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Kundu S, De Alwis PS, Kim AR, Lee SR, Kang HE, Go Y, Gietbong FZ, Wibowo A, Kim HW. Mitogenomic Characterization of Cameroonian Endemic Coptodon camerunensis (Cichliformes: Cichlidae) and Matrilineal Phylogeny of Old-World Cichlids. Genes (Basel) 2023; 14:1591. [PMID: 37628642 PMCID: PMC10454717 DOI: 10.3390/genes14081591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
The mitogenomic evolution of old-world cichlids is still largely incomplete in Western Africa. In this present study, the complete mitogenome of the Cameroon endemic cichlid, Coptodon camerunensis, was determined by next-generation sequencing. The mitogenome was 16,557 bp long and encoded with 37 genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region). The C. camerunensis mitogenome is AT-biased (52.63%), as exhibited in its congener, Coptodon zillii (52.76% and 53.04%). The majority of PCGs start with an ATG initiation codon, except COI, which starts with a GTG codon and five PCGs and ends with the TAA termination codon and except seven PCGs with an incomplete termination codon. In C. camerunensis mitogenome, most tRNAs showed classical cloverleaf secondary structures, except tRNA-serine with a lack of DHU stem. Comparative analyses of the conserved blocks of two Coptodonini species control regions revealed that the CSB-II block was longer than other blocks and contained highly variable sites. Using 13 concatenated PCGs, the mitogenome-based Bayesian phylogeny easily distinguished all the examined old-world cichlids. Except for Oreochromini and Coptodinini tribe members, the majority of the taxa exhibited monophyletic clustering within their respective lineages. C. camerunensis clustered closely with Heterotilapia buttikoferi (tribe Heterotilapiini) and had paraphyletic clustering with its congener, C. zillii. The Oreochromini species also displayed paraphyletic grouping, and the genus Oreochromis showed a close relationship with Coptodinini and Heterotilapiini species. In addition, illustrating the known distribution patterns of old-world cichlids, the present study is congruent with the previous hypothesis and proclaims that prehistoric geological evolution plays a key role in the hydroclimate of the African continent during Mesozoic, which simultaneously disperses and/or colonizes cichlids in different ichthyological provinces and Rift Lake systems in Africa. The present study suggests that further mitogenomes of cichlid species are required, especially from western Africa, to understand their unique evolution and adaptation.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
| | - Piyumi S. De Alwis
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea;
| | - Yunji Go
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University, Busan 48513, Republic of Korea;
| | | | - Arif Wibowo
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia;
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea; (S.K.); (P.S.D.A.)
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea; (A.R.K.); (S.R.L.)
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Moons T, Kmentová N, Pariselle A, Artois T, Bert W, Vanhove MP, Cruz-Laufer AJ. All quiet on the western front? The evolutionary history of monogeneans (Dactylogyridae: Cichlidogyrus, Onchobdella) infecting a West and Central African tribe of cichlid fishes (Chromidotilapiini). Parasite 2023; 30:25. [PMID: 37404116 PMCID: PMC10321234 DOI: 10.1051/parasite/2023023] [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: 01/24/2023] [Accepted: 05/21/2023] [Indexed: 07/06/2023] Open
Abstract
Owing to the largely unexplored diversity of metazoan parasites, their speciation mechanisms and the circumstances under which such speciation occurs - in allopatry or sympatry - remain vastly understudied. Cichlids and their monogenean flatworm parasites have previously served as a study system for macroevolutionary processes, e.g., for the role of East African host radiations on parasite communities. Here, we investigate the diversity and evolution of the poorly explored monogeneans infecting a West and Central African lineage of cichlid fishes: Chromidotilapiini, which is the most species-rich tribe of cichlids in this region. We screened gills of 149 host specimens (27 species) from natural history collections and measured systematically informative characters of the sclerotised attachment and reproductive organs of the parasites. Ten monogenean species (Dactylogyridae: Cichlidogyrus and Onchobdella) were found, eight of which are newly described and one redescribed herein. The phylogenetic positions of chromidotilapiines-infecting species of Cichlidogyrus were inferred through a parsimony analysis of the morphological characters. Furthermore, we employed machine learning algorithms to detect morphological features associated with the main lineages of Cichlidogyrus. Although the results of these experimental algorithms remain inconclusive, the parsimony analysis indicates that West and Central African lineages of Cichlidogyrus and Onchobdella are monophyletic, unlike the paraphyletic host lineages. Several instances of host sharing suggest occurrences of intra-host speciation (sympatry) and host switching (allopatry). Some morphological variation was recorded that may also indicate the presence of species complexes. We conclude that collection material can provide important insights on parasite evolution despite the lack of well-preserved DNA material.
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Affiliation(s)
- Tanisha Moons
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
- Nematology Research Unit, Department of Biology, Ghent University K.L. Ledeganckstraat 35 9000 Ghent Belgium
- Department of Parasitology, Faculty of Science, University of South Bohemia České Budějovice 37005 Czech Republic
| | - Nikol Kmentová
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Antoine Pariselle
- ISEM, Université de Montpellier, CNRS, IRD 34095 Montpellier France
- Faculty of Sciences, Laboratory “Biodiversity, Ecology and Genome”, Research Centre “Plant and Microbial Biotechnology, Biodiversity and Environment”, Mohammed V University 10000 Rabat Morocco
| | - Tom Artois
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University K.L. Ledeganckstraat 35 9000 Ghent Belgium
| | - Maarten P.M. Vanhove
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Armando J. Cruz-Laufer
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
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Day JJ, Steell EM, Vigliotta TR, Withey LA, Bills R, Friel JP, Genner MJ, Stiassny MLJ. Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family. Mol Phylogenet Evol 2023; 182:107754. [PMID: 36906193 DOI: 10.1016/j.ympev.2023.107754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/13/2023]
Abstract
Endeavours in species discovery, particularly the characterisation of cryptic species, have been greatly aided by the application of DNA molecular sequence data to phylogenetic reconstruction and inference of evolutionary and biogeographic processes. However, the extent of cryptic and undescribed diversity remains unclear in tropical freshwaters, where biodiversity is declining at alarming rates. To investigate how data on previously undiscovered biodiversity impacts inferences of biogeography and diversification dynamics, we generated a densely sampled species-level family tree of Afrotropical Mochokidae catfishes (220 valid species) that was ca. 70 % complete. This was achieved through extensive continental sampling specifically targeting the genus Chiloglanis a specialist of the relatively unexplored fast-flowing lotic habitat. Applying multiple species-delimitation methods, we report exceptional levels of species discovery for a vertebrate genus, conservatively delimiting a staggering ca. 50 putative new Chiloglanis species, resulting in a near 80 % increase in species richness for the genus. Biogeographic reconstructions of the family identified the Congo Basin as a critical region in the generation of mochokid diversity, and further revealed complex scenarios for the build-up of continental assemblages of the two most species rich mochokid genera, Synodontis and Chiloglanis. While Syndontis showed most divergence events within freshwater ecoregions consistent with largely in situ diversification, Chiloglanis showed much less aggregation of freshwater ecoregions, suggesting dispersal as a key diversification process in this older group. Despite the significant increase in mochokid diversity identified here, diversification rates were best supported by a constant rate model consistent with patterns in many other tropical continental radiations. While our findings highlight fast-flowing lotic freshwaters as potential hotspots for undescribed and cryptic species diversity, a third of all freshwater fishes are currently threatened with extinction, signifying an urgent need to increase exploration of tropical freshwaters to better characterise and conserve its biodiversity.
