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Huggett MJ, Hobbs JPA, Vitelli F, Stat M, Sinclair-Taylor TH, Bunce M, DiBattista JD. Gut microbial communities of hybridising pygmy angelfishes reflect species boundaries. Commun Biol 2023; 6:542. [PMID: 37202414 DOI: 10.1038/s42003-023-04919-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/06/2023] [Indexed: 05/20/2023] Open
Abstract
Hybridisation and introgression of eukaryotic genomes can generate new species or subsume existing ones, with direct and indirect consequences for biodiversity. An understudied component of these evolutionary forces is their potentially rapid effect on host gut microbiomes, and whether these pliable microcosms may serve as early biological indicators of speciation. We address this hypothesis in a field study of angelfishes (genus Centropyge), which have one of the highest prevalence of hybridisation within coral reef fish. In our study region of the Eastern Indian Ocean, the parent fish species and their hybrids cohabit and display no differences in their diet, behaviour, and reproduction, often interbreeding in mixed harems. Despite this ecological overlap, we show that microbiomes of the parent species are significantly different from each other in form and function based on total community composition, supporting the division of parents into distinct species, despite the confounding effects of introgression acting to homogenize parent species identity at other molecular markers. The microbiome of hybrid individuals, on the other hand, are not significantly different to each of the parents, instead harbouring an intermediate community composition. These findings suggest that shifts in gut microbiomes may be an early indicator of speciation in hybridising species.
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Affiliation(s)
- Megan J Huggett
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, 2258, Australia.
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, Australia.
| | - Jean-Paul A Hobbs
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4069, Australia
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Federico Vitelli
- Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, Australia
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW, 2258, Australia
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
| | - Tane H Sinclair-Taylor
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- Australian Institute of Marine Sciences, Townsville, QLD, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
- Institute of Environmental Science and Research (ESR), Kenepuru, Porirua, 5022, New Zealand
| | - Joseph D DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, 6102, Australia
- Australian Museum Research Institute, Australian Museum, 1 William St, Sydney, NSW, 2010, Australia
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Gaither MR, Coker DJ, Greaves S, Sarigol F, Payet SD, Chaidez V, Sinclair-Taylor TH, DiBattista JD, Berumen ML. Does color matter? Molecular and ecological divergence in four sympatric color morphs of a coral reef fish. Ecol Evol 2020; 10:9663-9681. [PMID: 33005338 PMCID: PMC7520180 DOI: 10.1002/ece3.6566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 01/13/2023] Open
Abstract
Non-sex-linked color polymorphism is common in animals and can be maintained in populations via balancing selection or, when under diversifying selection, can promote divergence. Despite their potential importance in ecological interactions and the evolution of biodiversity, their function and the mechanisms by which these polymorphisms are maintained are still poorly understood. Here, we combine field observations with life history and molecular data to compare four sympatric color morphs of the coral reef fish Paracirrhites forsteri (family Cirrhitidae) in the central Red Sea. Our findings verify that the color morphs are not sex-limited, inhabit the same reefs, and do not show clear signs of avoidance or aggression among them. A barcoding approach based on 1,276 bp of mitochondrial DNA could not differentiate the color morphs. However, when 36,769 SNPs were considered, we found low but significant population structure. Focusing on 1,121 F ST outliers, we recovered distinct population clusters that corresponded to shifts in allele frequencies with each color morph harboring unique alleles. Genetic divergence at these outlier loci is accompanied by differences in growth and marginal variation in microhabitat preference. Together, life history and molecular analysis suggest subtle divergence between the color morphs in this population, the causes for which remain elusive.
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Affiliation(s)
- Michelle R Gaither
- Genomics and Bioinformatics Cluster Department of Biology University of Central Florida Orlando FL USA
| | - Darren J Coker
- Division of Biological and Environmental Science and Engineering Red Sea Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Samuel Greaves
- Genomics and Bioinformatics Cluster Department of Biology University of Central Florida Orlando FL USA
| | - Fatih Sarigol
- Faculty of Biology Ludwig-Maximilians-Universität München Planegg-Martinsried Germany
| | - Samuel D Payet
- Division of Biological and Environmental Science and Engineering Red Sea Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Veronica Chaidez
- Division of Biological and Environmental Science and Engineering Red Sea Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia
| | | | - Joseph D DiBattista
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Perth WA Australia
- Australian Museum Research Institute Australian Museum Sydney NSW Australia
| | - Michael L Berumen
- Division of Biological and Environmental Science and Engineering Red Sea Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia
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Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii). Sci Rep 2018; 8:1498. [PMID: 29367590 PMCID: PMC5784092 DOI: 10.1038/s41598-018-19430-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022] Open
Abstract
The diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservation.
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