A small cichlid species flock from the Upper Miocene (9--10 MYA) of Central Kenya

Fossil cichlids from East Africa offer unique insights into the evolutionary history and ancient diversity of the family on the African continent. Here we present three fossil species of the extinct haplotilapiine cichlid †Baringochromis gen. nov. from the upper Miocene of the palaeolake Waril in Central Kenya, based on the analysis of a total of 78 articulated skeletons. †Baringochromis senutae sp. nov., †B. sonyii sp. nov. and †B. tallamae sp. nov. are superficially similar, but differ from each other in oral-tooth dentition and morphometric characters related to the head, dorsal fin base and body depth. These findings indicate that they represent an ancient small species flock. Possible modern analogues of palaeolake Waril and its species flock are discussed. The three species of †Baringochromis may have begun to subdivide their initial habitat by trophic differentiation. Possible sources of food could have been plant remains and insects, as their fossilized remains are known from the same place where †Baringochromis was found

Fish fossils from Miocene palaeolakes in the East African Rift Valley in Kenya

Africa’s modern-day freshwater fish fauna comprises more than 3000 species, many of them endemic, and is dominated by a few teleost lineages among which the Cyprinodontiformes and the Cichlidae are especially prominent. Even though members of both groups are used as model organisms in evolutionary studies, their evolutionary history is not yet fully understood. This is in part due to their scant fossil record. The main purpose of this dissertation is to investigate the palaeodiversity of freshwater fishes on the African continent during the Miocene epoch, focusing particularly on the Lukeino and Ngorora Formations in the Central Kenya Rift. The material described in this study forms part of a collection consisting of about 650 articulated fish fossils, which were recovered from the upper Miocene Lukeino Formation and the middle–upper Miocene Ngorora Formation in the course of two field campaigns in 2013 and 2014. To provide a context for a better understanding of the new fossils of Cyprinodontiformes and Cichlidae, a comprehensive comparative dataset, including data on meristics, osteology, scale characters and otolith morphology, was assembled for extant representatives of both groups. The dataset for the Cichlidae includes all previously recognized lineages of African cichlids, and is the first of its kind designed to facilitate the phylogenetic placement of cichlid fossils. This new dataset was used to organize the taxonomic studies and to analyse the phylogenetic relationships of the fossils. The results presented here shed new light on the evolutionary history of both Cyprinodontiformes and Cichlidae, and provide new information on Miocene palaeoenvironments and hydrological networks in the Central Kenya Rift. The upper Miocene Lukeino Formation has yielded numerous well-preserved cyprinodontiform fossils of an extinct lineage of the suborder Aplocheiloidei, which represent the first fossil record of this group. On the basis of the morphological study and the phylogenetic analysis, the new taxon was assigned to the new family †Kenyaichthyidae, the new genus †Kenyaichthys and the new species †K. kipkechi sp. nov. The specimens of †K. kipkechi show wide variation in their meristic counts and morphometric traits, which is comparable to that found in recent sympatric species with variable grades of hybridization. †K. kipkechi thus presumably represents a fossil species flock in statu nascendi. The phylogenetic analysis unexpectedly places †K. kipkechi in a sister relationship to the exclusively Neotropical family Rivulidae, a probable explanation might be lack of available synapomorphies for the Rivulidae, Nothobranchiidae and Aplocheilidae. Moreover, the comparison with the recent material revealed that previously proposed apomorphic characters concerning the neural and haemal spines of the preural vertebrae in the caudal skeleton should be revised. The scarcity of other typical freshwater fishes in the Lukeino Formation and the close relationship of †K. kipkechi to the aplocheiloid families Nothobranchiidae and Rivulidae suggest a seasonally dry climate for the palaeoenvironment. Some recent members of the Nothobranchiidae and Rivulidae are known to withstand such harsh conditions due to their ability to produce desiccation-resistant eggs. The new taxon may perhaps have had a similar life cycle. In addition, deformities of the vertebral column are prominent in our sample and point to a strong influence of volcanic activity on the aquatic environment. The study of the middle–upper Miocene Ngorora fish Lagerstätte uncovered two remarkable new fossil taxa of the family Cichlidae. The first is †Protochromis pickfordi nov. gen. nov. sp. Comparative osteological and meristic studies revealed that †P. pickfordi is closely related to the present-day tribes Ectodini and Limnochromini in Lake Tanganyika. This is further supported by a Principal Coordinates Analysis based on meristic data. Due to its unique character set, which includes a tripartite lateral line and a lacrimal with six lateral line tubules, it is suggested that †P. pickfordi belongs to a precursor lineage of the ‘ancient Tanganyika mouth-brooders’. The presence of a Miocene precursor of Lake Tanganyika cichlids far outside the drainage area of the present-day Lake Tanganyika implies an ancient hydrological connection between the Central Kenya Rift and Lake Tanganyika, which supports the hypothesis that a significant portion of the genomic diversity of modern-day Lake Tanganyika cichlids is derived from riverine cichlids. The second new taxon, †Baringochromis nov. gen., is based on the analysis of 335 well-preserved fossil specimens. Its unique combination of characters, most prominently one predorsal bone, six infraorbitals including a lacrimal with four or five lateral line tubules, a partially scaled suboperculum and a low number of anal and dorsal fin spines, puts it in an intermediate position between the almost pan-African Oreochromini and the exclusively East African Haplochromini. This placement is supported by a Principal Coordinates Analysis based on meristic data. The discovery of †Baringochromis therefore suggests a scenario in which precursor lineages of the present-day Oreochromini and Haplochromini were widely distributed throughout East Africa and underwent hybridization in rivers prior to the formation of the Rift Lakes. Taken together, the data reveal that, due to their mosaic-like character sets, the new fossil cyprinodontiform and cichlid taxa cannot be confidently placed within available phylogenetic trees. This implies that the evolutionary history of these two freshwater fish groups cannot be described solely in terms of lineage splitting, and probably involved introgression and hybridization, as already suggested by studies based on molecular data for the Cichlidae. Moreover, the results highlight the value of fossil archives with high preservation quality, like the Lukeino Formation and the Ngorora fish Lagerstätte, for the understanding of past evolutionary processes