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Affiliation(s)
- Julia J Day
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Elizabeth M Steell
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas R Vigliotta
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Lewis A Withey
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Roger Bills
- South African Institute for Aquatic Biodiversity, Private Bag, 1015, 6140 Grahamstown, South Africa
| | - John P Friel
- Alabama Museum of Natural History, The University of Alabama, Box 870340, 35487-0340 Tuscaloosa, AL, USA
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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The Evolutionary Dynamics of the Mitochondrial tRNA in the Cichlid Fish Family. BIOLOGY 2022; 11:biology11101522. [PMID: 36290425 PMCID: PMC9598224 DOI: 10.3390/biology11101522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary Cichlids are a unique example of fish diversity and species richness which have been explained by sympatric speciation at different freshwater sources in Africa. The mitochondria contribute to cell vitality by providing energy. It contains a circular genome with an established translation system that is spatially independent of the cytosolic counterpart. The current study aimed to investigate the evolutionary dynamics of the mitochondrial tRNA and its role in cichlids’ diversity. The available cichlid mitogenomes in the public database were filtered, in addition to newly sequenced accessions from a specific cichlid group known as the haplotilapiine lineage that is widely distributed in the Egyptian sector of the Nile River. Based on the comparative analysis of mitogenomic data, we identified 22 tRNA genes, in which a single gene was D-armless, while the cloverleaf secondary structure subdivided into stem-loop formations was predicted and used to define the levels of genetic divergence for the remained tRNAs. Peculiarly, in cichlids, the formation known as “T-arm” showed the lowest polymorphism levels among other structures in contrast to other organisms (e.g., scorpions). Comparing the whole family to the specific haplotilapiine lineage showed that the tryptophan tRNA was the most conserved tRNA, with signatures of possible purifying selection. Abstract The mitochondrial transfer RNA genes (tRNAs) attract more attention due to their highly dynamic and rapidly evolving nature. The current study aimed to detect and evaluate the dynamics, characteristic patterns, and variations of mitochondrial tRNAs. The study was conducted in two main parts: first, the published mitogenomic sequences of cichlids mt tRNAs have been filtered. Second, the filtered mitochondrial tRNA and additional new mitogenomes representing the most prevalent Egyptian tilapiine were compared and analyzed. Our results revealed that all 22 tRNAs of cichlids folded into a classical cloverleaf secondary structure with four domains, except for trnSGCU, missing the D domain in all cichlids. When consensus tRNAs were compared, most of the mutations were observed in the trnP at nucleotide levels (substitutions and indels), in contrast to trnLUAA. From a structural perspective, the anticodon loop and T-loop formations were the most conserved structures among all parts of the tRNA in contrast to the A-stem and D-loop formations. The trnW was the lowest polymorphic unneutral tRNA among all cichlids (both the family and the haplotilapiine lineage), in contrast with the neutral trnD that was extremely polymorphic among and within the haplotilapiine lineage species compared to other cichlids species. From a phylogenetic perspective, the trnC was extremely hypervariable and neutral tRNA in both haplotilapiine lineage and cichlids but was unable to report correct phylogenetic signal for the cichlids. In contrast to trnI and trnY, less variable neutral tRNAs that were able to cluster the haplotilapiine lineage and cichlids species as previously reported. By observing the DNA polymorphism in the coding DNA sequences (CDS), the highest affected amino acid by non-synonymous mutations was isoleucine and was equally mutated to valine and vice versa; no correlation between mutations in CDS and tRNAs was statistically found. The current study provides an insight into the mitochondrial tRNA evolution and its effect on the cichlid diversity and speciation model at the maternal level.
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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Nam SE, Eom HJ, Park HS, Rhee JS. Characterization and phylogenetic analysis of the complete mitochondrial genome of the rainbow krib, Pelvicachromis pulcher (Perciformes: Cichlidae). Mitochondrial DNA B Resour 2022; 7:918-920. [PMID: 35692647 PMCID: PMC9176354 DOI: 10.1080/23802359.2022.2079099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report the complete mitochondrial genome information of the rainbow krib, Pelvicachromis pulcher (Boulenger 1901). Illumina HiSeq genome sequencing allowed the assembly of a circular mitogenome of 17,196 base pairs (bp) from P. pulcher consisting of 47% GC nucleotides, 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a putative control region in the typical teleost gene composition. The gene order of the P. pulcher mitogenome was identical to that of other cichlid species. A maximum likelihood phylogenetic tree based on mitochondrial PCGs showed a relationship of P. pulcher with a cichlid Tylochromis polylepis (Boulenger 1900), suggesting that more complete mitogenomes are needed to explore mitogenome evolution in West African tribes and riverine cichlids, as this genomic information is the first complete mitogenome in the tribe Chromidotilapiini.
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Affiliation(s)
- Sang-Eun Nam
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
| | - Hye-Jin Eom
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
| | - Hyoung Sook Park
- Department of Song-Do Bio-Environmental Engineering, Incheon Jaeneung University, Incheon, South Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
- Research Institute of Basic Sciences, Incheon National University, Incheon, South Korea
- Yellow Sea Research Institute, Incheon, South Korea
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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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Santos D, Ribeiro GC. Areas of endemism in the Afrotropical region based on the geographical distribution of Tipulomorpha (Insecta: Diptera). AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daubian Santos
- Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166, Bairro Bangu Santo André SP 09210‐170 Brazil
| | - Guilherme Cunha Ribeiro
- Centro de Ciências Naturais e Humanas Universidade Federal do ABC Rua Santa Adélia, 166, Bairro Bangu Santo André SP 09210‐170 Brazil
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Nam SE, Eom HJ, Park HS, Rhee JS. The complete mitochondrial genome of Lamprologus signatus (Perciformes: Cichlidae). Mitochondrial DNA B Resour 2021; 6:3487-3489. [PMID: 34869886 PMCID: PMC8635558 DOI: 10.1080/23802359.2021.1981789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In this study, the complete 16,583 bp mitochondrial genome of Lamprologus signatus (Poll, 1952) was determined from a specimen sourced from Lake Tanganyika. The mitogenome contains 37 genes [13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes] and a putative control region, which consists of 27.1% A, 27.0% T, 29.9% C, and 16.0% G, with a total G + C content of 45.9%. A maximum likelihood phylogenetic tree based on mitochondrial PCGs suggested that L. signatus is clustered with members of the tribes Haplochromini and Tropheini. As this is the first report of the entire mitogenome in the tribe Lamprologini, the complete mitochondrial sequence information of L. sigantus will be useful in determining phylogenetic relationships of Pseudocrenilabrinae tribes.
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Affiliation(s)
- Sang-Eun Nam
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
| | - Hye-Jin Eom
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
| | - Hyoung Sook Park
- Department of Song-Do Bio-Environmental Engineering, Incheon Jaeneung University, Incheon, South Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea
- Research Institute of Basic Sciences, Incheon National University, Incheon, South Korea
- Institute of Green Environmental Research Center, Incheon, South Korea
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An efficient vector-based CRISPR/Cas9 system in an Oreochromis mossambicus cell line using endogenous promoters. Sci Rep 2021; 11:7854. [PMID: 33846462 PMCID: PMC8041756 DOI: 10.1038/s41598-021-87068-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 03/23/2021] [Indexed: 02/01/2023] Open
Abstract
CRISPR/Cas9 gene editing is effective in manipulating genetic loci in mammalian cell cultures and whole fish but efficient platforms applicable to fish cell lines are currently limited. Our initial attempts to employ this technology in fish cell lines using heterologous promoters or a ribonucleoprotein approach failed to indicate genomic alteration at targeted sites in a tilapia brain cell line (OmB). For potential use in a DNA vector approach, endogenous tilapia beta Actin (OmBAct), EF1 alpha (OmEF1a), and U6 (TU6) promoters were isolated. The strongest candidate promoter determined by EGFP reporter assay, OmEF1a, was used to drive constitutive Cas9 expression in a modified OmB cell line (Cas9-OmB1). Cas9-OmB1 cell transfection with vectors expressing gRNAs driven by the TU6 promoter achieved mutational efficiencies as high as 81% following hygromycin selection. Mutations were not detected using human and zebrafish U6 promoters demonstrating the phylogenetic proximity of U6 promoters as critical when used for gRNA expression. Sequence alteration to TU6 improved mutation rate and cloning efficiency. In conclusion, we report new tools for ectopic expression and a highly efficient, economical system for manipulation of genomic loci and evaluation of their causal relationship with adaptive cellular phenotypes by CRISPR/Cas9 gene editing in fish cells.
