1
|
Baraf LM, Hung JY, Pratchett MS, Cowman PF. Comparative mitogenomics of marine angelfishes (F: Pomacanthidae). Ecol Evol 2024; 14:e70127. [PMID: 39119180 PMCID: PMC11307104 DOI: 10.1002/ece3.70127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/16/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
The targeted capture of ultraconserved elements (UCEs) has substantially increased the amount of genetic data available for phylogenomic reconstructions. These capture datasets frequently contain mitochondrial DNA as a by-product, often in the form of complete mitogenomes. These can be efficiently harvested to expand existing datasets without additional costs. Here, we present new mitochondrial genomes for six marine angelfish species (F: Pomacanthidae), assembled and annotated from off-target UCE reads. We provide the first comparative analysis of all mitochondrial genomes available for the Pomacanthidae. Results showed that the average length of pomacanthid mitogenomes is 16.8 kbp. Total GC and AT content varied between 44.5% and 46.3%, and 53.7% and 55.5%, respectively. The architecture of angelfish mitogenomes was comparable to that seen in other fish species with 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and the control region. All 13 PCGs evolved under purifying selection, highlighting a high level of selection pressure and gene expression to preserve genetic integrity. The ND6 and ATP8 genes had the highest ratio of non-synonymous (dN) to synonymous (dS) substitutions, indicating a relaxation of purifying selection constraints. Finally, these newly assembled mitogenomes will allow further investigations of the population genetics, systematics and evolutionary biology of one of the most prominent reef fish family in the aquarium trade.
Collapse
Affiliation(s)
- Lauriane M. Baraf
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Julia Y. Hung
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Morgan S. Pratchett
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Peter F. Cowman
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland Museum TropicsTownsvilleQueenslandAustralia
| |
Collapse
|
2
|
Stiller J, Wilson NG, Rouse GW. Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture. BMC Biol 2023; 21:129. [PMID: 37248474 DOI: 10.1186/s12915-023-01628-9] [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: 01/26/2023] [Accepted: 05/16/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture. RESULTS Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia. CONCLUSIONS We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.
Collapse
Affiliation(s)
- Josefin Stiller
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
- Centre for Biodiversity Genomics, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Nerida G Wilson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA
- Research & Collections, Western Australian Museum, Perth, Western Australia, 6106, Australia
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, 6009, Australia
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, 92093 , USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Shen KN, Chang CW. The complete mitogenome of the Greytail angelfish Chaetodontoplus poliourus and its phylogenetic relationships (Perciformes: Pomacanthidae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3333-3335. [PMID: 34746406 PMCID: PMC8567932 DOI: 10.1080/23802359.2021.1933632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The mitogenome of the Greytail angelfish Chaetodontoplus poliourus (Pomacanthidae) was decoded using next-generation sequencing techniques. The de novo assembled mitogenome consists of 16,961 bp, including 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. The gene arrangement is identical to the other available Pomacanthidae mitogenomes submitted to NCBI. The overall base composition of the C. poliourus mitogenome was estimated to be 28.0% A, 30.9% C, 15.8% G and 25.3% T. The phylogenetic analysis of the C. poliourus mitogenome suggests a closer genetic relationship with Vermiculated angelfish Chaetodontoplus mesoleucus as expected from their similar color patterns. The overall pairwise identity except D-loop is 93.7% for these two sister species. The decoding of the C. poliourus mitogenome has enriched gene database for further evolutionary studies and conservation assessments of this uncommon and newly described marine angelfish.
