1
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Konstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida MV, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska EA, van Wolfswinkel JC, Haase AD. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals. Cell Rep 2024; 43:114777. [PMID: 39302833 DOI: 10.1016/j.celrep.2024.114777] [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: 05/02/2024] [Revised: 08/09/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs) play a crucial role in safeguarding genome integrity by silencing mobile genetic elements. From flies to humans, piRNAs originate from long single-stranded precursors encoded by genomic piRNA clusters. How piRNA clusters form to adapt to genomic invaders and evolve to maintain protection remain key outstanding questions. Here, we generate a roadmap of piRNA clusters across seven species that highlights both similarities and variations. In mammals, we identify transcriptional readthrough as a mechanism to generate piRNAs from transposon insertions (piCs) downstream of genes (DoG). Together with the well-known stress-dependent DoG transcripts, our findings suggest a molecular mechanism for the formation of piRNA clusters in response to retroviral invasion. Finally, we identify a class of dynamic piRNA clusters in humans, underscoring unique features of human germ cell biology. Our results advance the understanding of conserved principles and species-specific variations in piRNA biology and provide tools for future studies.
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Affiliation(s)
- Parthena Konstantinidou
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zuzana Loubalova
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Franziska Ahrend
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Oak Ridge Institute for Science and Education, US Department of Energy, Oak Ridge, TN, USA
| | - Aleksandr Friman
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA; Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic; Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Yuejun Wang
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; Oak Ridge Institute for Science and Education, US Department of Energy, Oak Ridge, TN, USA; TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Hernan Lorenzi
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA; TriLab Bioinformatics Group, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eric A Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Josien C van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA; Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Astrid D Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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2
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Bucklow CV, Genner MJ, Turner GF, Maclaine J, Benson R, Verd B. A whole-body micro-CT scan library that captures the skeletal diversity of Lake Malawi cichlid fishes. Sci Data 2024; 11:984. [PMID: 39256465 PMCID: PMC11387623 DOI: 10.1038/s41597-024-03687-1] [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: 01/25/2024] [Accepted: 07/26/2024] [Indexed: 09/12/2024] Open
Abstract
Here we describe a dataset of freely available, readily processed, whole-body μCT-scans of 56 species (116 specimens) of Lake Malawi cichlid fishes that captures a considerable majority of the morphological variation present in this remarkable adaptive radiation. We contextualise the scanned specimens within a discussion of their respective ecomorphological groupings and suggest possible macroevolutionary studies that could be conducted with these data. In addition, we describe a methodology to efficiently μCT-scan (on average) 23 specimens per hour, limiting scanning time and alleviating the financial cost whilst maintaining high resolution. We demonstrate the utility of this method by reconstructing 3D models of multiple bones from multiple specimens within the dataset. We hope this dataset will enable further morphological study of this fascinating system and permit wider-scale comparisons with other cichlid adaptive radiations.
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Affiliation(s)
- Callum V Bucklow
- University of Oxford, Department of Biology, OX1 3SZ, Oxford, United Kingdom
- University of Oxford, Department of Earth Sciences, OX1 3AN, Oxford, United Kingdom
| | - Martin J Genner
- University of Bristol, School of Biological Sciences, Bristol, BS8 1TQ, United Kingdom
| | - George F Turner
- Bangor University, School of Natural Sciences, Bangor, LL57 2UR, United Kingdom
| | | | - Roger Benson
- University of Oxford, Department of Earth Sciences, OX1 3AN, Oxford, United Kingdom.
- American Museum of Natural History, New York City, NY 10024, USA.
| | - Berta Verd
- University of Oxford, Department of Biology, OX1 3SZ, Oxford, United Kingdom.
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3
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Ciezarek AG, Mehta TK, Man A, Ford AGP, Kavembe GD, Kasozi N, Ngatunga BP, Shechonge AH, Tamatamah R, Nyingi DW, Cnaani A, Ndiwa TC, Di Palma F, Turner GF, Genner MJ, Haerty W. Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes. Mol Biol Evol 2024; 41:msae116. [PMID: 38865496 PMCID: PMC11221657 DOI: 10.1093/molbev/msae116] [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: 09/21/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.