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Mojekwu TO, Cunningham MJ, Bills RI, Pretorius PC, Hoareau TB. Utility of DNA barcoding in native Oreochromis species. JOURNAL OF FISH BIOLOGY 2021; 98:498-506. [PMID: 33070327 DOI: 10.1111/jfb.14594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.
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Affiliation(s)
- Tonna O Mojekwu
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biotechnology, Nigerian Institute for Oceanography and Marine Research, Lagos, Nigeria
| | - Michael J Cunningham
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- South African Institute for Aquatic Biodiversity, Grahamstown, South Africa
| | - Roger I Bills
- South African Institute for Aquatic Biodiversity, Grahamstown, South Africa
| | - Petrus C Pretorius
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Thierry B Hoareau
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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13
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Altner M, Ruthensteiner B, Reichenbacher B. New haplochromine cichlid from the upper Miocene (9-10 MYA) of Central Kenya. BMC Evol Biol 2020; 20:65. [PMID: 32503417 PMCID: PMC7275555 DOI: 10.1186/s12862-020-01602-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/06/2020] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Melanie Altner
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, DE Germany
| | - Bernhard Ruthensteiner
- Section Evertebrata Varia, SNSB – ZSM Bavarian State Collection of Zoology, Münchhausen-Strasse 21, 81247 Munich, DE Germany
| | - Bettina Reichenbacher
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, DE Germany
- GeoBio-Center at Ludwig-Maximilians-Universität München, Richard-Wagner-Strasse 10, 80333 Munich, DE Germany
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14
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Diversification and gene flow of tilapia species driven by ecological changes in lowland and mountain areas of southern Mauritania. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10017-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
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Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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16
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Conith MR, Conith AJ, Albertson RC. Evolution of a soft-tissue foraging adaptation in African cichlids: Roles for novelty, convergence, and constraint. Evolution 2019; 73:2072-2084. [PMID: 31418824 DOI: 10.1111/evo.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Abstract
Understanding the origins of biodiversity demands consideration of both extrinsic (e.g., ecological opportunity) and intrinsic (e.g., developmental constraint) factors. Here, we use a combination of phylogenetic and genetic tools to address the origin of novelty in African cichlids. In particular, we focus on an extreme hypertrophied snout that is structurally integrated with the upper jaw. We show that this bizarre trait has evolved independently in at least two distinct and ecologically successful cichlid clades. We find that snout dimensions are decoupled both phenotypically and genetically, which has enabled it to evolve independently in multiple directions. Further, patterns of variation among species and within a genetic mapping pedigree suggest that relative to snout length, depth is under greater genetic and/or developmental constraint. Models of evolution suggest that snout shape is under selection for feeding behavior, with snout depth being important for algae scraping and snout length for sand sifting. Indeed, the deep snout of some algivores is achieved via an expansion of the intermaxillary ligament, which is important for jaw stability and may increase feeding performance. Overall, our data imply that the evolution of exaggerated snout depth required overcoming a genetic/developmental constraint, which led to expanded ecological opportunity via foraging adaptation.
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Affiliation(s)
- Moira R Conith
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Andrew J Conith
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - R Craig Albertson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003.,Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
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17
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Penk SBR, Altner M, F Cerwenka A, Schliewen UK, Reichenbacher B. New fossil cichlid from the middle Miocene of East Africa revealed as oldest known member of the Oreochromini. Sci Rep 2019; 9:10198. [PMID: 31308387 PMCID: PMC6629881 DOI: 10.1038/s41598-019-46392-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/28/2019] [Indexed: 11/09/2022] Open
Abstract
A new genus and species of fossil cichlid fishes of middle Miocene age (12.5 Ma) is described from the Ngorora fish Lagerstätte (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.
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Affiliation(s)
- Stefanie B R Penk
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
| | - Melanie Altner
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
| | - Alexander F Cerwenka
- Section Evertebrata varia, SNSB Bavarian State Collection of Zoology, 81247, Munich, Germany
| | - Ulrich K Schliewen
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333, Munich, Germany
- Department of Ichthyology, SNSB Bavarian State Collection of Zoology, 81247, Munich, Germany
| | - Bettina Reichenbacher
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333, Munich, Germany.
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18
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Ford AG, Bullen TR, Pang L, Genner MJ, Bills R, Flouri T, Ngatunga BP, Rüber L, Schliewen UK, Seehausen O, Shechonge A, Stiassny ML, Turner GF, Day JJ. Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments. Mol Phylogenet Evol 2019; 136:215-226. [DOI: 10.1016/j.ympev.2019.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 03/26/2019] [Accepted: 04/06/2019] [Indexed: 12/15/2022]
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19
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Schedel FDB, Musilova Z, Schliewen UK. East African cichlid lineages (Teleostei: Cichlidae) might be older than their ancient host lakes: new divergence estimates for the east African cichlid radiation. BMC Evol Biol 2019; 19:94. [PMID: 31023223 PMCID: PMC6482553 DOI: 10.1186/s12862-019-1417-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/31/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil †Tugenchromis pickfordi in the cichlid divergence age estimates. RESULTS Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43-33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89-20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88-25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23-18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40-26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93-5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: 'Orthochromis' indermauri and 'Haplochormis' vanheusdeni. CONCLUSIONS Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated "Melting-Pot Tanganyika" hypothesis. The radiation of the 'Lower Congo Lamprologus clade' might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi.
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Affiliation(s)
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Vinicna 7, CZ-128 44 Prague, Czech Republic
| | - Ulrich Kurt Schliewen
- Department of Ichthyology, SNSB - Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 Munich, Germany
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20
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Böhne A, Weber AAT, Rajkov J, Rechsteiner M, Riss A, Egger B, Salzburger W. Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine Cichlid Pseudocrenilabrus philander. Genome Biol Evol 2019; 11:439-458. [PMID: 30649313 PMCID: PMC6375353 DOI: 10.1093/gbe/evz003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2019] [Indexed: 12/15/2022] Open
Abstract
Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX-XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX-XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.