Collapse
Affiliation(s)
- Kang-Ning Shen
- Aquatic Technology Laboratories, Agricultural Technology Research Institute, Hsinchu, Taiwan, R.O.C
| | - Chih-Wei Chang
- Marine Ecology and Conservation Research Center, National Academy of Marine Research, Kaohsiung, Taiwan, R.O.C.,Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan, R.O.C.,National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, R.O.C
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Palmerín‐Serrano PN, Tavera J, Espinoza E, Angulo A, Martínez‐Gómez JE, González‐Acosta AF, Domínguez‐Domínguez O. Evolutionary history of the reef fish
Anisotremus interruptus
(Perciformes: Haemulidae) throughout the Tropical Eastern Pacific. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paola Nallely Palmerín‐Serrano
- Programa Institucional de Maestría en Ciencias Biológicas Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
| | - Jose Tavera
- Laboratorio de Ictiología Departamento de Biología Universidad del Valle Cali Colombia
| | - Eduardo Espinoza
- Investigación Marina Aplicada Parque Nacional Galápagos “Charles Darwin” Puerto Ayora Isla Santa Cruz Ecuador
| | - Arturo Angulo
- Museo de Zoología y Centro de Investigación en Ciencias del Mar y Limnología Universidad de Costa Rica San Pedro de Montes de Oca San José Costa Rica
- Laboratorio de Ictiología Departamento de Zoología e Botánica Universidad Estadual Paulista “Julio de MesquitaFilho” São José do Rio Preto São Paul Brazil
| | - Juan E. Martínez‐Gómez
- Instituto de Ecología A. C. (INECOL)Red de Interacciones Multitróficas Xalapa Veracruz México
| | - Adrián F. González‐Acosta
- Instituto Politécnico NacionalCentro Interdisciplinario de Ciencias Marinas (CICIMAR)Pesquerías y Biología Marina La Paz México
| | - Omar Domínguez‐Domínguez
- Laboratorio de Biología Acuática Facultad de Biología Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán México
- Laboratorio Nacional de Análisis y Síntesis Ecológica para la Conservación de Recursos Genéticos de México Escuela Nacional de Estudios SuperioresUniversidad Nacional Autónoma de México Morelia Michoacán México
- Instituto Nacional de BiodiversidadColección de Peces Quito Ecuador
| |
Collapse
|
8
|
Embryonic and early larval development of two marine angelfish, Centropyge bicolor and Centropyge bispinosa. ZYGOTE 2020; 28:196-202. [PMID: 32083523 DOI: 10.1017/s0967199419000789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Marine angelfish (family: Pomacanthidae) are among the most sought-after fish species in the saltwater aquarium trade. However, there is a lack of information in the literature on their early ontogeny. The objective of this study was to describe the embryonic and early larval development of two dwarf angelfish, the bicolour angelfish, Centropyge bicolor and the coral beauty angelfish, Centropyge bispinosa. The eggs of these two species were obtained from spontaneous spawning of the broodstock fish in captivity and incubated at 26.0 ± 0.2°C throughout the study. Fertilized eggs (n = 15) of both species are transparent, pelagic and spherical; the mean diameters of the eggs were measured at 703.6 ± 7.8 μm for C. bicolor and 627.6 ± 7.8 μm for C. bispinosa. The eggs of both species possessed a narrow perivitelline space, smooth and thin chorion, a homogenous and non-segmented yolk as well as a single oil globule. Overall, the observed embryonic development pattern of C. bicolor and C. bispinosa was very similar, and the main difference was the embryonic pigmentation pattern, which only became evident close to hatching. Larvae of both species started hatching at 13 h 30 min after fertilization, and the larval characteristics of both species also showed high levels of similarities. However, the mouth opening time for C. bicolor was 72 h after hatching (AH) and 96 AH for C. bispinosa. In general, the observed early ontogeny of C. bicolor and C. bispinosa also resembled that of other Centropyge species documented in the literature.
Collapse
|
9
|
Baraf LM, Pratchett MS, Cowman PF. Ancestral biogeography and ecology of marine angelfishes (F: Pomacanthidae). Mol Phylogenet Evol 2019; 140:106596. [DOI: 10.1016/j.ympev.2019.106596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022]
|
10
|
Thermal influence on the embryonic development and hatching rate of the flameback pygmy angelfish Centropyge aurantonotus eggs. ZYGOTE 2019; 28:80-82. [PMID: 31603058 DOI: 10.1017/s096719941900056x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The flameback pygmy angelfish Centropyge aurantonotus, highly appreciated and valued by the aquarium market, is heavily harvested and traded. Temperature is one of the abiotic factors that has the most influence on fish development, especially in the early stages of life. For captive production, it is essential to know the appropriate environmental parameters for each species. In this sense, this study aimed to evaluate the influence of temperature on the embryonic development and hatching rates of C. aurantonotus incubated at six different temperatures (20, 22, 24, 26, 28, 30°C). Embryonic development events were very similar in terms of morphological and chronological characteristics compared with other species of the genus Centropyge. Incubation time was inversely proportional to temperature. The treatment at 22°C required twice the time of that required by 30°C treatment for hatching to occur. The best incubation temperature range was 24-28°C. Values below 22°C and at 30°C showed lower hatching rates compared with other treatments. Based on these results, the recommended temperature at which to incubate C. aurantonotus eggs is between 24-28°C.