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Affiliation(s)
- Adam G Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Centre of Environment, Fisheries and Aquaculture Science (Cefas), Scientific Advice for Fisheries Management Team (SAFM), Lowestoft NR33 0H5, UK
| | - Tarang K Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Angela Man
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G P Ford
- School of Life and Health Sciences, Whitelands College, University of Roehampton, London SW15 4NA, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Buginyanya Zonal Agricultural Research and Development Institute, Mbale, Uganda
| | | | | | | | | | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion 7528809, Israel
| | - Titus C Ndiwa
- Department of Clinical Studies, University of Nairobi, Nairobi, Kenya
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - George F Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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4
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Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587621. [PMID: 38617250 PMCID: PMC11014572 DOI: 10.1101/2024.04.01.587621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
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Affiliation(s)
- Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Moritz Blumer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Pío Sierra
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan L. Price
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Aleksandr Friman
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Alexandra Dallaire
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
| | - Grégoire Vernaz
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Present address: Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Audrey L. K. Putman
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Alan M. Smith
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Domino A. Joyce
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Falk Butter
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Ackermannweg 4, Mainz, 55128, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Südufer, Greifswald, 17493, Germany
| | - Astrid D. Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - M. Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Eric A. Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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5
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Costa VA, Ronco F, Mifsud JCO, Harvey E, Salzburger W, Holmes EC. Host adaptive radiation is associated with rapid virus diversification and cross-species transmission in African cichlid fishes. Curr Biol 2024; 34:1247-1257.e3. [PMID: 38428417 DOI: 10.1016/j.cub.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Adaptive radiations are generated through a complex interplay of biotic and abiotic factors. Although adaptive radiations have been widely studied in the context of animal and plant evolution, little is known about how they impact the evolution of the viruses that infect these hosts, which in turn may provide insights into the drivers of cross-species transmission and hence disease emergence. We examined how the rapid adaptive radiation of the cichlid fishes of African Lake Tanganyika over the last 10 million years has shaped the diversity and evolution of the viruses they carry. Through metatranscriptomic analysis of 2,242 RNA sequencing libraries, we identified 121 vertebrate-associated viruses among various tissue types that fell into 13 RNA and 4 DNA virus groups. Host-switching was commonplace, particularly within the Astroviridae, Metahepadnavirus, Nackednavirus, Picornaviridae, and Hepacivirus groups, occurring more frequently than in other fish communities. A time-calibrated phylogeny revealed that hepacivirus diversification was not constant throughout the cichlid radiation but accelerated 2-3 million years ago, coinciding with a period of rapid cichlid diversification and niche packing in Lake Tanganyika, thereby providing more closely related hosts for viral infection. These data depict a dynamic virus ecosystem within the cichlids of Lake Tanganyika, characterized by rapid virus diversification and frequent host jumping, and likely reflecting their close phylogenetic relationships that lower the barriers to cross-species virus transmission.
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Affiliation(s)
- Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Fabrizia Ronco
- Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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6
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Jiang Z, Zang W, Ericson PGP, Song G, Wu S, Feng S, Drovetski SV, Liu G, Zhang D, Saitoh T, Alström P, Edwards SV, Lei F, Qu Y. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae). BMC Biol 2024; 22:49. [PMID: 38413944 PMCID: PMC10900574 DOI: 10.1186/s12915-024-01848-7] [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: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Resolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary. RESULTS Here we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression. CONCLUSIONS Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
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Affiliation(s)
- Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenqing Zang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shaoyuan Wu
- Jiangsu International Joint Center of Genomics, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China
| | - Sergei V Drovetski
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20004, USA
- Present address: U.S. Geological Survey, Eastern Ecological Science Center at Patuxent Research Refuge, Laurel, MD, 20708, USA
| | - Gang Liu
- Chinese Academy of Forestry, Institute of Ecological Conservation and Restoration, Beijing, 100091, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Takema Saitoh
- Yamashina Institute for Ornithology, Abiko, Chiba, Japan
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden.
