Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation
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...
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| Format: | Article |
| Language: | English |
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BMC
2022-11-01
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| Series: | BMC Ecology and Evolution |
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| Online Access: | https://doi.org/10.1186/s12862-022-02085-8 |
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| author | Leona J. M. Milec Maarten P. M. Vanhove Fidel Muterezi Bukinga Els L. R. De Keyzer Vercus Lumami Kapepula Pascal Mulungula Masilya N’Sibula Mulimbwa Catherine E. Wagner Joost A. M. Raeymaekers |
| author_facet | Leona J. M. Milec Maarten P. M. Vanhove Fidel Muterezi Bukinga Els L. R. De Keyzer Vercus Lumami Kapepula Pascal Mulungula Masilya N’Sibula Mulimbwa Catherine E. Wagner Joost A. M. Raeymaekers |
| author_sort | Leona J. M. Milec |
| collection | DOAJ |
| description | 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, Stolothrissa tanganicae and Limnothrissa miodon. 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 Potamothrissa obtusirostris 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. |
| first_indexed | 2024-04-11T23:06:52Z |
| format | Article |
| id | doaj.art-e78347a4463d4bf2be85f3c2a6d2c44f |
| institution | Directory Open Access Journal |
| issn | 2730-7182 |
| language | English |
| last_indexed | 2024-04-11T23:06:52Z |
| publishDate | 2022-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ecology and Evolution |
| spelling | doaj.art-e78347a4463d4bf2be85f3c2a6d2c44f2022-12-22T03:58:00ZengBMCBMC Ecology and Evolution2730-71822022-11-0122111710.1186/s12862-022-02085-8Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciationLeona J. M. Milec0Maarten P. M. Vanhove1Fidel Muterezi Bukinga2Els L. R. De Keyzer3Vercus Lumami Kapepula4Pascal Mulungula Masilya5N’Sibula Mulimbwa6Catherine E. Wagner7Joost A. M. Raeymaekers8Faculty of Biosciences and Aquaculture, Nord UniversityCentre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt UniversityCentre de Recherche en Hydrobiologie-Uvira (CRH-Uvira)Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU LeuvenCentre de Recherche en Hydrobiologie-Uvira (CRH-Uvira)Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira)Centre de Recherche en Hydrobiologie-Uvira (CRH-Uvira)University of WyomingFaculty of Biosciences and Aquaculture, Nord UniversityAbstract 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, Stolothrissa tanganicae and Limnothrissa miodon. 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 Potamothrissa obtusirostris 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.https://doi.org/10.1186/s12862-022-02085-8Great LakesClupeiformesMitogenomeTime calibrationPhylogenetics |
| spellingShingle | Leona J. M. Milec Maarten P. M. Vanhove Fidel Muterezi Bukinga Els L. R. De Keyzer Vercus Lumami Kapepula Pascal Mulungula Masilya N’Sibula Mulimbwa Catherine E. Wagner Joost A. M. Raeymaekers Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation BMC Ecology and Evolution Great Lakes Clupeiformes Mitogenome Time calibration Phylogenetics |
| title | Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation |
| title_full | Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation |
| title_fullStr | Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation |
| title_full_unstemmed | Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation |
| title_short | Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation |
| title_sort | complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to lake tanganyika africa suggest intralacustrine speciation |
| topic | Great Lakes Clupeiformes Mitogenome Time calibration Phylogenetics |
| url | https://doi.org/10.1186/s12862-022-02085-8 |
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