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Edgley DE, Carruthers M, Gabagambi NP, Saxon AD, Smith AM, Joyce DA, Vernaz G, Santos ME, Turner GF, Genner MJ. Lateral line system diversification during the early stages of ecological speciation in cichlid fish. BMC Ecol Evol 2024; 24:24. [PMID: 38378480 PMCID: PMC10877828 DOI: 10.1186/s12862-024-02214-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND The mechanosensory lateral line system is an important sensory modality in fishes, informing multiple behaviours related to survival including finding food and navigating in dark environments. Given its ecological importance, we may expect lateral line morphology to be under disruptive selection early in the ecological speciation process. Here we quantify the lateral line system morphology of two ecomorphs of the cichlid fish Astatotilapia calliptera in crater Lake Masoko that have diverged from common ancestry within the past 1,000 years. RESULTS Based on geometric morphometric analyses of CT scans, we show that the zooplanktivorous benthic ecomorph that dominates the deeper waters of the lake has large cranial lateral line canal pores, relative to those of the nearshore invertebrate-feeding littoral ecomorph found in the shallower waters. In contrast, fluorescence imaging revealed no evidence for divergence between ecomorphs in the number of either superficial or canal neuromasts. We illustrate the magnitude of the variation we observe in Lake Masoko A. calliptera in the context of the neighbouring Lake Malawi mega-radiation that comprises over 700 species. CONCLUSIONS These results provide the first evidence of divergence in this often-overlooked sensory modality in the early stages of ecological speciation, suggesting that it may have a role in the broader adaptive radiation process.
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Affiliation(s)
- Duncan E Edgley
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Madeleine Carruthers
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Nestory P Gabagambi
- Tanzania Fisheries Research Institute, Kyela Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alan M Smith
- School of Natural Sciences, University of Hull, Hull, UK
| | - Domino A Joyce
- School of Natural Sciences, University of Hull, Hull, UK
| | - Grégoire Vernaz
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
- Wellcome/Cancer Research UK, Gurdon Institute, University of Cambridge, Cambridge, UK
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK.
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Liu Z, Kishe MA, Gabagambi NP, Shechonge AH, Ngatunga BP, Smith K, Saxon AD, Hudson AG, Linderoth T, Turner GF, Collins RA, Genner MJ. Nuclear environmental DNA resolves fine-scale population genetic structure in an aquatic habitat. iScience 2024; 27:108669. [PMID: 38226161 PMCID: PMC10788193 DOI: 10.1016/j.isci.2023.108669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
There is considerable potential for nuclear genomic material in environmental DNA (eDNA) to inform us of population genetic structure within aquatic species. We tested if nuclear allelic composition data sourced from eDNA can resolve fine scale spatial genetic structure of the cichlid fish Astatotilapia calliptera in Lake Masoko, Tanzania. In this ∼35 m deep crater lake the species is diverging into two genetically distinguishable ecomorphs, separated by a thermo-oxycline at ∼15 m that divides biologically distinct water masses. We quantified population genetic structure along a depth transect using single nucleotide polymorphisms (SNPs) derived from genome sequencing of 530 individuals. This population genetic structure was reflected in a focal set of SNPs that were also reliably amplified from eDNA - with allele frequencies derived from eDNA reflecting those of fish within each depth zone. Thus, by targeting known genetic variation between populations within aquatic eDNA, we measured genetic structure within the focal species.
