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Milec LJM, Vanhove MPM, Bukinga FM, De Keyzer ELR, Kapepula VL, Masilya PM, Mulimbwa N, Wagner CE, Raeymaekers JAM. Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation. BMC Ecol Evol 2022; 22:127. [PMID: 36329403 PMCID: PMC9635120 DOI: 10.1186/s12862-022-02085-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Background The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissatanganicae and Limnothrissamiodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids. Results We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S.tanganicae and L.miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissaobtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P.obtusirostris around 10.92 MYA [95% CI: 6.37–15.48]. Conclusions These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02085-8.
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Affiliation(s)
- Leona J. M. Milec
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway ,grid.12155.320000 0001 0604 5662Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Maarten P. M. Vanhove
- grid.12155.320000 0001 0604 5662Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium ,grid.5596.f0000 0001 0668 7884Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Déberiotstraat 32, 3000 Leuven, Belgium
| | - Fidel Muterezi Bukinga
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo
| | - Els L. R. De Keyzer
- grid.5596.f0000 0001 0668 7884Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Charles Déberiotstraat 32, 3000 Leuven, Belgium ,grid.5284.b0000 0001 0790 3681Evolutionary Ecology Group (EVECO), Universiteit Antwerpen, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Vercus Lumami Kapepula
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo ,grid.7942.80000 0001 2294 713XUniversité Catholique de Louvain, Place Sainte Barbe 2, 1348 Louvain-la-Neuve, Belgium
| | - Pascal Mulungula Masilya
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo ,Unité d’Enseignement et de Recherche en Hydrobiologie Appliquée (UERHA)-ISP/Bukavu, Bukavu, Sud-Kivu Democratic Republic of Congo
| | - N’Sibula Mulimbwa
- Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira), Uvira, Sud-Kivu Democratic Republic of Congo
| | - Catherine E. Wagner
- grid.135963.b0000 0001 2109 0381University of Wyoming, 1000 E University Ave, Laramie, WY 82071 USA
| | - Joost A. M. Raeymaekers
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026 Bodø, Norway
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Rick JA, Junker J, Kimirei IA, Sweke EA, Mosille JB, Dinkel C, Mwaiko S, Seehausen O, Wagner CE. The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators. J Hered 2022; 113:145-159. [PMID: 35575081 PMCID: PMC9113442 DOI: 10.1093/jhered/esab072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding genetic connectivity plays a crucial role in species conservation decisions, and genetic connectivity is an important component of modern fisheries management. In this study, we investigated the population genetics of four endemic Lates species of Lake Tanganyika (Lates stappersii, L. microlepis, L. mariae, and L. angustifrons) using reduced-representation genomic sequencing methods. We find the four species to be strongly differentiated from one another (mean interspecific FST = 0.665), with no evidence for contemporary admixture. We also find evidence for strong genetic structure within L. mariae, with the majority of individuals from the most southern sampling site forming a genetic group that is distinct from the individuals at other sampling sites. We find evidence for much weaker structure within the other three species (L. stappersii, L. microlepis, and L. angustifrons). Our ability to detect this weak structure despite small and unbalanced sample sizes and imprecise geographic sampling locations suggests the possibility for further structure undetected in our study. We call for further research into the origins of the genetic differentiation in these four species-particularly that of L. mariae-which may be important for conservation and management of this culturally and economically important clade of fishes.
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Affiliation(s)
- Jessica A Rick
- Department of Botany and Program in Ecology, University of Wyoming, 1000 E University Dr., Laramie, WY 82072, USA
| | - Julian Junker
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Ismael A Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Emmanuel A Sweke
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
- Deep Sea Fishing Authority (DSFA), Zanzibar, Tanzania
| | - Julieth B Mosille
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Christian Dinkel
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
| | - Salome Mwaiko
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Ole Seehausen
- EAWAG Swiss Federal Institute of Aquatic Science and Technology, CH-6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Catherine E Wagner
- Department of Botany and Program in Ecology, University of Wyoming, 1000 E University Dr., Laramie, WY 82072, USA
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Rahmouni C, Vanhove MP, Koblmüller S, Šimková A. Molecular phylogeny and speciation patterns in host-specific monogeneans (Cichlidogyrus, Dactylogyridae) parasitizing cichlid fishes (Cichliformes, Cichlidae) in lake tanganyika. Int J Parasitol 2022; 52:359-375. [DOI: 10.1016/j.ijpara.2021.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 12/01/2022]
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Contrasting Host-Parasite Population Structure: Morphology and Mitogenomics of a Parasitic Flatworm on Pelagic Deepwater Cichlid Fishes from Lake Tanganyika. BIOLOGY 2021; 10:biology10080797. [PMID: 34440029 PMCID: PMC8389663 DOI: 10.3390/biology10080797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/11/2022]
Abstract
Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We assessed the congruence between the phylogeographic structure of bathybatine cichlids and their parasitic flatworm Cichlidogyrus casuarinus to test the magnifying glass hypothesis. Additionally, we evaluated the use of a PoolSeq approach to study intraspecific variation in dactylogyrid monogeneans. The lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the cox1 gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 parasite samples from one spatially constrained metapopulation was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in H. stenosoma may be explained by the broad host range of this flatworm including eupelagic bathybatine host species that form panmictic populations across the lake. In addition, we present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying the intraspecific mitogenomic variation of dactylogyrid monogeneans.