New haplochromine cichlid from the upper Miocene (9-10 MYA) of Central Kenya

Background: The diversification process known as the Lake Tanganyika Radiation has given rise to the most speciose clade of African cichlids. Almost all cichlid species found in the lakes Tanganyika, Malawi and Victoria, comprising a total of 12-16 tribes, belong to this clade. Strikingly, all the species in the latter two lakes are members of the tribe Haplochromini, whose origin remains unclear. The 'out of Tanganyika' hypothesis argues that the Haplochromini emerged simultaneously with other cichlid tribes and lineages in Lake Tanganyika, presumably about 5-6 million years ago (MYA), and that their presence in the lakes Malawi and Victoria and elsewhere in Africa today is due to later migrations. In contrast, the 'melting pot Tanganyika hypothesis' postulates that Haplochromini emerged in Africa prior to the formation of Lake Tanganyika, and that their divergence could have begun about 17 MYA. Haplochromine fossils could potentially resolve this debate, but such fossils are extremely rare. Results: Here we present a new fossil haplochromine from the upper Miocene site Waril (9-10 million years) in Central Kenya. Comparative morphology, supported by Micro-CT imaging, reveals that it bears a unique combination of characters relating to dentition, cranial bones, caudal skeleton and meristic traits. Its most prominent feature is the presence of exclusively unicuspid teeth, with canines in the outer tooth row. †Warilochromis unicuspidatus gen. et sp. nov. shares this combination of characters solely with members of the Haplochromini and its lacrimal morphology indicates a possible relation to the riverine genus Pseudocrenilabrus. Due to its fang-like dentition and non-fusiform body, †W. unicuspidatus gen. et sp. nov. might have employed either a sit-and-pursue or sit-and-wait hunting strategy, which has not been reported for any other fossil haplochromine cichlid. Conclusions: The age of the fossil (9-10 MYA) is incompatible with the 'out of Tanganyika' hypothesis, which postulates that the divergence of the Haplochromini began only 5-6 MYA. The presence of this fossil in an upper Miocene palaeolake in the Central Kenya Rift, as well as its predatory lifestyle, indicate that Haplochromini were already an important component of freshwater drainages in East Africa at that time

New fossil cichlid from the middle Miocene of East Africa revealed as oldest known member of the Oreochromini