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Affiliation(s)
- Astrid Böhne
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Alexandra Anh-Thu Weber
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
- Museums Victoria, Melbourne, Victoria, Australia
| | - Jelena Rajkov
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Michael Rechsteiner
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Andrin Riss
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
| | - Bernd Egger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
- Program Man Society Environment, University of Basel, Switzerland
| | - Walter Salzburger
- Department of Environmental Sciences, Zoological Institute, University of Basel, Switzerland
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21
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Bbole I, Zhao JL, Tang SJ, Katongo C. Mitochondrial genome annotation and phylogenetic placement of Oreochromis andersonii and O. macrochir among the cichlids of southern Africa. PLoS One 2018; 13:e0203095. [PMID: 30481181 PMCID: PMC6258479 DOI: 10.1371/journal.pone.0203095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/12/2018] [Indexed: 11/18/2022] Open
Abstract
Genetic characterization of southern African cichlids has not received much attention. Here, we describe the mitogenome sequences and phylogenetic positioning of Oreochromis andersonii and O. macrochir among the African cichlids. The complete mitochondrial DNA sequences were determined for O. andersonii and O. macrochir, two important aquaculture and fisheries species endemic to southern Africa. The complete mitogenome sequence lengths were 16642 bp and 16644 bp for O. andersonii and O. macrochir respectively. The general structural organization follows that of other teleost species with 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a non-coding control region. Phylogenetic placement of the two species among other African cichlids was performed using Maximum Likelihood (ML) and Bayesian Markov-Chain-Monte-Carlo (MCMC). The consensus trees confirmed the relative positions of the two cichlid species with O. andersonii being very closely related to O. mossambicus and O. macrochir showing a close relation to both species. Among the 13 mitochondrial DNA protein coding genes ND6 may have evolved more rapidly and COIII was the most conserved. There are signs that ND6 may have been subjected to positive selection in order for these cichlid lineages to diversify and adapt to new environments. More work is needed to characterize the southern Africa cichlids as they are important species for capture fisheries, aquaculture development and understanding biogeographic history of African cichlids. Bio-conservation of some endangered cichlids is also essential due to the threat by invasive species.
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Affiliation(s)
- Ian Bbole
- Department of Fisheries, Mansa, Zambia
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Jin-Liang Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN), Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
- National Demonstration Centre for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Shou-Jie Tang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, China
| | - Cyprian Katongo
- Biological Sciences Department, University of Zambia, Lusaka, Zambia
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22
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Gammerdinger WJ, Kocher TD. Unusual Diversity of Sex Chromosomes in African Cichlid Fishes. Genes (Basel) 2018; 9:E480. [PMID: 30287777 PMCID: PMC6210639 DOI: 10.3390/genes9100480] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.
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Affiliation(s)
- William J Gammerdinger
- Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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23
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Irisarri I, Singh P, Koblmüller S, Torres-Dowdall J, Henning F, Franchini P, Fischer C, Lemmon AR, Lemmon EM, Thallinger GG, Sturmbauer C, Meyer A. Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes. Nat Commun 2018; 9:3159. [PMID: 30089797 PMCID: PMC6082878 DOI: 10.1038/s41467-018-05479-9] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/30/2018] [Indexed: 11/21/2022] Open
Abstract
Lake Tanganyika is the oldest and phenotypically most diverse of the three East African cichlid fish adaptive radiations. It is also the cradle for the younger parallel haplochromine cichlid radiations in Lakes Malawi and Victoria. Despite its evolutionary significance, the relationships among the main Lake Tanganyika lineages remained unresolved, as did the general timescale of cichlid evolution. Here, we disentangle the deep phylogenetic structure of the Lake Tanganyika radiation using anchored phylogenomics and uncover hybridization at its base, as well as early in the haplochromine radiation. This suggests that hybridization might have facilitated these speciation bursts. Time-calibrated trees support that the radiation of Tanganyika cichlids coincided with lake formation and that Gondwanan vicariance concurred with the earliest splits in the cichlid family tree. Genes linked to key innovations show signals of introgression or positive selection following colonization of lake habitats and species' dietary adaptations are revealed as major drivers of colour vision evolution. These findings shed light onto the processes shaping the evolution of adaptive radiations.
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Affiliation(s)
- Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, 2, Madrid, 28006, Spain
| | - Pooja Singh
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, 21944-970, Brazil
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany
| | - Christoph Fischer
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306, USA
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, Graz, 8010, Austria
- OMICS Center Graz, BioTechMed Graz, Stiftingtalstraße 24, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria.
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz, 78457, Germany.
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, 02138, MA, USA.
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24
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Matschiner M, Musilová Z, Barth JMI, Starostová Z, Salzburger W, Steel M, Bouckaert R. Bayesian Phylogenetic Estimation of Clade Ages Supports Trans-Atlantic Dispersal of Cichlid Fishes. Syst Biol 2018; 66:3-22. [PMID: 28173588 DOI: 10.1093/sysbio/syw076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/21/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two nonexclusive alternative approaches have recently been developed, the “fossilized birth–death” (FBD) model and “total-evidence dating.” While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the FBD model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated data sets, and compare its performance to that of the FBD model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the FBD model. By applying our approach to a large data set including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for transoceanic dispersal of cichlids and other groups of teleost fishes.
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Affiliation(s)
- Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Zuzana Musilová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Julia M I Barth
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - Mike Steel
- Department of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Remco Bouckaert
- Department of Computer Science, University of Auckland, Auckland, New Zealand.,Computational Evolution Group, University of Auckland, Auckland, New Zealand
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Meyer BS, Matschiner M, Salzburger W. Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes. Syst Biol 2018; 66:531-550. [PMID: 27539485 DOI: 10.1093/sysbio/syw069] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022] Open
Abstract
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.
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Affiliation(s)
- Britta S Meyer
- Zoological Institute, University of Basel, Basel, Switzerland.,Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Michael Matschiner
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Zoological Institute, University of Basel, Basel, Switzerland.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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26
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Diversity and host specificity of monogenean gill parasites (Platyhelminthes) of cichlid fishes in the Bangweulu-Mweru ecoregion. J Helminthol 2017; 92:417-437. [PMID: 28829000 DOI: 10.1017/s0022149x17000712] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This study represents the first exploration of the parasite fauna of cichlid fishes in the Mweru-Luapula subregion (Central Africa). Twelve species of cichlids and 14 species of Monogenea from three genera (Cichlidogyrus, Gyrodactylus and Scutogyrus) were collected. We present a first record of the gill parasite fauna of eight host species, Oreochromis mweruensis, Orthochromis sp. 'Mambilima', Sargochromis mellandi, Serranochromis angusticeps, S. stappersi, S. thumbergi and Tylochromis mylodon. The host range of ten parasite species was expanded. The study further includes the description of Cichlidogyrus consobrini sp. n. from S. mellandi and Orthochromis sp. 'Mambilima'. A new morphotype of C. halli is characterized, and three species - C. papernastrema, C. quaestio and C. zambezensis - are redescribed. Furthermore, the biodiversity and host specificity of these parasites is compared with that of cichlid parasites from Lake Kariba and Cameroon. Two species, including C. consobrini sp. n. and a new morphotype of C. halli, are putative endemics. The parasite fauna in Bangweulu-Mweru is highly similar in species composition to Lake Kariba, but in Bangweulu-Mweru the same parasite species are more host-specific, probably because of hydrogeographical differences between the two regions.