Collapse
|
11
|
Baliga VB, Mehta RS. Morphology, Ecology, and Biogeography of Independent Origins of Cleaning Behavior Around the World. Integr Comp Biol 2019; 59:625-637. [DOI: 10.1093/icb/icz030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Members of an ecological guild may be anticipated to show morphological convergence, as similar functional demands exert similar selective pressures on phenotypes. Nature is rife with examples, however, where such taxa instead exhibit ‘incomplete’ convergence or even divergence. Incorporating factors such as character displacement by other guild members or variation in ecological specialization itself may therefore be necessary to gain a more complete understanding of what constrains or promotes diversity. Cleaning, a behavior in which species remove and consume ectoparasites from “clientele,” has been shown to exhibit variation in specialization and has evolved in a variety of marine habitats around the globe. To determine the extent to which specialization in this tropic strategy has affected phenotypic evolution, we examined the evolution of cleaning behavior in five marine fish families: Labridae, Gobiidae, Pomacanthidae, Pomacentridae, and Embiotocidae. We used a comparative framework to determine patterns of convergence and divergence in body shape and size across non-cleaning and cleaning members within these five clades. Highly specialized obligate cleaning, found in the Indo-Pacific and the Caribbean, evolved in the Labridae and Gobiidae at strikingly similar times. In these two regions, obligate cleaning evolves early, shows convergence on an elongate body shape, and is restricted to species of small body size. Facultative cleaning, shown either throughout ontogeny or predominately in the juvenile phase, exhibits a much more varied phenotype, especially in geographic regions where obligate cleaning occurs. Collectively, our results are consistent with varying extents of an ecological specialization constraining or spurring morphological evolution in recurrent ways across regions.
Collapse
Affiliation(s)
- Vikram B Baliga
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Rita S Mehta
- Department of Ecology and Evolutionary Biology, Long Marine Laboratory, University of California, Santa Cruz, CA 95060, USA
| |
Collapse
|
12
|
Ludt WB, Bernal MA, Kenworthy E, Salas E, Chakrabarty P. Genomic, ecological, and morphological approaches to investigating species limits: A case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes. Ecol Evol 2019; 9:4001-4012. [PMID: 31015983 PMCID: PMC6467843 DOI: 10.1002/ece3.5029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 01/02/2023] Open
Abstract
A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark spots on their body. We examined the species limits in this system using comparative specimen-based approaches, a mitochondrial gene (COI), more than 800 nuclear loci (Ultraconserved Elements), and abiotic niche comparisons. The results indicate there is a complete overlap of meristic counts and morphometric measurements between the two species. Further, we detected multiple individuals with intermediate spotting patterns suggesting that coloration is not diagnostic. Mitochondrial data recovered a single main haplotype shared between the species and all locations resulting in a complete lack of structure (ΦST = 0). Genomic analyses also suggest low levels of genetic differentiation (F ST = 0.013), and no alternatively fixed SNPs were detected between the two phenotypes. Furthermore, niche comparisons could not reject niche equivalency or similarity between the species. These results suggest that these two phenotypes are conspecific and widely distributed in the TEP. Here, we recognize Prionurus punctatus Gill 1862 as a junior subjective synonym of P. laticlavius (Valenciennes 1846). The underlying causes of phenotypic variation in this species are unknown. However, this system gives insight into general evolutionary dynamics within the TEP.
Collapse
Affiliation(s)
- William B. Ludt
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDistrict of Columbia
| | - Moisés A. Bernal
- Department of Biological Sciences109 Cooke HallState University of New York at BuffaloBuffaloNew York
| | - Erica Kenworthy
- Ichthyology Section, 119 Foster Hall, Museum of Natural Science, Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | | | - Prosanta Chakrabarty
- Ichthyology Section, 119 Foster Hall, Museum of Natural Science, Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| |
Collapse
|
13
|
Hemingson CR, Cowman PF, Hodge JR, Bellwood DR. Colour pattern divergence in reef fish species is rapid and driven by both range overlap and symmetry. Ecol Lett 2018; 22:190-199. [DOI: 10.1111/ele.13180] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/10/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Christopher R. Hemingson
- College of Science and Engineering James Cook University Townsville4811 Australia
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville4811 Australia
| | - Peter F. Cowman
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville4811 Australia
| | - Jennifer R. Hodge
- Department of Evolution and Ecology University of California Davis Davis CA95616 USA
| | - David R. Bellwood
- College of Science and Engineering James Cook University Townsville4811 Australia
- ARC Centre of Excellence for Coral Reef Studies James Cook University Townsville4811 Australia
| |
Collapse
|
14
|
Campbell MA, Robertson DR, Vargas MI, Allen GR, McMillan WO. Multilocus molecular systematics of the circumtropical reef-fish genus Abudefduf (Pomacentridae): history, geography and ecology of speciation. PeerJ 2018; 6:e5357. [PMID: 30128183 PMCID: PMC6097498 DOI: 10.7717/peerj.5357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/11/2018] [Indexed: 01/05/2023] Open