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Koblmüller S, Schöggl CA, Lorber CJ, Van Steenberge M, Kmentová N, Vanhove MPM, Zangl L. African lates perches (Teleostei, Latidae, Lates): Paraphyly of Nile perch and recent colonization of Lake Tanganyika. Mol Phylogenet Evol 2021; 160:107141. [PMID: 33711447 DOI: 10.1016/j.ympev.2021.107141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022]
Abstract
Lates perches of the genus Lates (Latidae) are large piscivorous fishes, with a strikingly disjunct distribution range in coastal areas and estuaries of the Indo-Pacific region and in some large African freshwater systems. Previous phylogenetic hypotheses based on osteological and ontogenetic data suggested paraphyly of the African representatives, or even the small Lake Tanganyika species assemblage, with respect to the remaining Lates species. Based on a multilocus phylogeny, however, we show that extant African lates perches are monophyletic. The Nile perch, L. niloticus, which is widely distributed in the Nilo-Sudan region and Central Africa, comprises three distinct lineages and is paraphyletic with respect to the four endemic Lake Tanganyika species. We find that diversification of extant African Lates happened only as recently as the Pliocene. With the extensive, in part much older fossil record, this suggests repeated extinction and (re-)colonization of hydrological systems. We further find that Lates started to diversify in Lake Tanganyika only in the Pleistocene, which is much more recent than other fish radiations endemic to Lake Tanganyika, implying that they radiated in the presence of other top predators already in this ecosystem.
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Affiliation(s)
- Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria.
| | - Christian A Schöggl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Clemens J Lorber
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Maarten Van Steenberge
- Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium; Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, Helsinki FI-00014, Finland
| | - Lukas Zangl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria; Universalmuseum Joanneum, Studienzentrum Naturkunde, Weinzöttlstraße 16, 8045 Graz, Austria; ÖKOTEAM - Institute for Animal Ecology and Landscape Planning, Bergmanngasse 22, 8010 Graz, Austria
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Ronco F, Büscher HH, Indermaur A, Salzburger W. The taxonomic diversity of the cichlid fish fauna of ancient Lake Tanganyika, East Africa. JOURNAL OF GREAT LAKES RESEARCH 2020; 46:1067-1078. [PMID: 33100489 PMCID: PMC7574848 DOI: 10.1016/j.jglr.2019.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ancient Lake Tanganyika in East Africa houses the world's ecologically and morphologically most diverse assemblage of cichlid fishes, and the third most species-rich after lakes Malawi and Victoria. Despite long-lasting scientific interest in the cichlid species flocks of the East African Great Lakes, for example in the context of adaptive radiation and explosive diversification, their taxonomy and systematics are only partially explored; and many cichlid species still await their formal description. Here, we provide a current inventory of the cichlid fish fauna of Lake Tanganyika, providing a complete list of all valid 208 Tanganyikan cichlid species, and discuss the taxonomic status of more than 50 undescribed taxa on the basis of the available literature as well as our own observations and collections around the lake. This leads us to conclude that there are at least 241 cichlid species present in Lake Tanganyika, all but two are endemic to the basin. We finally summarize some of the major taxonomic challenges regarding Lake Tanganyika's cichlid fauna. The taxonomic inventory of the cichlid fauna of Lake Tanganyika presented here will facilitate future research on the taxonomy and systematics and the ecology and evolution of the species flock, as well as its conservation.