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27
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Zahradníčková P, Barson M, Luus-Powell WJ, Přikrylová I. Species of Gyrodactylus von Nordmann, 1832 (Platyhelminthes: Monogenea) from cichlids from Zambezi and Limpopo river basins in Zimbabwe and South Africa: evidence for unexplored species richness. Syst Parasitol 2016; 93:679-700. [PMID: 27522367 DOI: 10.1007/s11230-016-9652-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 06/12/2016] [Indexed: 10/21/2022]
Abstract
New findings on Gyrodactylus spp. parasitising African cichlids in southern Africa are presented, comprising data from Zimbabwe and South Africa. Morphometry of opisthaptoral hard parts in combination with nuclear ribosomal DNA sequences confirmed the presence of six species of Gyrodactylus von Nordmann, 1832. Three new species are described from fishes in Zimbabwe: Gyrodactylus chitandiri n. sp. from the gill arches of Coptodon rendalli (Boulenger) and Pseudocrenilabrus philander (Weber); Gyrodactylus occupatus n. sp. from the fins of Oreochromis niloticus (L.), Pharyngochromis acuticeps (Steindachner) and P. philander; and Gyrodactylus parisellei n. sp. from the fins of O. niloticus, P. philander and Tilapia sp. Gyrodactylus nyanzae Paperna, 1973 was also identified from the gills of O. niloticus and C. rendalli collected from two localities in Zimbabwe; these findings represent new host and locality records for this parasite. Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 was identified from P. philander collected in South Africa and Zimbabwe thereby providing new host and locality records for this parasite. Finally, Gyrodactylus yacatli García-Vásquez, Hansen, Christison, Bron & Shinn, 2011 was collected from the fins of O. niloticus and P. philander studied in Zimbabwe; this represents the first record of this species from the continent of Africa. Notably, this study improves upon the knowledge of Gyrodactylus spp. parasitising cichlids from these southern African regions. All species studied were recorded from at least two different cichlid host species indicating trend for a wide range of Gyrodactylus hosts in Africa. Accordingly, this supports the idea of intensive host switching in the course of their evolution.
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Affiliation(s)
- Petra Zahradníčková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Maxwell Barson
- Department of Biological Sciences, University of Zimbabwe, PO Box MP167, Mt. Pleasant Harare, Harare, Zimbabwe
| | - Wilmien J Luus-Powell
- Department of Biodiversity, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa
| | - Iva Přikrylová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic. .,Department of Biodiversity, University of Limpopo, Private Bag X1106, Sovenga, 0727, South Africa. .,Water Research Group, School of for Environmental Sciences and Development, North West University, Private Bag X6001, Potchefstroom, 2531, South Africa.
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28
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Takahashi T, Sota T. A robust phylogeny among major lineages of the East African cichlids. Mol Phylogenet Evol 2016; 100:234-242. [PMID: 27068840 DOI: 10.1016/j.ympev.2016.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/16/2016] [Accepted: 04/07/2016] [Indexed: 11/30/2022]
Abstract
The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.
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Affiliation(s)
- Tetsumi Takahashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; National Institute of Genetics, Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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29
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Kide NG, Dunz A, Agnèse JF, Dilyte J, Pariselle A, Carneiro C, Correia E, Brito JC, Yarba LO, Kone Y, Durand JD. Cichlids of the Banc d'Arguin National Park, Mauritania: insight into the diversity of the genus Coptodon. JOURNAL OF FISH BIOLOGY 2016; 88:1369-1393. [PMID: 26856797 DOI: 10.1111/jfb.12899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
To determine the species diversity of cichlids in the Banc d'Arguin National Park (PNBA) and their phylogenetic relationships with other species in West Africa, a morphometric and meristic and molecular phylogenetic study was conducted. Both approaches not only confirm the presence of Sarotherodon melanotheron in PNBA but also demonstrate the presence of a second species from the genus Coptodon. While morphometric characteristics match the description of the Guinean tilapia Coptodon guineensis, phylogenetic reconstructions based on three mitochondrial and one nuclear DNA fragment demonstrate that C. guineensis is paraphyletic over its range. Because different lineages of C. guineensis are allopatric, the distribution of C. guineensis should be restricted to Ghana and Côte d'Ivoire. The many other lineages of this species should be considered as C. sp. aff. guineensis.
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Affiliation(s)
- N G Kide
- Université Abdel Maleck Essaâdi - Faculté des Sciences, Département de Biologie, Laboratoire Biologie Appliqué et Pathologie, Tétouan, Morocco
| | - A Dunz
- Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstr. 21, 81247, München, Germany
| | - J-F Agnèse
- Institut de Recherche pour le Développement (IRD), Université Montpellier, UMR 226, Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, CC 65, F-34095, Montpellier cedex 5, France
| | - J Dilyte
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - A Pariselle
- Institut de Recherche pour le Développement (IRD), Université Montpellier, UMR 226, Institut des Sciences de l'Evolution de Montpellier, Place Eugène Bataillon, CC 65, F-34095, Montpellier cedex 5, France
- IRD, ISE-M, BP 1857, Yaoundé, Cameroon
| | - C Carneiro
- Observatoire du Parc National du Banc d'Arguin, Nouakchott, Mauritania
| | - E Correia
- Observatoire du Parc National du Banc d'Arguin, Nouakchott, Mauritania
| | - J C Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - L O Yarba
- Observatoire du Parc National du Banc d'Arguin, Nouakchott, Mauritania
| | - Y Kone
- Faculté des Sciences de l'Université de Nouakchott, Nouakchott, Mauritania
| | - J-D Durand
- Institut de Recherche pour le Développement (IRD), Université Montpellier, UMR MARBEC, Place Eugène Bataillon, CC 93, F-34095, Montpellier cedex 5, France
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30
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Genner MJ, Ngatunga BP, Mzighani S, Smith A, Turner GF. Geographical ancestry of Lake Malawi's cichlid fish diversity. Biol Lett 2016; 11:20150232. [PMID: 26063752 DOI: 10.1098/rsbl.2015.0232] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Lake Malawi haplochromine cichlid flock is one of the largest vertebrate adaptive radiations. The geographical source of the radiation has been assumed to be rivers to the south and east of Lake Malawi, where extant representatives of the flock are now present. Here, we provide mitochondrial DNA evidence suggesting the sister taxon to the Lake Malawi radiation is within the Great Ruaha river in Tanzania, north of Lake Malawi. Estimates of the time of divergence between the Lake Malawi flock and this riverine sister taxon range from 2.13 to 6.76 Ma, prior to origins of the current radiation 1.20-4.06 Ma. These results are congruent with evaluations of 2-3.75 Ma fossil material that suggest past faunal connections between Lake Malawi and the Ruaha. We propose that ancestors of the Malawi radiation became isolated within the catchment during Pliocene rifting that formed both Lake Malawi and the Kipengere/Livingstone mountain range, before colonizing rivers to the south and east of the lake region and radiating within the lake basin. Identification of this sister taxon allows tests of whether standing genetic diversity has predisposed Lake Malawi cichlids to rapid speciation and adaptive radiation.
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Affiliation(s)
- Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol BS81TQ, UK
| | - Benjamin P Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), PO Box 9750, Dar-es-Salaam, Tanzania
| | - Semvua Mzighani
- Tanzania Fisheries Research Institute (TAFIRI), PO Box 9750, Dar-es-Salaam, Tanzania
| | - Alan Smith
- School of Biological, Biomedical and Environmental Science, University of Hull, Hull HU67RX, UK
| | - George F Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL572UW, UK
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31
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Schneider K, Koblmüller S, Sefc KM. HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test. Methods Ecol Evol 2015; 7:358-368. [PMID: 27066216 PMCID: PMC4824276 DOI: 10.1111/2041-210x.12490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/27/2015] [Indexed: 12/01/2022]
Abstract
The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data.We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis.With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed.With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in bootstrap support. hext significantly facilitates the taxon-jackknife approach to hybrid taxon detection, even though the simple test for excess bootstrap increase may not reliably identify hybrid taxa in all applications.
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Affiliation(s)
- Kevin Schneider
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria ; Department of Systematic Botany and Geobotany, Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Kristina M Sefc
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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32
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Ford AGP, Dasmahapatra KK, Rüber L, Gharbi K, Cezard T, Day JJ. High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment. Mol Ecol 2015; 24:3421-40. [PMID: 25997156 PMCID: PMC4973668 DOI: 10.1111/mec.13247] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/30/2022]
Abstract
Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.