Abstract
We investigated a pantropical sub-family and genus of damselfishes, the sergeant-majors (Pomacentridae: Abudefdufinae: Abudefduf), to identify the tempo and mechanisms of speciation in the lineage. We examined sequence capture data from 500 loci and 20 species, with multiple individuals sampled from across the geographic ranges of widespread species. Utilizing a maximum likelihood framework, as well as a time-calibrated Bayesian phylogeny, the following key questions are addressed: What is the historical tempo of speciation? What are the relative contributions of vicariant, peripatric and parapatric speciation to sergeant-major diversity? How is speciation related to major variation in trophic ecology? The approximately 20 species of sergeant-majors fall into three main lineages. The ancestral condition appears to be benthivory, which is predominant in two lineages comprising six species. The remaining species of sergeant-majors, of which there are at least 15, fall within a clade composed entirely of planktivores. This clade is sister to a benthivore clade that included one species, Abudefduf notatus, in transition to planktivory. Most speciation of sergeant-majors, which appeared ∼24 million years ago, occurred in the last 10 million years. Present distributional patterns indicate vicariant speciation precipitated by the closure of land barriers between both sides of the Atlantic and the Pacific, and the emergence of land between the Indian and Pacific Oceans. Within this backdrop, frequent oscillations in sea level over the last 10 million years also appear to have generated conditions suitable for both peripatric and vicariant speciation, and most speciation within the genus appears linked to these changes in sea level. Diversification within the genus has been concentrated in planktivorous seargeant-majors rather than benthivores. The root cause is unclear, but does not appear to be related to differences in dispersal potential, which is greater in the planktivorous species, due to the ability of their post-larval juveniles to raft with floating debris. This elevated speciation rate in planktivores and their propensity to form local endemics may reflect relaxation of selective pressures (e.g., on crypticity) that limit speciation in benthivorous sergeant-majors. Finally, our data allow us to clarify relationships of geminate sergeant-major species, indicating that there are subdivisions within the Atlantic for both benthivore and planktivore geminate pairs that may have misled previous studies.
Collapse
Affiliation(s)
| | - D Ross Robertson
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Marta I Vargas
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Gerald R Allen
- Western Australian Museum, Welshpool, Western Australia, Australia
| | - W O McMillan
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| |
Collapse
|
15
|
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: 8] [Impact Index Per Article: 1.3] [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.
Collapse
|
16
|
Frédérich B, Santini F, Konow N, Schnitzler J, Lecchini D, Alfaro ME. Body shape convergence driven by small size optimum in marine angelfishes. Biol Lett 2017; 13:20170154. [PMID: 28615351 PMCID: PMC5493737 DOI: 10.1098/rsbl.2017.0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 11/12/2022] Open
Abstract
Convergent evolution of small body size occurs across many vertebrate clades and may reflect an evolutionary response to shared selective pressures. However it remains unclear if other aspects of phenotype undergo convergent evolution in miniaturized lineages. Here we present a comparative analysis of body size and shape evolution in marine angelfishes (Pomacanthidae), a reef fish family characterized by repeated transitions to small body size. We ask if lineages that evolve small sizes show convergent evolution in body shape. Our results reveal that angelfish lineages evolved three different stable size optima with one corresponding to the group of pygmy angelfishes (Centropyge). Then, we test if the observed shifts in body size are associated with changes to new adaptive peaks in shape. Our data suggest that independent evolution to small size optima have induced repeated convergence upon deeper body and steeper head profile in Centropyge These traits may favour manoeuvrability and visual awareness in these cryptic species living among corals, illustrating that functional demands on small size may be related to habitat specialization and predator avoidance. The absence of shape convergence in large marine angelfishes also suggests that more severe requirements exist for small than for large size optima.
Collapse
Affiliation(s)
- Bruno Frédérich
- Laboratoire de Morphologie Fonctionnelle et Evolutive, Université de Liège, Liège, Belgium
| | | | - Nicolai Konow
- Department of Biological Sciences, UMass, Lowell, MA, USA
| | - Joseph Schnitzler
- Institute for Terrestrial and Aquatic Wildlife Research, TiHo Hannover, Büsum, Germany
| | - David Lecchini
- USR 3278, PSL, Labex 'Corail', CRIOBE, Moorea, French Polynesia
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| |
Collapse
|
17
|
Floeter SR, Bender MG, Siqueira AC, Cowman PF. Phylogenetic perspectives on reef fish functional traits. Biol Rev Camb Philos Soc 2017; 93:131-151. [PMID: 28464469 DOI: 10.1111/brv.12336] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/24/2017] [Accepted: 03/29/2017] [Indexed: 01/13/2023]
Abstract
Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.