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7
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DeLorenzo L, Powder KE. Epigenetics and the evolution of form: Experimental manipulation of a chromatin modification causes species-specific changes to the craniofacial skeleton. Evol Dev 2024; 26:e12461. [PMID: 37850843 PMCID: PMC10842503 DOI: 10.1111/ede.12461] [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: 03/08/2023] [Revised: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
A central question in biology is the molecular origins of phenotypic diversity. While genetic changes are key to the genotype-phenotype relationship, alterations to chromatin structure and the physical packaging of histone proteins may also be important drivers of vertebrate divergence. We investigate the impact of such an epigenetic mechanism, histone acetylation, within a textbook example of an adaptive radiation. Cichlids of Lake Malawi have adapted diverse craniofacial structures, and here we investigate how histone acetylation influences morphological variation in these fishes. Specifically, we assessed the effect of inhibiting histone deacetylation using the drug trichostatin A (TSA) on developing facial structures. We examined this during three critical developmental windows in two cichlid species with alternate adult morphologies. Exposure to TSA during neural crest cell (NCC) migration and as postmigratory NCCs proliferate in the pharyngeal arches resulted in significant changes in lateral and ventral shape in Maylandia, but not in Tropheops. This included an overall shortening of the head, widening of the lower jaw, and steeper craniofacial profile, all of which are paedomorphic morphologies. In contrast, treatment with TSA during early chondrogenesis did not result in significant morphological changes in either species. Together, these data suggest a sensitivity to epigenetic alterations that are both time- and species-dependent. We find that morphologies are due to nonautonomous or potentially indirect effects on NCC development, including in part a global developmental delay. Our research bolsters the understanding that proper histone acetylation is essential for early craniofacial development and identifies a species-specific robustness to developmental change. Overall, this study demonstrates how epigenetic regulation may play an important role in both generating and buffering morphological variation.
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Affiliation(s)
- Leah DeLorenzo
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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8
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Burress ED, Muñoz MM. Phenotypic rate and state are decoupled in response to river-to-lake transitions in cichlid fishes. Evolution 2023; 77:2365-2377. [PMID: 37624672 DOI: 10.1093/evolut/qpad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Geographic access to isolated ecosystems is an important catalyst of adaptive radiation. Cichlid fishes repeatedly colonized rift, crater, and volcanic lakes from surrounding rivers. We test the "lake effect" on the phenotypic rate and state across 253 cichlid species. The rate of evolution was consistently higher (~10-fold) in lakes, and consistent across different dimensions of the phenotype. Rate shifts tended to occur coincident with or immediately following river-to-lake transitions, generally resulting in 2- to 5-fold faster rates than in the founding riverine lineage. By contrast, river- and lake-dwelling cichlids exhibit considerable overlap in phenotypes, generally with less disparity in lakes, but often different evolutionary optima. Taken together, these results suggest that lake radiations rapidly expand into niches largely already represented by ancestral riverine lineages, albeit in different frequencies. Lakes may provide ecological opportunity via ecological release (e.g., from predators/competitors) but need not be coupled with access to novel ecological niches.
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Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolution, Yale University, New Haven, CT, United States
| | - Martha M Muñoz
- Department of Ecology and Evolution, Yale University, New Haven, CT, United States
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9
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Porretta D, Canestrelli D. The ecological importance of hybridization. Trends Ecol Evol 2023; 38:1097-1108. [PMID: 37620217 DOI: 10.1016/j.tree.2023.07.003] [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: 03/12/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Hybridization as an evolutionary process has been studied in depth over the past few decades. Research has focused on its role in shaping reproductive barriers, its adaptive value, and its genomic consequences. In contrast, our knowledge of ecological dimensions of hybridization is still in its infancy, despite hybridization being an inherently ecological interaction. Using examples from various organisms, we show that hybridization can affect and be affected by non-reproductive interactions, including predation, competition, parasitism, mutualism, commensalism, and organism-environment interactions, with significant implications for community structure and ecosystem functioning. However, since these dimensions of hybridization have mostly been revealed from studies designed to decipher other evolutionary processes, we argue that much of the eco-evolutionary importance of hybridization is yet to be discovered.