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Affiliation(s)
- Antonia G P Ford
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, Bern, 3005, Switzerland
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Timothee Cezard
- Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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33
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Martin CH, Cutler JS, Friel JP, Dening Touokong C, Coop G, Wainwright PC. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution 2015; 69:1406-1422. [PMID: 25929355 DOI: 10.1111/evo.12674] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/20/2015] [Indexed: 12/19/2022]
Abstract
One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph S Cutler
- Department of Conservation Biology, University of California, Santa Cruz, California
| | - John P Friel
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama
| | | | - Graham Coop
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
| | - Peter C Wainwright
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
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34
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Weiss JD, Cotterill FPD, Schliewen UK. Lake Tanganyika--a 'melting pot' of ancient and young cichlid lineages (Teleostei: Cichlidae)? PLoS One 2015; 10:e0125043. [PMID: 25928886 PMCID: PMC4415804 DOI: 10.1371/journal.pone.0125043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/08/2015] [Indexed: 11/19/2022] Open
Abstract
A long history of research focused on the East Africa cichlid radiations (EAR) revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and the mitochondrial ND2 gene were genotyped for 91 species representing almost all major lacustrine and riverine haplotilapiine east African cichlid lineages with a focus on L. Tanganyika endemics. Explicitly testing for the possibility of ancient hybridisation events, a comprehensive phylogenetic network hypothesis is proposed for the origin and diversification of L. Tanganyika cichlids. Inference of discordant phylogenetic signal strongly suggests that the genomes of two endemic L. Tanganyika tribes, Eretmodini and Tropheini, are composed of an ancient mixture of riverine and lacustrine lineages. For the first time a strong monophyly signal of all non-haplochromine mouthbrooding species endemic to L. Tanganyika (“ancient mouthbrooders”) was detected. Further, in the genomes of early diverging L. Tanganyika endemics Trematocarini, Bathybatini, Hemibatini and Boulengerochromis genetic components of other lineages belonging to the East African Radiation appear to be present. In combination with recent palaeo-geological results showing that tectonic activity in the L. Tanganyika region resulted in highly dynamic and heterogeneous landscape evolution over the Neogene and Pleistocene, the novel phylogenetic data render a single lacustrine basin as the geographical cradle of the endemic L. Tanganyika cichlid lineages unlikely. Instead a scenario of a pre-rift origin of several independent L. Tanganyika precursor lineages which diversified in ancient rivers and precursor lakes and then amalgamated in the extant L. Tanganyika basin is put forward as an alternative: the 'melting pot Tanganyika' hypothesis.
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Affiliation(s)
- Juliane D. Weiss
- Department of Ichthyology, Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 München, Germany
| | - Fenton P. D. Cotterill
- Geoecodynamics Research Hub, c/o Department of Botany and Zoology, University of Stellenbosch, Private Bag X1 Matieland, 7602, Stellenbosch, South Africa
| | - Ulrich K. Schliewen
- Department of Ichthyology, Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247 München, Germany
- * E-mail:
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Koblmüller S, Odhiambo EA, Sinyinza D, Sturmbauer C, Sefc KM. Big fish, little divergence: phylogeography of Lake Tanganyika's giant cichlid, Boulengerochromis microlepis. HYDROBIOLOGIA 2015; 748:29-38. [PMID: 25983338 PMCID: PMC4430823 DOI: 10.1007/s10750-014-1863-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The largely endemic cichlid species flocks of the East African Great Lakes are among the prime examples for explosive speciation and adaptive radiation. Speciation rates differ among cichlid lineages, and the propensity to radiate has been linked to intrinsic and extrinsic factors such as sexual selection and ecological opportunity. Remarkably, only one cichlid tribe-the Boulengerochromini-comprises just a single species, Boulengerochromis microlepis, a predominantly piscivorous endemic of Lake Tanganyika and the world's largest cichlid. While the lineage diverged from its closest relatives at the onset of the Lake Tanganyika radiation >8 MYA, mitochondrial control region sequences collected in this study dated the most recent common ancestor of B. microlepis to ~60-110 KYA. There was no evidence of phylogeographic structure in the lake-wide sample. Patterns of genetic diversity and demographic analyses were consistent with slow and steady population growth throughout the reconstructed timescale. Additionally, the shallow divergence within the species may be related to a possibly large variance in reproductive success in this highly fecund species. Trophic niche space restriction by sympatric piscivores, lack of geographic structure, low potential for sexual selection arising from the monogamous mating system and extinction may have contributed to keeping the lineage monotypic.
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Affiliation(s)
- Stephan Koblmüller
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria.
| | - Elizabeth A Odhiambo
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria; Ichthyology Section, National Museums of Kenya, Nairobi, Kenya
| | - Danny Sinyinza
- Department of Fisheries, Ministry of Agriculture and Lifestock, Mpulungu, Zambia
| | - Christian Sturmbauer
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Kristina M Sefc
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, 8010 Graz, Austria
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Kratochwil CF, Meyer A. Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts. Mol Ecol Resour 2014; 15:761-71. [PMID: 25403420 DOI: 10.1111/1755-0998.12350] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 10/29/2014] [Accepted: 11/15/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For nonmodel organisms with adaptive key innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has been primarily used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genomewide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation.
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Affiliation(s)
- Claudius F Kratochwil
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany
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Hubbard PC, Mota VC, Keller-Costa T, da Silva JP, Canário AVM. Chemical communication in tilapia: a comparison of Oreochromis mossambicus with O. niloticus. Gen Comp Endocrinol 2014; 207:13-20. [PMID: 24979336 DOI: 10.1016/j.ygcen.2014.06.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 06/19/2014] [Accepted: 06/21/2014] [Indexed: 10/25/2022]
Abstract
In allopatric speciation species differentiation generally results from different selective pressures in different environments, and identifying the traits responsible helps to understand the isolation mechanism(s) involved. Male Mozambique tilapia (Oreochromis mossambicus) use urine to signal dominance; furthermore, 5β-pregnane-3α,17,20β-triol-3α-glucuronide (and its α-epimer, 5β-pregnane-3α,17,20α-triol-3α-glucuronide), in their urine is a potent pheromone, the concentration of which is correlated with social status. The Nile tilapia (Oreochromisniloticus) is a close relative; species divergence probably resulted from geographical separation around 6 million years ago. This raises the question of whether the two species use similar urinary chemical cues during reproduction. The olfactory potency of urine, and crude extracts, from either species was assessed by the electro-olfactogram and the presence of the steroid glucuronides in urine from the Nile tilapia by liquid-chromatography/mass-spectrometry. Both species showed similar olfactory sensitivity to urine and respective extracts from either species, and similar sensitivity to the steroid glucuronides. 5β-Pregnan-3α,17α,20β-triol-3α-glucuronide was present at high concentrations (approaching 0.5mM) in urine from Nile tilapia, with 5β-pregnan-3α,17α,20α-triol-3α-glucuronide present at lower concentrations, similar to the Mozambique tilapia. Both species also had similar olfactory sensitivity to estradiol-3-glucuronide, a putative urinary cue from females. Together, these results support the idea that reproductive chemical cues have not been subjected to differing selective pressure. Whether these chemical cues have the same physiological and behavioural roles in O. niloticus as O. mossambicus remains to be investigated.