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Affiliation(s)
- Zifang Liu
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Mary A. Kishe
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Nestory P. Gabagambi
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Asilatu H. Shechonge
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Benjamin P. Ngatunga
- Tanzania Fisheries Research Institute (TAFIRI), P.O. Box 9750, Dar es Salaam, Tanzania
| | - Katie Smith
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Andrew D. Saxon
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Alan G. Hudson
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
| | - Tyler Linderoth
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA
| | - George F. Turner
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Rupert A. Collins
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS81TQ, UK
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Nazarizadeh M, Nováková M, Loot G, Gabagambi NP, Fatemizadeh F, Osano O, Presswell B, Poulin R, Vitál Z, Scholz T, Halajian A, Trucchi E, Kočová P, Štefka J. Historical dispersal and host-switching formed the evolutionary history of a globally distributed multi-host parasite - The Ligula intestinalis species complex. Mol Phylogenet Evol 2023; 180:107677. [PMID: 36572162 DOI: 10.1016/j.ympev.2022.107677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/25/2022]
Abstract
Studies on parasite biogeography and host spectrum provide insights into the processes driving parasite diversification. Global geographical distribution and a multi-host spectrum make the tapeworm Ligula intestinalis a promising model for studying both the vicariant and ecological modes of speciation in parasites. To understand the relative importance of host association and biogeography in the evolutionary history of this tapeworm, we analysed mtDNA and reduced-represented genomic SNP data for a total of 139 specimens collected from 18 fish-host genera across a distribution range representing 21 countries. Our results strongly supported the existence of at least 10 evolutionary lineages and estimated the deepest divergence at approximately 4.99-5.05 Mya, which is much younger than the diversification of the fish host genera and orders. Historical biogeography analyses revealed that the ancestor of the parasite diversified following multiple vicariance events and was widespread throughout the Palearctic, Afrotropical, and Nearctic between the late Miocene and early Pliocene. Cyprinoids were inferred as the ancestral hosts for the parasite. Later, from the late Pliocene to Pleistocene, new lineages emerged following a series of biogeographic dispersal and host-switching events. Although only a few of the current Ligula lineages show narrow host-specificity (to a single host genus), almost no host genera, even those that live in sympatry, overlapped between different Ligula lineages. Our analyses uncovered the impact of historical distribution shifts on host switching and the evolution of host specificity without parallel host-parasite co-speciation. Historical biogeography reconstructions also found that the parasite colonized several areas (Afrotropical and Australasian) much earlier than was suggested by only recent faunistic data.
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Affiliation(s)
- Masoud Nazarizadeh
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic; Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Milena Nováková
- Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Géraldine Loot
- UMR-5174, EDB (Laboratoire Evolution and Diversité Biologique), CNRS, IRD, Université Toulouse III Paul Sabatier, France
| | | | - Faezeh Fatemizadeh
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Odipo Osano
- School of Environmental Studies, University of Eldoret, Kenya
| | | | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Zoltán Vitál
- Research Center for Fisheries and Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Szarvas, Hungary
| | - Tomáš Scholz
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic; Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Ali Halajian
- Research Administration and Development, and 2-DSI-NRF SARChI Chair (Ecosystem health), Department of Biodiversity, University of Limpopo, South Africa
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | | | - Jan Štefka
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic; Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic.
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Vernaz G, Hudson AG, Santos ME, Fischer B, Carruthers M, Shechonge AH, Gabagambi NP, Tyers AM, Ngatunga BP, Malinsky M, Durbin R, Turner GF, Genner MJ, Miska EA. Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. Nat Ecol Evol 2022; 6:1940-1951. [PMID: 36266459 PMCID: PMC9715432 DOI: 10.1038/s41559-022-01894-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/26/2022] [Indexed: 12/15/2022]
Abstract
Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.
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Affiliation(s)
- Grégoire Vernaz
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
| | - Alan G Hudson
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | | | - Alexandra M Tyers
- School of Natural Sciences, Bangor University, Bangor, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Milan Malinsky
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Eric A Miska
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
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Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol 2022; 39:msac251. [PMID: 36376993 PMCID: PMC10101686 DOI: 10.1093/molbev/msac251] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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Affiliation(s)
- Madeleine Carruthers
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Duncan E Edgley
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Nestory P Gabagambi
- Tanzanian Fisheries Research Institute, Kyela Research
Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Asilatu Shechonge
- Tanzanian Fisheries Research Institute, Dar es Salaam Research
Centre, P.O. Box 9750, Dar es Salaam, Tanzania
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge,
Cambridge CB2 1QN, United
Kingdom
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - George F Turner
- School of Natural Sciences, Bangor University,
Bangor, Wales LL57 2UW, United
Kingdom
| | - Martin J Genner
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
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Gabagambi NP, Salvanes AGV, Midtøy F, Skorping A. The tapeworm Ligula intestinalis alters the behavior of the fish intermediate host Engraulicypris sardella, but only after it has become infective to the final host. Behav Processes 2019; 158:47-52. [DOI: 10.1016/j.beproc.2018.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/06/2018] [Accepted: 11/09/2018] [Indexed: 11/28/2022]
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