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Affiliation(s)
- Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, Italy.
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10
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Nakamura H, Aibara M, Nikaido M. Ancient standing genetic variation facilitated the adaptive radiation of Lake Victoria cichlids. Genes Genet Syst 2023; 98:93-99. [PMID: 37495512 DOI: 10.1266/ggs.23-00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023] Open
Abstract
Cichlid fishes are textbook examples of explosive speciation and adaptive radiation, providing a great opportunity to understand how the genomic substrate yields extraordinary species diversity. Recently, we performed comparative genomic analyses of three Lake Victoria cichlids to reveal the genomic substrates underlying their rapid speciation and adaptation. We found that long divergent haplotypes derived from large-scale standing genetic variation, which originated before the adaptive radiation of Lake Victoria cichlids, may have contributed to their rapid diversification. In addition, the present study on genomic data from other East African cichlids suggested the reuse of alleles that may have originated in the ancestral lineages of Lake Tanganyika cichlids during cichlid evolution. Therefore, our results highlight that the primary factor that could drive repeated adaptive radiation across East African cichlids was allelic reuse from standing genetic variation to adapt to their own specific environment. In this report, we summarize the main results and discuss the evolutionary mechanisms of cichlids, based on our latest findings.
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Affiliation(s)
- Haruna Nakamura
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies
| | - Mitsuto Aibara
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology
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11
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Santos ME, Lopes JF, Kratochwil CF. East African cichlid fishes. EvoDevo 2023; 14:1. [PMID: 36604760 PMCID: PMC9814215 DOI: 10.1186/s13227-022-00205-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.
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Affiliation(s)
- M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK.
| | - João F Lopes
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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12
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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: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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13
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Disentangling the Diversity of the Labeobarbus Taxa (Cypriniformes: Cyprinidae) from the Epulu Basin (DR Congo, Africa). DIVERSITY 2022. [DOI: 10.3390/d14121022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In an attempt to disentangle the complex taxonomy of the Labeobarbus species of the Epulu River, a right bank headwater affluent of the Aruwimi, Central Congo basin, a morphological study was undertaken on 221 specimens from the Epulu and 32 type specimens. As a result, five different species have been distinguished, including four so-called rubberlips, L. caudovittatus, L. macroceps, L. mawambiensis, and L. sp. ‘thick lip’, and one chiselmouth, L. longidorsalis. While rubberlips have a curved mouth with well-developed lips and often a mental lobe, chiselmouths have a straight mouth with a keratinised cutting edge on the lower jaw. Among the specimens examined, several presented an intermediate mouth morphology between L. mawambiensis and L. longidorsalis, either with one or two pairs of barbels. One specimen exhibited an intermediate morphology between L. mawambiensis and L. macroceps. This morphological study, complemented with a molecular study of the mitochondrial gene cytochrome b (cyt b), suggests that these intermediates are probably hybrid specimens. The Epulu case is reminiscent to a case of possible hybridisation recently discovered in the Inkisi River (Lower Congo basin), but differs in having a lower relative abundance of hybrid specimens in the population, and in phylogenetic patterns.
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14
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Lewanski AL, Golcher-Benavides J, Rick JA, Wagner CE. Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact. Mol Ecol 2022; 31:5041-5059. [PMID: 35913373 DOI: 10.1111/mec.16636] [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: 12/06/2021] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 12/01/2022]
Abstract
Closely related taxa frequently exist in sympatry before the evolution of robust reproductive barriers, which can lead to substantial gene flow. Post-divergence gene flow can promote several disparate trajectories of divergence ranging from the erosion of distinctiveness and eventual collapse of the taxa to the strengthening of reproductive isolation. Among many relevant factors, understanding the demographic history of divergence (e.g. divergence time, extent of historical gene flow) can be particularly informative when examining contemporary gene flow between closely related taxa because this history can influence gene flow's prevalence and consequences. Here, we used genotyping-by-sequencing data to investigate speciation and contemporary hybridization in two closely related and sympatrically distributed Lake Tanganyikan cichlid species in the genus Petrochromis. Demographic modeling supported a speciation scenario involving divergence in isolation followed by secondary contact with bidirectional gene flow. Further investigation of this recent gene flow found evidence of ongoing hybridization between the species that varied in extent between different co-occurring populations. Relationships between abundance and the degree of admixture across populations suggest that the availability of conspecific mates may influence patterns of hybridization. These results, together with the observation that sets of recently diverged cichlid taxa are generally geographically separated in the lake, suggest that ongoing speciation in Lake Tanganyikan cichlids relies on initial spatial isolation. Additionally, the spatially heterogeneous patterns of admixture between the Petrochromis species illustrates the complexities of hybridization when species are in recent secondary contact.