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Affiliation(s)
- Peter C Hubbard
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, 8500-139 Faro, Portugal.
| | - Vasco C Mota
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, 8500-139 Faro, Portugal; Aquaculture and Fisheries Group, Wageningen University, Wageningen, Netherlands
| | - Tina Keller-Costa
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, 8500-139 Faro, Portugal; Departamento de Biologia, Universidade de Évora, Évora, Portugal
| | | | - Adelino V M Canário
- CCMAR-Centro de Ciências do Mar, Universidade do Algarve, 8500-139 Faro, Portugal
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Misof B, Meusemann K, von Reumont BM, Kück P, Prohaska SJ, Stadler PF. A priori assessment of data quality in molecular phylogenetics. Algorithms Mol Biol 2014. [DOI: 10.1186/s13015-014-0022-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Kück P, Meid SA, Groß C, Wägele JW, Misof B. AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support. BMC Bioinformatics 2014; 15:294. [PMID: 25176556 PMCID: PMC4167143 DOI: 10.1186/1471-2105-15-294] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 08/14/2014] [Indexed: 01/14/2023] Open
Abstract
Background Masking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence divergence which can mislead tree reconstructions. We present AliGROOVE, a new method based on a sliding window and a Monte Carlo resampling approach, that visualizes heterogeneous sequence divergence or alignment ambiguity related to single taxa or subsets of taxa within a multiple sequence alignment and tags suspicious branches on a given tree. Results We used simulated multiple sequence alignments to show that the extent of alignment ambiguity in pairwise sequence comparison is correlated with the frequency of misplaced taxa in tree reconstructions. The approach implemented in AliGROOVE allows to detect nodes within a tree that are supported despite the absence of phylogenetic signal in the underlying multiple sequence alignment. We show that AliGROOVE equally well detects heterogeneous sequence divergence in a case study based on an empirical data set of mitochondrial DNA sequences of chelicerates. Conclusions The AliGROOVE approach has the potential to identify single taxa or subsets of taxa which show predominantly randomized sequence similarity in comparison with other taxa in a multiple sequence alignment. It further allows to evaluate the reliability of node support in a novel way. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-294) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrick Kück
- Zoologisches Forschungsmuseum A, Koenig, Adenauerallee 160-163, 53113 Bonn, Germany.
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Huang H, Tran LAP, Knowles LL. Do estimated and actual species phylogenies match? Evaluation of East African cichlid radiations. Mol Phylogenet Evol 2014; 78:56-65. [PMID: 24837624 DOI: 10.1016/j.ympev.2014.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/02/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
Abstract
A large number of published phylogenetic estimates are based on a single locus or the concatenation of multiple loci, even though genealogies of single or concatenated loci may not accurately reflect the true history of species diversification (i.e., the species tree). The increased availability of genomic data, coupled with new computational methods, improves resolution of species relationships beyond what was possible in the past. Such developments will no doubt benefit future phylogenetic studies. It remains unclear how robust phylogenies that predate these developments (i.e., the bulk of phylogenetic studies) are to departures from the assumption of strict gene tree-species tree concordance. Here, we present a parametric bootstrap (PBST) approach that assesses the reliability of past phylogenetic estimates in which gene tree-species tree discord was ignored. We focus on a universal cause of discord-the random loss of gene lineages from genetic drift-and apply the method in a meta-analysis of East African cichlids, a group encompassing historical scenarios that are particularly challenging for phylogenetic estimation. Although we identify some evolutionary relationships that are robust to gene tree discord, many past phylogenetic estimates of cichlids are not. We discuss the utility of the PBST method for evaluating the robustness of gene tree-based phylogenetic estimations in general as well as for testing the clade-specific performance of species tree estimation methods and designing sampling strategies that increase the accuracy of estimated species relationships.
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Affiliation(s)
- Huateng Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA.
| | - Lucy A P Tran
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA.
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109-1079, USA.
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Schott RK, Refvik SP, Hauser FE, López-Fernández H, Chang BSW. Divergent positive selection in rhodopsin from lake and riverine cichlid fishes. Mol Biol Evol 2014; 31:1149-65. [PMID: 24509690 DOI: 10.1093/molbev/msu064] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly different spectral properties from the African rift lakes. These ecological and/or biogeographic differences may have imposed divergent selective pressures on the evolution of the cichlid visual system. To test these hypotheses, we investigated the molecular evolution of the dim-light visual pigment, rhodopsin. We sequenced rhodopsin from Neotropical and African riverine cichlids and combined these data with published sequences from African cichlids. We found significant evidence for positive selection using random sites codon models in all cichlid groups, with the highest levels in African lake cichlids. Tests using branch-site and clade models that partitioned the data along ecological (lake, river) and/or biogeographic (African, Neotropical) boundaries found significant evidence of divergent selective pressures among cichlid groups. However, statistical comparisons among these models suggest that ecological, rather than biogeographic, factors may be responsible for divergent selective pressures that have shaped the evolution of the visual system in cichlids. We found that branch-site models did not perform as well as clade models for our data set, in which there was evidence for positive selection in the background. One of our most intriguing results is that the amino acid sites found to be under positive selection in Neotropical and African lake cichlids were largely nonoverlapping, despite falling into the same three functional categories: spectral tuning, retinal uptake/release, and rhodopsin dimerization. Taken together, these results would imply divergent selection across cichlid clades, but targeting similar functions. This study highlights the importance of molecular investigations of ecologically important groups and the flexibility of clade models in explicitly testing ecological hypotheses.
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Affiliation(s)
- Ryan K Schott
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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42
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Keck BP, Hulsey CD. Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens. Mol Phylogenet Evol 2014; 73:53-9. [PMID: 24472673 DOI: 10.1016/j.ympev.2014.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 01/15/2014] [Accepted: 01/18/2014] [Indexed: 11/19/2022]
Abstract
The incredibly species-rich cichlid fish faunas of both the Neotropics and Africa are generally thought to be reciprocally monophyletic. However, the phylogenetic affinity of the African cichlid Heterochromis multidens is ambiguous, and this distinct lineage could make African cichlids paraphyletic. In past studies, Heterochromis has been variously suggested to be one of the earliest diverging lineages within either the Neotropical or the African cichlid radiations, and it has even been hypothesized to be the sister lineage to a clade containing all Neotropical and African cichlids. We examined the phylogenetic relationships among a representative sample of cichlids with a dataset of 29 nuclear loci to assess the support for the different hypotheses of the phylogenetic position of Heterochromis. Although individual gene trees in some instances supported alternative relationships, a majority of gene trees, integration of genes into species trees, and hypothesis testing of putative topologies all supported Heterochromis as belonging to the clade of African cichlids.
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Affiliation(s)
- Benjamin P Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996, USA.
| | - C Darrin Hulsey
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996, USA.
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Kirchberger PC, Sefc KM, Sturmbauer C, Koblmüller S. Outgroup effects on root position and tree topology in the AFLP phylogeny of a rapidly radiating lineage of cichlid fish. Mol Phylogenet Evol 2014; 70:57-62. [PMID: 24055738 PMCID: PMC3842234 DOI: 10.1016/j.ympev.2013.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/26/2022]
Abstract
Phylogenetic analyses of rapid radiations are particularly challenging as short basal branches and incomplete lineage sorting complicate phylogenetic inference. Multilocus data of presence-absence polymorphisms such as obtained by AFLP genotyping overcome some of the difficulties, but also present their own intricacies. Here we analyze >1000 AFLP markers to address the evolutionary history of the Limnochromini, a cichlid fish lineage endemic to Lake Tanganyika, and to test for potential effects of outgroup composition on tree topology. The data support previous mitochondrial evidence on the tribe's taxonomy by confirming the polyphyly of the genus Limnochromis and - in contradiction to a recent taxonomic revision - nesting the genus Greenwoodochromis within the Limnochromini. Species relationships suggest that ecological segregation occurred during the rapid basal radiation of the Limnochromini. The large phylogenetic distance between candidate outgroup taxa and the Limnochromini radiation caused random outgroup effects. Bootstrap support for ingroup nodes was lower in outgroup-rooted than in midpoint-rooted trees, and root positions and ingroup tree topologies varied in response to the composition of the outgroup. These observations suggest that the predisposition for homoplastic evolution makes AFLP-based phylogenetic analyses particularly susceptible to random biases introduced by too-distant outgroup taxa.