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Kmentová N, Bray RA, Koblmüller S, Artois T, De Keyzer ELR, Gelnar M, Vanhove MPM, Georgieva S. Uncharted digenean diversity in Lake Tanganyika: cryptogonimids (Digenea: Cryptogonimidae) infecting endemic lates perches (Actinopterygii: Latidae). Parasit Vectors 2020; 13:221. [PMID: 32357898 DOI: 10.1186/s13071-020-3913-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lake Tanganyika is considered a biodiversity hotspot with exceptional species richness and level of endemism. Given the global importance of the lake in the field of evolutionary biology, the understudied status of its parasite fauna is surprising with a single digenean species reported to date. Although the most famous group within the lake's fish fauna are cichlids, the pelagic zone is occupied mainly by endemic species of clupeids (Actinopterygii: Clupeidae) and lates perches (Actinopterygii: Latidae, Lates Cuvier), which are an important commercial source for local fisheries. In this study, we focused on the lake's four lates perches and targeted their thus far unexplored endoparasitic digenean fauna. METHODS A total of 85 lates perches from four localities in Lake Tanganyika were examined. Cryptogonimid digeneans were studied by means of morphological and molecular characterisation. Partial sequences of the nuclear 28S rRNA gene and the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene were sequenced for a representative subset of the specimens recovered. Phylogenetic analyses were conducted at the family level under Bayesian inference. RESULTS Our integrative approach revealed the presence of six species within the family Cryptogonimidae Ward, 1917. Three out of the four species of Lates were found to be infected with at least one cryptogonimid species. Two out of the three reported genera are new to science. Low interspecific but high intraspecific phenotypic and genetic diversity was found among Neocladocystis spp. Phylogenetic inference based on partial 28S rDNA sequences revealed a sister group relationship for two of the newly erected genera and their close relatedness to the widely distributed genus Acanthostomum Looss, 1899. CONCLUSIONS The present study provides the first comprehensive characterisation of the digenean diversity in a fish family from Lake Tanganyika which will serve as a baseline for future explorations of the lake's digenean fauna. Our study highlights the importance of employing an integrative approach for revealing the diversity in this unique host-parasite system.
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Affiliation(s)
- Nikol Kmentová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic. .,Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium. .,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium.
| | - Rodney A Bray
- Parasitic Worms Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Tom Artois
- Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium
| | - Els Lea R De Keyzer
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium
| | - Milan Gelnar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Maarten P M Vanhove
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.,Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, P.O.Box 17, Helsinki, 00014, Finland
| | - Simona Georgieva
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Science Park, University of Valencia, P.O. Box 46071, Valencia, Spain
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Weak population structure and recent demographic expansion of the monogenean parasite Kapentagyrus spp. infecting clupeid fishes of Lake Tanganyika, East Africa. Int J Parasitol 2020; 50:471-486. [PMID: 32277985 DOI: 10.1016/j.ijpara.2020.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 11/22/2022]
Abstract
Lake Tanganyika, East Africa, is the oldest and deepest African Great Lake and harbours one of the most diverse fish assemblages on earth. Two clupeid fishes, Limnothrissa miodon and Stolothrissa tanganicae, constitute a major part of the total fish catch, making them indispensable for local food security. Parasites have been proposed as indicators of stock structure in highly mobile pelagic hosts. We examined the monogeneans Kapentagyrus limnotrissae and Kapentagyrus tanganicanus (Dactylogyridae) infecting these clupeids to explore the parasites' lake-wide population structure and patterns of demographic history. Samples were collected at seven sites distributed across three sub-basins of the lake. Intraspecific morphological variation of the monogeneans (n = 380) was analysed using morphometrics and geomorphometrics of sclerotised structures. Genetic population structure of both parasite species (n = 246) was assessed based on a 415 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Overall, we observed a lack of clear geographical morphological differentiation in both parasites along a north-south axis. This lack of geographical population structure was also reflected by a large proportion of shared haplotypes, and a pattern of seemingly unrestricted gene flow between populations. Significant morphological and genetic differentiation between some populations might reflect temporal differentiation rather than geographical isolation. Overall, the shallow population structure of both species of Kapentagyrus reflects the near-panmictic population structure of both host species as previously reported. Morphological differences related to host species identity of K. tanganicanus were consistent with incipient speciation at the genetic level. Both parasite species experienced a recent demographic expansion, which might be linked to paleohydrological events. Finally, interspecific hybridisation was found in Kapentagyrus, representing the first case in dactylogyrid monogeneans.
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