Collapse
Affiliation(s)
- Sergio R Floeter
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB, Universidade Federal de Santa Catarina, Florianopolis, 88040-900, Brazil
| | - Mariana G Bender
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB, Universidade Federal de Santa Catarina, Florianopolis, 88040-900, Brazil
| | - Alexandre C Siqueira
- Depto. de Ecologia e Zoologia, Marine Macroecology and Biogeography Laboratory, CCB, Universidade Federal de Santa Catarina, Florianopolis, 88040-900, Brazil
| | - Peter F Cowman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, U.S.A.,Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4811, Australia
| |
Collapse
|
18
|
DiBattista JD, Gaither MR, Hobbs JPA, Rocha LA, Bowen BW. Response to Delrieu-Trottin et al.: Hybrids, Color Variants and the Consistently Devilish Taxonomy of Pygmy Angelfishes. J Hered 2017; 108:337-339. [PMID: 28391308 DOI: 10.1093/jhered/esx009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph D DiBattista
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Michelle R Gaither
- Hawai'i Institute of Marine Biology, Kane'ohe, HI, USA.,Section of Ichthyology, California Academy of Sciences, San Francisco, CA, USA
| | - Jean-Paul A Hobbs
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, San Francisco, CA, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, Kane'ohe, HI, USA
| |
Collapse
|
19
|
Delrieu-Trottin E, Shen KN, Chang CW, Borsa P. One Species Hypothesis to Rule Them All: Consistency Is Essential to Delimitate Species. J Hered 2017; 108:334-336. [PMID: 28391307 DOI: 10.1093/jhered/esx008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Wei Chang
- National Museum of Marine Biology & Aquarium and Graduate Institute of Marine Biology, National Dong Hwa University, Checheng, Pingtung, Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement (IRD), UMR 250 "Ecologie marine tropicale des océans Pacifique et Indien"/LabEx "Corail", Nouméa, New Caledonia
| |
Collapse
|
20
|
Bertrand JAM, Borsa P, Chen WJ. Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Mol Ecol 2017; 26:2527-2542. [PMID: 28160340 DOI: 10.1111/mec.14044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 01/02/2023]
Abstract
On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species.
Collapse
Affiliation(s)
- Joris A M Bertrand
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Philippe Borsa
- Institut de recherche pour le développement, UMR 250 'Ecologie marine tropicale des océans Pacifique et Indien', 101 promenade Roger-Laroque Anse Vata, BP A5, 98848 Nouméa cedex, New Caledonia
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, N°1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| |
Collapse
|
21
|
Bernal MA, Gaither MR, Simison WB, Rocha LA. Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon). Mol Ecol 2016; 26:639-652. [PMID: 27873385 DOI: 10.1111/mec.13937] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/18/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
Abstract
Closely related marine species with large overlapping ranges provide opportunities to study mechanisms of speciation, particularly when there is evidence of gene flow between such lineages. Here, we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via restriction site-associated DNA sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister-species. On the other hand, complete lineage sorting was observed at the nuclear loci and most of the SNPs. Under neutral expectations, the smaller effective population size of mtDNA should lead to fixation of mutations faster than nDNA. Thus, these results suggest that hybridization in the recent past (0.174-0.263 Ma) led to introgression of the mtDNA, with little effect on the nuclear genome. Analyses of the SNP data revealed 28 loci potentially under divergent selection between the two species. The combination of mtDNA introgression and limited nuclear DNA introgression provides a mechanism for the evolution of independent lineages despite recurrent hybridization events. This study adds to the growing body of research that exemplifies how genetic divergence can be maintained in the presence of gene flow between closely related species.
Collapse
Affiliation(s)
- Moisés A Bernal
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900 Thuwal, Kingdom of Saudi Arabia.,Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Michelle R Gaither
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA.,School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Luiz A Rocha
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| |
Collapse
|
22
|
DiBattista JD, Gaither MR, Hobbs JPA, Rocha LA, Bowen BW. Angelfishes, Paper Tigers, and the Devilish Taxonomy of theCentropyge flavissimaComplex. J Hered 2016; 107:647-653. [DOI: 10.1093/jhered/esw062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/11/2016] [Indexed: 11/13/2022] Open
|
23
|
Shen KN, Chang CW, Chan YF, Lin ZH, Tsai SY, Chen CH, Hsiao CD. Complete mitogenomes of Woodhead's angelfish ( Centropyge woodheadi) and Herald's angelfish ( Centropyge heraldi) (Teleostei: Pomacanthidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3672-3. [DOI: 10.3109/19401736.2015.1079849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan,
| | - Chih-Wei Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan,
| | - Yen-Fan Chan
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Zi-Han Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Shiou-Yi Tsai
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | | | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| |
Collapse
|
24
|
Shen KN, Chang CW, Lin ZH, Chan YF, Tsai SY, Chen CH, Hsiao CD. Complete mitogenomes of Cocos lemonpeel angelfish ( Centropyge flavissima) and Eibl’s angelfish ( Centropyge eibli) (Teleostei: Pomacanthidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:3709-10. [DOI: 10.3109/19401736.2015.1079868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan,