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Affiliation(s)
| | - Jimena Golcher-Benavides
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Jessica A Rick
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Catherine E Wagner
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA.,Biodiversity Institute, University of Wyoming, Laramie, WY, USA
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15
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Singh P, Irisarri I, Torres‐Dowdall J, Thallinger GG, Svardal H, Lemmon EM, Lemmon AR, Koblmüller S, Meyer A, Sturmbauer C. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecol Evol 2022; 12:e9077. [PMID: 35866021 PMCID: PMC9288888 DOI: 10.1002/ece3.9077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.
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Affiliation(s)
- Pooja Singh
- Institute of BiologyUniversity of GrazGrazAustria
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
- Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum HamburgHamburgGermany
| | - Julián Torres‐Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
| | - Gerhard G. Thallinger
- Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria
- OMICS Center Graz, BioTechMed GrazGrazAustria
| | - Hannes Svardal
- Department of BiologyUniversity of AntwerpAntwerpBelgium
- Naturalis Biodiversity CenterLeidenThe Netherlands
| | - Emily Moriarty Lemmon
- Department of Biological ScienceFlorida State University, Biomedical Research FacilityTallahasseeFloridaUSA
| | - Alan R. Lemmon
- Department of Biological ScienceFlorida State University, Biomedical Research FacilityTallahasseeFloridaUSA
| | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of BiologyUniversity of KonstanzConstanceGermany
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16
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Burress ED, Piálek L, Casciotta J, Almirón A, Říčan O. Rapid Parallel Morphological and Mechanical Diversification of South American Pike Cichlids (Crenicichla). Syst Biol 2022; 72:120-133. [PMID: 35244182 DOI: 10.1093/sysbio/syac018] [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: 01/28/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Explosive bouts of diversification are one of the most conspicuous features of the tree of life. When such bursts are repeated in similar environments it suggests some degree of predictability in the evolutionary process. We assess parallel adaptive radiation of South American pike cichlids (Crenicichla) using phylogenomics and phylogenetic comparative methods. We find that species flocks in the Uruguay and Iguazú River basins rapidly diversified into the same set of ecomorphs that reflect feeding ecology. Both adaptive radiations involve expansion of functional morphology, resulting in unique jaw phenotypes. Yet, form and function were decoupled such that most ecomorphs share similar mechanical properties of the jaws (i.e., jaw motion during a feeding strike). Prey mobility explained six to nine-fold differences in the rate of morphological evolution, but had no effect on the rate of mechanical evolution. We find no evidence of gene flow between species flocks or with surrounding coastal lineages that may explain their rapid diversification. When compared to cichlids of the East African Great Lakes and other prominent adaptive radiations, pike cichlids share many themes, including rapid expansion of phenotypic diversity, specialization along the benthic-to-pelagic habitat and soft-to-hard prey axes, and the evolution of conspicuous functional innovations. Yet, decoupled evolution of form and function and the absence of hybridization as a catalyzing force are departures from patterns observed in other adaptive radiations. Many-to-one mapping of morphology to mechanical properties is a mechanism by which pike cichlids exhibit a diversity of feeding ecologies while avoiding exacerbating underlying mechanical trade-offs.
