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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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de Gier W, Groenhof M, Fransen CH. Coming out of your shell or crawling back in: multiple interphylum host switching events within a clade of bivalve- and ascidian-associated shrimps (Caridea: Palaemonidae). CONTRIBUTIONS TO ZOOLOGY 2022. [DOI: 10.1163/18759866-bja10030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
Marine symbiotic Palaemonidae, comprising over 600 species, live in association with marine invertebrates of different phyla, like Cnidaria, Echinodermata, Mollusca, Porifera, and Tunicata. A phylogenetic study is performed on a clade of bivalve- and ascidian-associated endosymbiotic shrimp species (Caridea: Palaemonidae), using morphological and molecular data. A Total Evidence approach is used in order to include all currently known ingroup species in an evolutionary framework. Ancestral state reconstruction analyses are performed to identify host-switching events and ancestral ranges. The clade, including Ascidonia, Conchodytes, Dactylonia, Odontonia, and Pontonia, and various smaller genera, is recovered as monophyletic, with an ascidian-associated ancestral host state. At least six interphylum host switches are tentatively identified, with members of Odontonia and Notopontonia switching back to an ascidian host affiliation after the ancestral host switch of the clade including Conchodytes, Odontonia and related genera, from an ascidian- to a bivalve host. The clade including Ascidonia and Pontonia was recovered to have an ancestor with an East Pacific/Atlantic distribution. The other studied genera remained in the original ancestral Indo-West Pacific range. We hypothesize that similar internal environments of shrimp hosts from different phyla will function as hot spots for interphylum host switching in various lineages of symbionts.
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Affiliation(s)
- Werner de Gier
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands,
| | - Mike Groenhof
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300, RA Leiden, The Netherlands
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Stiller J, Short G, Hamilton H, Saarman N, Longo S, Wainwright P, Rouse GW, Simison WB. Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates. BMC Biol 2022; 20:75. [PMID: 35346180 PMCID: PMC8962102 DOI: 10.1186/s12915-022-01271-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/04/2022] [Indexed: 12/03/2022] Open
Abstract
Background Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved. Results Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus. In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea. Conclusions Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01271-w.
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Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA. .,Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Graham Short
- Ichthyology, Australian Museum, Sydney, Australia.,Ichthyology, California Academy of Sciences, San Francisco, USA.,Ichthyology, Burke Museum of Natural History and Culture, Seattle, USA
| | | | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Sarah Longo
- Department of Biological Science, Towson University, Towson, MD, 21252, USA
| | - Peter Wainwright
- Department of Evolution & Ecology, University of California, Davis, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, USA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, USA
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Santaquiteria A, Siqueira AC, Duarte-Ribeiro E, Carnevale G, White W, Pogonoski J, Baldwin CC, Ortí G, Arcila D, Betancur RR. Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences. Syst Biol 2021; 70:1145-1162. [PMID: 33892493 DOI: 10.1093/sysbio/syab028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/14/2022] Open
Abstract
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.
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Affiliation(s)
- Aintzane Santaquiteria
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Alexandre C Siqueira
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Emanuell Duarte-Ribeiro
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10125, Torino, Italy
| | - William White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - John Pogonoski
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Guillermo Ortí
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Department of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - Dahiana Arcila
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.,Sam Noble Oklahoma Museum of Natural History, 2401 Chautauqua Ave, Norman, OK 73072, USA
| | - Ricardo R Betancur
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
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Tea YK, Hobbs JPA, Vitelli F, DiBattista JD, Ho SYW, Lo N. Angels in disguise: sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages. Proc Biol Sci 2020; 287:20201459. [PMID: 32752983 DOI: 10.1098/rspb.2020.1459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hybridization events are not uncommon in marine environments where physical barriers are attenuated. Studies of coral reef taxa have suggested that hybridization predominantly occurs between parapatric species distributed along biogeographic suture zones. By contrast, little is known about the extent of sympatric hybridization on coral reefs, despite the large amount of biogeographic overlap shared by many coral reef species. Here, we investigate if the propensity for hybridization along suture zones represents a general phenomenon among coral reef fishes, by focusing on the marine angelfishes (family Pomacanthidae). Although hybridization has been reported for this family, it has not been thoroughly surveyed, with more recent hybridization studies focusing instead on closely related species from a population genetics perspective. We provide a comprehensive survey of hybridization among the Pomacanthidae, characterize the upper limits of genetic divergences between hybridizing species and investigate the occurrence of sympatric hybridization within this group. We report the occurrence of hybridization involving 42 species (48% of the family) from all but one genus of the Pomacanthidae. Our results indicate that the marine angelfishes are among the groups of coral reef fishes with the highest incidences of hybridization, not only between sympatric species, but also between deeply divergent lineages.
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Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia.,Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Jean-Paul A Hobbs
- School of Biological Sciences, University of Queensland, Brisbane, Queensland 4069, Australia
| | - Federico Vitelli
- Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia 6027, Australia
| | - Joseph D DiBattista
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney, New South Wales 2010, Australia.,School of Molecular and Life Sciences, Curtin University, Perth, Western Australia 6102, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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