| | - Chih-Wei Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan,
| | - Zi-Han Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Yen-Fan Chan
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Shiou-Yi Tsai
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | | | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| |
Collapse
|
25
|
Shen KN, Chang CW, Chen CH, Hsiao CD. Complete mitogenomes of Multicolor angelfish ( Centropyge multicolor) and Yellowhead angelfish ( Centropyge joculator) (Teleostei: Pomacanthidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:2807-8. [DOI: 10.3109/19401736.2015.1053077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, ROC,
| | - Chih-Wei Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, ROC,
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan, ROC,
| | | | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, ROC
| |
Collapse
|
26
|
Shen KN, Chang CW, Tsai SY, Lin ZH, Chan YF, Chen CH, Hsiao CD. Complete mitogenomes of Barred angelfish ( Paracentropyge multifasciata) and Purplemask angelfish ( Paracentropyge venusta) (Teleostei: Pomacanthidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:2945-6. [DOI: 10.3109/19401736.2015.1060453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan,
| | - Chih-Wei Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan,
| | - Shiou-Yi Tsai
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Zi-Han Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Yen-Fan Chan
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | | | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| |
Collapse
|
27
|
Shen KN, Chang CW, Lin ZH, Chan YF, Tsai SY, Chen CH, Hsiao CD. Complete mitogenomes of Whitetail angelfish ( Centropyge flavicauda) and Orangeback angelfish ( Centropyge acanthops) (Teleostei: Pomacanthidae). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:2951-2. [DOI: 10.3109/19401736.2015.1060456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kang-Ning Shen
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan,
| | - Chih-Wei Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan,
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan,
| | - Zi-Han Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Yen-Fan Chan
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | - Shiou-Yi Tsai
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| | | | - Chung-Der Hsiao
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan, and
| |
Collapse
|
28
|
Coleman RR, Eble JA, DiBattista JD, Rocha LA, Randall JE, Berumen ML, Bowen BW. Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean. Mol Phylogenet Evol 2016; 100:243-253. [PMID: 27068838 DOI: 10.1016/j.ympev.2016.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/27/2022]
Abstract
The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.
Collapse
Affiliation(s)
- Richard R Coleman
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kāne'ohe, HI 96744, USA; Department of Biology, University of Hawai'i, Mānoa, 2500 Campus Rd, Honolulu, HI 96822, USA.
| | - Jeffrey A Eble
- University of West Florida, 11000 University Pkwy, Pensacola, FL 32514, USA
| | - Joseph D DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; Department of Environment and Agriculture, Curtin University, PO Box U1987, Perth, WA 6845, Australia
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr, San Francisco, CA 94118, USA
| | - John E Randall
- Bernice Pauahi Bishop Museum, 1525 Bernice St, Honolulu, HI 96817, USA
| | - Michael L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i, PO Box 1346, Kāne'ohe, HI 96744, USA
| |
Collapse
|
29
|
Henriques R, von der Heyden S, Matthee CA. When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus). PeerJ 2016; 4:e1827. [PMID: 27069785 PMCID: PMC4824878 DOI: 10.7717/peerj.1827] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/29/2016] [Indexed: 11/20/2022] Open
Abstract
In the marine environment, an increasing number of studies have documented introgression and hybridization using genetic markers. Hybridization appears to occur preferentially between sister-species, with the probability of introgression decreasing with an increase in evolutionary divergence. Exceptions to this pattern were reported for the Cape hakes (Merluccius capensis and M. paradoxus), two distantly related Merluciidae species that diverged 3-4.2 million years ago. Yet, it is expected that contemporary hybridization between such divergent species would result in reduced hybrid fitness. We analysed 1,137 hake individuals using nine microsatellite markers and control region mtDNA data to assess the validity of the described hybridization event. To distinguish between interbreeding, ancestral polymorphism and homplasy we sequenced the flanking region of the most divergent microsatellite marker. Simulation and empirical analyses showed that hybrid identification significantly varied with the number of markers, model and approach used. Phylogenetic analyses based on the sequences of the flanking region of Mmerhk-3b, combined with the absence of mito-nuclear discordance, suggest that previously reported hybridization between M. paradoxus and M. capensis cannot be substantiated. Our findings highlight the need to conduct a priori simulation studies to establish the suitability of a particular set of microsatellite loci for detecting multiple hybridization events. In our example, the identification of hybrids was severely influenced by the number of loci and their variability, as well as the different models employed. More importantly, we provide quantifiable evidence showing that homoplasy mimics the effects of heterospecific crossings which can lead to the incorrect identification of hybridization.