A new genus and species of fossil cichlid fishes of middle Miocene age (12.5 Ma) is described from the Ngorora fish Lagerstatte (Tugen Hills, Kenya) in the East African Rift Valley. Parsimony analysis of morphological characters using published phylogenetic frameworks for extant cichlids combined with the application of a comprehensive best-fit approach based on morphology was employed to place the new fossil taxon in the phylogenetic context of the African cichlids. The data reveal that the fossil specimens can be assigned to the tribe Oreochromini within the haplotilapiines. +Oreochromimos kabchorensis gen. et sp. nov. shows a mosaic set of characters bearing many similarities to the almost pan-African Oreochromis and the East African lake-endemic Alcolapia. As the striking diversity of present-day African cichlids, with 1100 recognised species, has remained largely invisible in the fossil record, the material described here adds significantly to our knowledge of the Miocene diversity of the group. It effectively doubles the age of a fossil calibration point, which has hitherto been used to calibrate divergence times of the East African cichlids in molecular phylogenetic investigations. Furthermore, the comparative dataset derived from extant cichlids presented here will greatly facilitate the classification of fossil cichlids in future studies

†Kenyaichthyidae fam. nov and †Kenyaichthys gen. nov - First Record of a Fossil Aplocheiloid Killifish (Teleostei, Cyprinodontiformes)

The extant Cyprinodontiformes (killifishes) with their two suborders Cyprinodontoidei and Aplocheiloidei represent a diverse and well-studied group of fishes. However, their fossil record is comparatively sparse and has so far yielded members of the Cyprinodontoidei only. Here we report on cyprinodontiform fossils from the upper Miocene Lukeino Formation in the Tugen Hills of the Central Rift Valley of Kenya, which represent the first fossil record of an aplocheiloid killifish. A total of 169 specimens - mostly extraordinarily well preserved and a sample of ten extant cyprinodontiform species were studied on the basis of morphometrics, meristics and osteology. A phylogenetic analysis using PAUP was also conducted for the fossils. Both the osteological data and the phylogenetic analysis provide strong evidence for the assignment of the fossils to the Aplocheiloidei, and justify the definition of the new family dagger Kenyaichthyidae, the new genus dagger Kenyaichthys and the new species dagger K. kipkechi sp. nov. The phylogenetic analysis unexpectedly places dagger Kenyaichthys gen. nov. in a sister relationship to the Rivulidae (a purely Neotropical group),a probable explanation might be lack of available synapomorphies for the Rivulidae, Nothobranchiidae and Aplocheilidae. The specimens of dagger K. kipkechi sp. nov. show several polymorphic characters and large overlap in meristic traits, which justifies their interpretation as a species flock in statu nascendi. Patterns of variation in neural and haemal spine dimensions in the caudal vertebrae of dagger Kenyaichthys gen. nov. and the extant species studied indicate that some previously suggested synapomorphies of the Cyprinodontoidei and Aplocheiloidei need to be revised

A new fossil cichlid from the Middle Miocene in the East African Rift Valley (Tugen Hills, Central Kenya): First record of a putative Ectodini

Identification of fossil cichlids is difficult, because the currently used diagnostic morphological characters for living cichlids are mostly soft tissue based and such characters are hardly preserved in fossils. During our recent fieldwork in the Central Kenya Rift (E-Africa), we discovered several exceptionally well-preserved fossil cichlids, which can be assigned to different lineages among the African Pseudocrenilabrinae. Here we present one of those new specimens. Its most conspicuous character is a lateral line divided into three segments. This specimen was found in the lacustrine sediments of the Middle Miocene site Waril, Tugen Hills, Kenya. The site represents the deposits of an ancient freshwater lake ca. 9-10 million years ago. Previous work on fossil leaves from the same site allow for the reconstruction of open vegetation surrounding the lake and pronounced dry seasons. Among the main further characteristics of the new fossil cichlid is a lachrimal with six lateral line canals, big cycloid scales and a low number of dorsal fin spines (XIII). The latter two characters are traceable in several members of tribes within the Pseudocrenilabrinae. However, a lachrimal with six lateral line canals is exclusively found in certain tribes of the EAR (East African Radiation within the Pseudocrenilabrinae). Moreover, the unique lateral line pattern is solely present in two genera of the EAR tribe Ectodini. However, the fossil shows cycloid scales, while modern Ectodini have ctenoid scales. Taken all evidence together, this fossil may perhaps represent an ancient lineage related to the Ectodini. Up to date, there is no definite fossil record of the members of the EAR. Our fossil may represent the first reliable calibration point for this group, which would be consistent with the previously reconstructed diversification time of the H-lineage (EAR tribes, except Boulengerochromini, Bathybatini, Trematocarini and Lamprologini) and the Lamprologini ca. 15 million years ago

Schematic drawings indicating measurements used in this study.

