relaxed clock analyses were used to estimate timings of radiations. Our analyses reveal a single origin of the LT flock with the inclusion of the nonendemic S. victoriae, and that these taxa evolved relatively recently (5.5 Ma), considerably later than the formation of LT (9–12 Ma). Two internal endemic clades diversified at a similar time (2–2.5 Ma), corresponding to a period of climate change, when lake levels dropped. We find evidence for a further species flock, composed of riverine southern African taxa, the diversification of which is very rapid, 0.8 Ma (95% HPD: 0.4–1.5) and infer a similar scenario for the diversification of this flock to southern African serrachromine cichlids in that they radiated in the now extinct lake Makgadikgadi. We also reveal that the biogeographic history of Synodontis catfish is more complex than previously thought, with nonmonophyletic geographic species groupings.

Mastacembelid eels support lake tanganyika as an evolutionary hotspot of diversification

BackgroundLake Tanganyika (LT) is the oldest of the African Rift Lakes and is one of the richest freshwater ecosystems on Earth, with high levels of faunal diversity and endemism. The endemic species flocks that occur in this lake, such as cichlid fishes, gastropods, catfish and crabs, provide unique comparative systems for the study of patterns and processes of speciation. Mastacembelid eels (Teleostei: Mastacembelidae) are a predominately riverine family of freshwater fish, occurring across Africa and Asia, but which also form a small species flock in LT.MethodsIncluding 25 species across Africa, plus Asian representatives as outgroups, we present the first molecular phylogenetic analysis for the group, focusing particularly on the evolutionary history and biodiversity of LT mastacembelid eels. A combined matrix of nuclear and mitochondrial genes based on 3118 bp are analysed implementing different phylogenetic methods, including Bayesian inference and maximum likelihood.ResultsLT Mastacembelus are recovered as monophyletic, and analyses reveal the rapid diversification of five main LT lineages. Relaxed molecular clock dates provide age estimates for the LT flock at ~7-8 Myr, indicating intralacustrine diversification, with further speciation events coinciding with periods of lower lake level. Our analyses also reveal as yet undescribed diversity of lacustrine and riverine species. A Southern-Eastern African clade, that is younger than the LT flock, is also recovered, while West African taxa are basal members of the African mastacembelid clade.ConclusionsThat the LT species flock of mastacembelid eels appears to have colonised and immediately diversified soon after the formation of the lake, supports the view of LT as an evolutionary hotspot of diversification. We find evidence for biogeographic clades mirroring a similar pattern to other ichthyological faunas. In addition, our analyses also highlight a split of African and Asian mastacembelid eels at ~19 Myr that is considerably younger than the split between their associated continents, suggesting a dispersal scenario for their current distribution.

A critical revision of the churchill snoutfish, genus Petrocephalus Marcusen, 1854 (Actinopterygii: Teleostei: Mormyridae), from southern and eastern Africa, with the recognition of Petrocephalus tanensis, and the description of five new species

We morphologically and genetically studied the southern African electric fish Petrocephalus catostoma, or churchill, and its six nominal species, five of which by synonymization (three valid subspecies). We reinstate the synonymized species, and recognize Petrocephalus tanensis (Whitehead and Greenwood, 1959) from the Tana River in Kenya, also using electric organ discharges. The Okavango delta (Botswana) is inhabited by Petrocephalus okavangensis sp. nov. and Petrocephalus magnitrunci sp. nov., and the Namibian Cunene River by Petrocephalus magnoculis sp. nov. We recognize Petrocephalus petersi sp. nov. for the Lower Zambezi River (Mozambique), and Petrocephalus longicapitis sp. nov. for the Upper Zambezi River (Namibia). The Lufubu River in Northern Zambia is inhabited by Petrocephalus longianalis sp. nov. For the southern churchill, Petrocephalus wesselsi Kramer and Van der Bank, 2000, we confirm intraspecific and interspecific differentiation. Sequence data from mitochondrial DNA confirm differentiation of two new western and two eastern species, forming mutual sister groups.

Nocturnal claroteine catfishes reveal dual colonisation but a single radiation in Lake Tanganyika

Lake Tanganyika (LT) is a biodiversity hotspot supporting many endemic radiations that provide comparative systems in which to investigate if there are common factors leading to the build-up of its considerable diversity. Despite LT containing the highest diversity of lacustrine catfishes on Earth, the evolutionary relationships of nocturnal catfishes within the sub-family Claroteinae have not been investigated and it is unknown if its constituent genera have diversified via single or independent colonisation events. We report the first molecular phylogeny of the LT claroteine catfishes based on a multigene dataset (three nuclear markers, two mitochondrial totalling 4227 bp), including 85 samples from LT and outside of the lake basin. These data support LT claroteine monophyly, with the exclusion of the LT endemic Chrysichthys brachynema that independently colonised the lake but has not radiated. Multiple sampling localities from LT and the use of Bayesian species delimitation methods reveal additional locally restricted diversity within the LT Claroteinae clade. Fossil calibrated molecular divergence dates suggest that diversification occurred within full lake conditions as demonstrated in other LT lineages.

The composition and health of fishes in residual dry season habitats in southern Africa (Strauch et al. 2015)

A recent paper on the composition and health of fish in refugia habitats in seasonal tributaries of the Zambezi River in southern Africa contains several errors. These include the misidentification of species and a misunderstanding of the zoogeography of the Zambezi River. There were also several weaknesses in the data analysis and some conclusions were based on misinterpretations of their own data and the literature. The authors should have considered regional literature and worked with southern African ichthyologists to prevent these errors.