Collapse
Affiliation(s)
- Romina Henriques
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University , Stellenbosch , South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University , Stellenbosch , South Africa
| | - Conrad A Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University , Stellenbosch , South Africa
| |
Collapse
|
30
|
Bellwood DR, Goatley CHR, Bellwood O. The evolution of fishes and corals on reefs: form, function and interdependence. Biol Rev Camb Philos Soc 2016; 92:878-901. [PMID: 26970292 DOI: 10.1111/brv.12259] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 11/30/2022]
Abstract
Coral reefs are renowned for their spectacular biodiversity and the close links between fishes and corals. Despite extensive fossil records and common biogeographic histories, the evolution of these two key groups has rarely been considered together. We therefore examine recent advances in molecular phylogenetics and palaeoecology, and place the evolution of fishes and corals in a functional context. In critically reviewing the available fossil and phylogenetic evidence, we reveal a marked congruence in the evolution of the two groups. Despite one group consisting of swimming vertebrates and the other colonial symbiotic invertebrates, fishes and corals have remarkably similar evolutionary histories. In the Paleocene and Eocene [66-34 million years ago (Ma)] most modern fish and coral families were present, and both were represented by a wide range of functional morphotypes. However, there is little evidence of diversification at this time. By contrast, in the Oligocene and Miocene (34-5.3 Ma), both groups exhibited rapid lineage diversification. There is also evidence of increasing reef area, occupation of new habitats, increasing coral cover, and potentially, increasing fish abundance. Functionally, the Oligocene-Miocene is marked by the appearance of new fish and coral taxa associated with high-turnover fast-growth ecosystems and the colonization of reef flats. It is in this period that the functional characteristics of modern coral reefs were established. Most species, however, only arose in the last 5.3 million years (Myr; Plio-Pleistocene), with the average age of fish species being 5.3 Myr, and corals just 1.9 Myr. While these species are genetically distinct, phenotypic differences are often limited to variation in colour or minor morphological features. This suggests that the rapid increase in biodiversity during the last 5.3 Myr was not matched by changes in ecosystem function. For reef fishes, colour appears to be central to recent diversification. However, the presence of pigment patterns in the Eocene suggests that colour may not have driven recent diversification. Furthermore, the lack of functional changes in fishes or corals over the last 5 Myr raises questions over the role and importance of biodiversity in shaping the future of coral reefs.
Collapse
Affiliation(s)
- David R Bellwood
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Christopher H R Goatley
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Orpha Bellwood
- College of Marine and Environmental Sciences and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| |
Collapse
|
31
|
Herrera M, Saenz-Agudelo P, Nanninga GB, Berumen ML. Development of polymorphic microsatellite loci for conservation genetic studies of the coral reef fish Centropyge bicolor. JOURNAL OF FISH BIOLOGY 2015; 87:748-753. [PMID: 26272332 DOI: 10.1111/jfb.12694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/11/2015] [Indexed: 06/04/2023]
Abstract
A total of 23 novel polymorphic microsatellite marker loci were developed for the angelfish Centropyge bicolor through 454 sequencing, and further tested on two spatially separated populations (90 individuals each) from Kimbe Bay in Papua New Guinea. The mean ± s.e. number of alleles per locus was 14·65 ± 1·05, and mean ± s.e. observed (HO ) and expected (HE ) heterozygosity frequencies were 0·676 ± 0·021 and 0·749 ± 0·018, respectively. The markers reported here constitute the first specific set for this genus and will be useful for future conservation genetic studies in the Indo-Pacific region.
Collapse
Affiliation(s)
- M Herrera
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - P Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - G B Nanninga
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| |
Collapse
|
32
|
Gaither MR, Bernal MA, Fernandez-Silva I, Mwale M, Jones SA, Rocha C, Rocha LA. Two deep evolutionary lineages in the circumtropical glasseye Heteropriacanthus cruentatus (Teleostei, Priacanthidae) with admixture in the south-western Indian Ocean. JOURNAL OF FISH BIOLOGY 2015; 87:715-727. [PMID: 26333139 DOI: 10.1111/jfb.12754] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 06/19/2015] [Indexed: 06/05/2023]
Abstract
A phylogeographic study of the circumtropical glasseye Heteropriacanthus cruentatus was conducted. Molecular analyses indicate two mitochondrial cytochrome c oxidase subunit I (coI) lineages that are 10·4% divergent: one in the western Atlantic (Caribbean) and another that was detected across the Indo-Pacific. A fixed single nucleotide polymorphism (SNP) was detected at a nuclear locus (S7 ribosomal protein) and is consistent with this finding. There is evidence of recent dispersal from the Atlantic to the Indian Ocean with individuals of mixed lineages detected in South Africa and the Mozambique Channel. Using coalescent analyses of the mitochondrial dataset, time of divergence between lineages was estimated to be c. 15·3 million years. The deep divergence between these two lineages indicates distinct evolutionary units, however, due to the lack of morphological differences and evidence of hybridization between lineages, taxonomic revision is not suggested at this time.