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Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Lubomír Piálek
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jorge Casciotta
- División Zoología Vertebrados, Facultad de Ciencias Naturales y Museo,UNLP, Paseo del Bosque, 1900 La Plata, Buenos Aires, Argentina.,CIC,Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Adriana Almirón
- División Zoología Vertebrados, Facultad de Ciencias Naturales y Museo,UNLP, Paseo del Bosque, 1900 La Plata, Buenos Aires, Argentina
| | - Oldřich Říčan
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
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17
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Cuevas A, Eroukhmanoff F, Ravinet M, Sætre GP, Runemark A. Predictors of genomic differentiation within a hybrid taxon. PLoS Genet 2022; 18:e1010027. [PMID: 35148321 PMCID: PMC8870489 DOI: 10.1371/journal.pgen.1010027] [Citation(s) in RCA: 3] [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: 03/30/2021] [Revised: 02/24/2022] [Accepted: 01/11/2022] [Indexed: 01/03/2023] Open
Abstract
Hybridization is increasingly recognized as an important evolutionary force. Novel genetic methods now enable us to address how the genomes of parental species are combined in hybrid lineages. However, we still do not know the relative importance of admixed proportions, genome architecture and local selection in shaping hybrid genomes. Here, we take advantage of the genetically divergent island populations of Italian sparrow on Crete, Corsica and Sicily to investigate the predictors of genomic variation within a hybrid taxon. We test if differentiation is affected by recombination rate, selection, or variation in ancestry proportions. We find that the relationship between recombination rate and differentiation is less pronounced within hybrid lineages than between the parent species, as expected if purging of minor parent ancestry in low recombination regions reduces the variation available for differentiation. In addition, we find that differentiation between islands is correlated with differences in signatures of selection in two out of three comparisons. Signatures of selection within islands are correlated across all islands, suggesting that shared selection may mould genomic differentiation. The best predictor of strong differentiation within islands is the degree of differentiation from house sparrow, and hence loci with Spanish sparrow ancestry may vary more freely. Jointly, this suggests that constraints and selection interact in shaping the genomic landscape of differentiation in this hybrid species.
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Affiliation(s)
- Angélica Cuevas
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Fabrice Eroukhmanoff
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Mark Ravinet
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Glenn-Peter Sætre
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
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18
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Abstract
Whole genome sequences are beginning to revolutionize our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic data sets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of single nucleotide polymorphisms extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomize the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than 2 million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the data set to nonintrogressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome data sets. [Incomplete lineage sorting; introgression; linkage disequilibrium; multispecies coalescence; rapid radiation; soft polytomy.]
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19
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Daane JM, William Detrich H. Adaptations and Diversity of Antarctic Fishes: A Genomic Perspective. Annu Rev Anim Biosci 2021; 10:39-62. [PMID: 34748709 DOI: 10.1146/annurev-animal-081221-064325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antarctic notothenioid fishes are the classic example of vertebrate adaptive radiation in a marine environment. Notothenioids diversified from a single common ancestor ∼25 Mya to more than 140 species today, and they represent ∼90% of fish biomass on the continental shelf of Antarctica. As they diversified in the cold Southern Ocean, notothenioids evolved numerous traits, including osteopenia, anemia, cardiomegaly, dyslipidemia, and aglomerular kidneys, that are beneficial or tolerated in their environment but are pathological in humans. Thus, notothenioids are models for understanding adaptive radiations, physiological and biochemical adaptations to extreme environments, and genetic mechanisms of human disease. Since 2014, 16 notothenioid genomes have been published, which enable a first-pass holistic analysis of the notothenioid radiation and the genetic underpinnings of novel notothenioid traits. Here, we review the notothenioid radiation from a genomic perspective and integrate our insights with recent observations from other fish radiations. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Jacob M Daane
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - H William Detrich
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
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20
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Jensen EL, Gaughran SJ, Garrick RC, Russello MA, Caccone A. Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises. Mol Ecol 2021; 30:6325-6339. [PMID: 34510620 DOI: 10.1111/mec.16176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022]
Abstract
Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of diversity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three individuals of the 12 extant lineages of Galapagos giant tortoise and estimate diversity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within individuals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in-depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.
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Affiliation(s)
- Evelyn L Jensen
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Stephen J Gaughran
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, Mississippi, USA
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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