<p><b>A</b>, morphometric parameters; <b>B1–B2</b> measurements of hypural plate length and width and measurements of the spine widths on the caudal skeleton of †<i>K</i>. <i>kipkechi</i> sp. nov. (paratype 1200´04); note that the proximal part of the parhypural (with an anteroventral projection) does not overlap the terminal centrum, left lateral view. Abbreviations: ep, epural; Go, gill opening; H, maximum body depth; h, minimum body depth; hA, depth of anal fin; hc, head depth; hD, depth of dorsal fin; hs2–5, haemal spine of preural vertebrae 2–5; lA, length of anal fin base; lc, length of head; lC, length of caudal fin; lD, length of dorsal fin base; lmd, lower jaw length, i.e. distance from anteriormost point of lower jaw symphysis to posteriormost margin of mandibular joint; lH, length of hypural plate; lmx, upper jaw length, i.e. distance between anteriormost point of premaxillary and posteriormost point of maxillary; lP, length of pectoral fin; lPbs, length of pectoral fin base; lpc, length of caudal peduncle; lV, length of pelvic fin; lVbs, length of pelvic fin base; ns2–5, neural spine of preural vertebrae 2–5; Or, eye diameter; pA, preanal distance; P–A, distance between pectoral fin base and anal fin base; pD, predorsal distance; phy, parhypural; poA, postanal distance, i.e. from posterior end of anal fin to end of caudal fin rays; poD, postdorsal distance, i.e. from posterior end of dorsal fin to end of caudal fin rays; pP, prepectoral distance; prO, preorbital distance; pu2–4, preural vertebrae 2–4; pV, prepelvic distance; P–V, distance between pectoral fin base and pelvic fin base; s, stegural; SL, standard length; TL, total length; V–A, distance between pelvic fin base and anal fin base; wH, width of hypural plate.</p

Summary of the osteological synapomorphies for the Cyprinodontoidei and Aplocheiloidei and comparisons with †<i>Kenyaichthys</i> gen. et sp. nov. compiled from [1], [3], [48] and [50].

<p>Summary of the osteological synapomorphies for the Cyprinodontoidei and Aplocheiloidei and comparisons with †<i>Kenyaichthys</i> gen. et sp. nov. compiled from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123056#pone.0123056.ref001" target="_blank">1</a>], [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123056#pone.0123056.ref003" target="_blank">3</a>], [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123056#pone.0123056.ref048" target="_blank">48</a>] and [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123056#pone.0123056.ref050" target="_blank">50</a>].</p

Spine ratios (means and ranges) of †<i>Kenyaichthys</i> gen. et sp. nov. and the recent cyprinodontiform species used for comparison.

<p>Spine ratios (means and ranges) of †<i>Kenyaichthys</i> gen. et sp. nov. and the recent cyprinodontiform species used for comparison.</p

Anatomical details of †<i>Kenyaichthys</i> nov. gen. (holotype 1209a´05, †<i>K</i>. <i>kipkechi</i>), left lateral view.

<p><b>A1</b> General overview (photograph by Dr. W. Altner); <b>A2–A3</b> Close up of the head and pectoral girdle (the lacrimal is from the counterpart and mirrored for clarity); <b>A4–A5</b> Close-up of lower and upper jaw; <b>A6</b> Detail of abdominal part showing vertebrae, pleural ribs and epipleural ribs; <b>A7</b> Truncate to rounded caudal fin. Abbreviations: apl, autopalatinum; art, anguloarticular; asc, premaxillary ascending process; br, branchiostegal rays; cer, ceratohyal; cl, cleithrum; den, dentary; dmx, dorsal maxillary process; end, endopterygoid; fro, frontal; hyo, hyomandibula; l, lacrimal; max, maxilla; op, operculum; pas, parasphenoid; pmx, premaxilla; pop, preoperculum; ptt, posttemporal; qua, quadratum; ret, retroarticular; soc-pro, supraoccipital process.</p