Collapse
Affiliation(s)
- M R Gaither
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, U.K
| | - M A Bernal
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- University of Texas Marine Science Institute, 750 Channel View Drive, Port Aransas, TX, 78373, U.S.A
| | - I Fernandez-Silva
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, 903-0213, Japan
| | - M Mwale
- South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown, 6140, South Africa
- National Zoological Gardens of South Africa, P. O. Box 754, Pretoria, 001, South Africa
| | - S A Jones
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| | - C Rocha
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| | - L A Rocha
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, U.S.A
| |
Collapse
|
33
|
Gaither MR, Bernal MA, Coleman RR, Bowen BW, Jones SA, Simison WB, Rocha LA. Genomic signatures of geographic isolation and natural selection in coral reef fishes. Mol Ecol 2015; 24:1543-57. [PMID: 25753379 DOI: 10.1111/mec.13129] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 01/17/2023]
Abstract
The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection.
Collapse
Affiliation(s)
- Michelle R Gaither
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK; Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Isolation and characterization of fifteen microsatellite loci in two-spined angelfish Centropyge bispinosa (family Pomacanthidae) with cross-amplification success in four Centropyge congeners. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0363-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
35
|
Tornabene L, Valdez S, Erdmann M, Pezold F. Support for a 'Center of Origin' in the Coral Triangle: cryptic diversity, recent speciation, and local endemism in a diverse lineage of reef fishes (Gobiidae: Eviota). Mol Phylogenet Evol 2014; 82 Pt A:200-10. [PMID: 25300452 DOI: 10.1016/j.ympev.2014.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/10/2014] [Accepted: 09/13/2014] [Indexed: 11/17/2022]
Abstract
The Coral Triangle is widely regarded as the richest marine biodiversity hot-spot in the world. One factor that has been proposed to explain elevated species-richness within the Coral Triangle is a high rate of in situ speciation within the region itself. Dwarfgobies (Gobiidae: Eviota) are a diverse genus of diminutive cryptobenthic reef fishes with limited dispersal ability, and life histories and ecologies that increase potential for speciation. We use molecular phylogenetic and biogeographic data from two clades of Eviota species to examine patterns, processes and timing associated with species origination within the Coral Triangle. Sequence data from mitochondrial and nuclear DNA were used to generate molecular phylogenies and median-joining haplotype networks for the genus Eviota, with emphasis on the E. nigriventris and E. bifasciata complexes - two species groups with distributions centered in the Coral Triangle. The E. nigriventris and E. bifasciata complexes both contain multiple genetically distinct, geographically restricted color morphs indicative of recently-diverged species originating within the Coral Triangle. Relaxed molecular-clock dating estimates indicate that most speciation events occurred within the Pleistocene, and the geographic pattern of genetic breaks between species corresponds well with similar breaks in other marine fishes and sessile invertebrates. Regional isolation due to sea-level fluctuations may explain some speciation events in these species groups, yet other species formed with no evidence of physical isolation. The timing of diversification events and present day distributions of Eviota species within the Coral Triangle suggest that both allopatric speciation (driven by ephemeral and/or 'soft' physical barriers to gene flow) and sympatric speciation (driven by niche partitioning and assortative mating) may be driving diversification at local scales within the Coral Triangle. The presence of multiple young, highly-endemic cryptic species of Eviota within the Coral Triangle suggests that (i) the Coral Triangle is indeed a "cradle" of reef fish biodiversity and that (ii) our current approximations of reef fish diversity in the region may be significantly underestimated.
Collapse
Affiliation(s)
- Luke Tornabene
- College of Science and Engineering, Texas A & M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.
| | - Samantha Valdez
- College of Science and Engineering, Texas A & M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Mark Erdmann
- Conservation International Indonesia Marine Program, Jl. Muwardi No. 17 Renon Denpasar, Bali 80235, Indonesia; California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA
| | - Frank Pezold
- College of Science and Engineering, Texas A & M University - Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| |
Collapse
|
36
|
Hubert N, Espiau B, Meyer C, Planes S. Identifying the ichthyoplankton of a coral reef using DNA barcodes. Mol Ecol Resour 2014; 15:57-67. [PMID: 24935524 DOI: 10.1111/1755-0998.12293] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/28/2014] [Accepted: 05/30/2014] [Indexed: 11/30/2022]
Abstract
Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.
Collapse
Affiliation(s)
- Nicolas Hubert
- Institut de Recherche pour le Développement (IRD), UMR226 ISE-M, Bât. 22 - CC065, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | | | | | | |
Collapse
|