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Affiliation(s)
| | | | | | - Stephan Koblmüller
- Department of Zoology, Karl-Franzens-University Graz, Universitätsplatz 2, A-8010 Graz, Austria
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44
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Edwards DP, Sloan S, Weng L, Dirks P, Sayer J, Laurance WF. Mining and the African Environment. Conserv Lett 2013. [DOI: 10.1111/conl.12076] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- David P. Edwards
- Centre for Tropical Environmental and Sustainability Science and School of Marine and Tropical Biology; James Cook University; Cairns Queensland 4878 Australia
| | - Sean Sloan
- Centre for Tropical Environmental and Sustainability Science and School of Marine and Tropical Biology; James Cook University; Cairns Queensland 4878 Australia
| | - Lingfei Weng
- Centre for Tropical Environmental and Sustainability Science and School of Earth and Environmental Sciences; James Cook University; Cairns Queensland 4878 Australia
| | - Paul Dirks
- Centre for Tropical Environmental and Sustainability Science and School of Earth and Environmental Sciences; James Cook University; Cairns Queensland 4878 Australia
- Economic Geology Research Centre, School of Earth and Environmental Sciences; James Cook University; Cairns Queensland 4878 Australia
| | - Jeffrey Sayer
- Centre for Tropical Environmental and Sustainability Science and School of Earth and Environmental Sciences; James Cook University; Cairns Queensland 4878 Australia
| | - William F. Laurance
- Centre for Tropical Environmental and Sustainability Science and School of Marine and Tropical Biology; James Cook University; Cairns Queensland 4878 Australia
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McMahan CD, Chakrabarty P, Sparks JS, Smith WL, Davis MP. Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae). PLoS One 2013; 8:e71162. [PMID: 23990936 PMCID: PMC3747193 DOI: 10.1371/journal.pone.0071162] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/01/2013] [Indexed: 11/26/2022] Open
Abstract
The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.
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Affiliation(s)
- Caleb D. McMahan
- LSU Museum of Natural Science (Ichthyology), Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Prosanta Chakrabarty
- LSU Museum of Natural Science (Ichthyology), Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - John S. Sparks
- American Museum of Natural History, Department of Ichthyology, Division of Vertebrate Zoology, New York, New York, United States of America
| | - Wm. Leo Smith
- The Field Museum, Division of Fishes, Chicago, Illinois, United States of America
| | - Matthew P. Davis
- The Field Museum, Division of Fishes, Chicago, Illinois, United States of America
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Musilová Z, Kalous L, Petrtýl M, Chaloupková P. Cichlid fishes in the Angolan headwaters region: molecular evidence of the ichthyofaunal contact between the Cuanza and Okavango-Zambezi systems. PLoS One 2013; 8:e65047. [PMID: 23724120 PMCID: PMC3664563 DOI: 10.1371/journal.pone.0065047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 04/25/2013] [Indexed: 12/03/2022] Open
Abstract
The headwaters of five large African river basins flow through the Bié Plateau in Angola and still remain faunistically largely unexplored. We investigated fish fauna from the Cuanza and Okavango-Zambezi river systems from central Angola. We reconstructed molecular phylogenies of the most common cichlid species from the region, Tilapia sparrmanii and Serranochromis macrocephalus, using both mitochondrial and nuclear markers. We found evidence for ichthyofaunal contact and gene flow between the Cuanza and Okavango-Zambezi watersheds in the Bié Plateau in central Angola. Waterfalls and rapids also appeared to restrict genetic exchange among populations within the Cuanza basin. Further, we found that the Angolan Serranochromis cichlid fishes represent a monophyletic lineage with respect to other haplochromines, including the serranochromines from the Congo and Zambezi rivers. This study represents an important initial step in a biodiversity survey of this extremely poorly explored region, as well as giving further understanding to species distributions and gene flow both between and within river basins.
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Affiliation(s)
- Zuzana Musilová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics AV ČR v.v.i, Liběchov, Czech Republic.
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Day JJ, Peart CR, Brown KJ, Friel JP, Bills R, Moritz T. Continental Diversification of an African Catfish Radiation (Mochokidae: Synodontis). Syst Biol 2013; 62:351-65. [DOI: 10.1093/sysbio/syt001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Julia J. Day
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Claire R. Peart
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Katherine J. Brown
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - John P. Friel
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Roger Bills
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Timo Moritz
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
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Přikrylová I, Vanhove MPM, Janssens SB, Billeter PA, Huyse T. Tiny worms from a mighty continent: high diversity and new phylogenetic lineages of African monogeneans. Mol Phylogenet Evol 2012; 67:43-52. [PMID: 23287552 DOI: 10.1016/j.ympev.2012.12.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 12/17/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
Abstract
The family Gyrodactylidae contains one of the most significant radiations of platyhelminth fish parasites. The so-called hyperviviparity is very rare in the animal kingdom, and the rapid generation time can lead to an explosive population growth, which can cause massive losses in farmed fish. Here we present the first molecular phylogeny including all-but-one African genera, inferred from ITS and 18S rDNA sequences. The validity of nominal genera is discussed in relation to the systematic value of morphological characters traditionally used for generic identification. New complete 18S rDNA sequences of 18 gyrodactylid species of eight genera together with ITS rDNA gene sequences of eight species representing seven genera were generated and complemented with GenBank sequences. The maximum likelihood and Bayesian analyses pointed to a paraphyletic nature of African Gyrodactylus species. They formed well-supported clades possibly indicating speciation within host taxa: (1) parasites of cichlids (Cichlidae); (2) parasites of catfishes (Siluriformes), consisting of a lineage infecting mochokids and one infecting clariids. Macrogyrodactylus spp. firmly clustered into a monophyletic group. We found that Swingleus and Fundulotrema are very closely related and clearly cluster within Gyrodactylus. This supports earlier claims as to the paraphyly of the nominal genus Gyrodactylus as it is currently defined, and necessitates a revision of Swingleus and Fundulotrema. Molecular dating estimates confirmed a relatively young, certainly post-Gondwanan, origin of gyrodactylid lineages. Building on the previously suggested South-American origin of viviparous gyrodactylids, the dataset suggests subsequent intercontinental dispersal to Africa and from there repeated colonisation of the Holarctic. Even though the African continent has been heavily under sampled, the present diversity is far greater than in the intensively studied European fauna, probably because of the high endemicity of sub-Saharan Africa.
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Affiliation(s)
- Iva Přikrylová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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Muterezi Bukinga F, Vanhove MPM, Van Steenberge M, Pariselle A. Ancyrocephalidae (Monogenea) of Lake Tanganyika: III: Cichlidogyrus infecting the world’s biggest cichlid and the non-endemic tribes Haplochromini, Oreochromini and Tylochromini (Teleostei, Cichlidae). Parasitol Res 2012; 111:2049-61. [DOI: 10.1007/s00436-012-3052-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 07/16/2012] [Indexed: 12/22/2022]
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Schwarzer J, Swartz ER, Vreven E, Snoeks J, Cotterill FPD, Misof B, Schliewen UK. Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution. Proc Biol Sci 2012; 279:4389-98. [PMID: 22951733 DOI: 10.1098/rspb.2012.1667] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometres apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.
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Affiliation(s)
- Julia Schwarzer
- Bavarian State Collection of Zoology, Münchhausenstrasse 21, Munich, Germany
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