51
|
Wepfer PH, Nakajima Y, Sutthacheep M, Radice VZ, Richards Z, Ang P, Terraneo T, Sudek M, Fujimura A, Toonen RJ, Mikheyev AS, Economo EP, Mitarai S. Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Mol Phylogenet Evol 2020; 151:106905. [DOI: 10.1016/j.ympev.2020.106905] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 11/16/2022]
|
52
|
El-Hossary EM, Abdel-Halim M, Ibrahim ES, Pimentel-Elardo SM, Nodwell JR, Handoussa H, Abdelwahab MF, Holzgrabe U, Abdelmohsen UR. Natural Products Repertoire of the Red Sea. Mar Drugs 2020; 18:md18090457. [PMID: 32899763 PMCID: PMC7551641 DOI: 10.3390/md18090457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.
Collapse
Affiliation(s)
- Ebaa M. El-Hossary
- National Centre for Radiation Research & Technology, Egyptian Atomic Energy Authority, Ahmed El-Zomor St. 3, El-Zohoor Dist., Nasr City, Cairo 11765, Egypt;
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Eslam S. Ibrahim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany
| | - Sheila Marie Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS Centre West, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (S.M.P.-E.); (J.R.N.)
| | - Justin R. Nodwell
- Department of Biochemistry, University of Toronto, MaRS Centre West, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (S.M.P.-E.); (J.R.N.)
| | - Heba Handoussa
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Miada F. Abdelwahab
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
| | - Ulrike Holzgrabe
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Correspondence: (U.H.); (U.R.A.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, P.O. Box 61111 New Minia City, Minia 61519, Egypt
- Correspondence: (U.H.); (U.R.A.)
| |
Collapse
|
53
|
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
|
54
|
Sales MAN, Freitas JEPD, Cavalcante CC, Santander-Neto J, Charvet P, Faria VV. The southernmost record and an update of the geographical range of the Atlantic chupare, Styracura schmardae (Chondrichthyes: Myliobatiformes). JOURNAL OF FISH BIOLOGY 2020; 97:302-308. [PMID: 32347542 DOI: 10.1111/jfb.14361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
The present study established the southernmost distribution range for the Chupare stingray Styracura schmardae based on a specimen caught on the easternmost portion of Ceará State, northeastern Brazil. Identification was based on diagnostic morphological characters and molecular data (sequence of the mitochondrial DNA gene nd2; 1046 bp). This record expands the known distribution range for this species by more than 1200 km and confirms that S. schmardae is distributed in more than one biogeographical province. SIGNIFICANCE STATEMENT: There are few records of the Atlantic Chupare stingray for Brazil and most of them are associated with the Amazon River mouth. New records indicate that this species is also present in the South Atlantic portion of the Brazilian coast. Apparently having a low abundance throughout its range, these new records increase the range of occurrence of this species.
Collapse
Affiliation(s)
- Manuela Alves Nobre Sales
- Marine Vertebrate Evolution and Conservation Lab - EvolVe, Departamento de Biologia, Centro de Ciências, Programa de Pós-graduação em Sistemática, Uso e Conservação da Biodiversidade, Universidade Federal do Ceará, Fortaleza, Brazil
- Instituto de Ciências do Mar - Labomar, Programa de Pós-graduação em Ciências Marinhas Tropicais, Universidade Federal do Ceará, Fortaleza, Brazil
| | - João Eduardo Pereira de Freitas
- Marine Vertebrate Evolution and Conservation Lab - EvolVe, Departamento de Biologia, Centro de Ciências, Programa de Pós-graduação em Sistemática, Uso e Conservação da Biodiversidade, Universidade Federal do Ceará, Fortaleza, Brazil
- Instituto de Ciências do Mar - Labomar, Programa de Pós-graduação em Ciências Marinhas Tropicais, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Carlos Costa Cavalcante
- Instituto Federal de Educação, Ciência e Tecnologia do Maranhão, Campus São Luis - Maracanã, São Luís, Brazil
| | - Jones Santander-Neto
- Instituto Federal de Educação, Ciência e Tecnologia do Espírito Santo, Campus Piúma, Piúma, Brazil
| | - Patricia Charvet
- Marine Vertebrate Evolution and Conservation Lab - EvolVe, Departamento de Biologia, Centro de Ciências, Programa de Pós-graduação em Sistemática, Uso e Conservação da Biodiversidade, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Vicente Vieira Faria
- Marine Vertebrate Evolution and Conservation Lab - EvolVe, Departamento de Biologia, Centro de Ciências, Programa de Pós-graduação em Sistemática, Uso e Conservação da Biodiversidade, Universidade Federal do Ceará, Fortaleza, Brazil
- Instituto de Ciências do Mar - Labomar, Programa de Pós-graduação em Ciências Marinhas Tropicais, Universidade Federal do Ceará, Fortaleza, Brazil
| |
Collapse
|
55
|
DiBattista JD, Saenz‐Agudelo P, Piatek MJ, Cagua EF, Bowen BW, Choat JH, Rocha LA, Gaither MR, Hobbs JA, Sinclair‐Taylor TH, McIlwain JH, Priest MA, Braun CD, Hussey NE, Kessel ST, Berumen ML. Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula. Ecol Evol 2020; 10:4314-4330. [PMID: 32489599 PMCID: PMC7246217 DOI: 10.1002/ece3.6199] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and primary productivity that vary both by latitude and by season. The adjacent Arabian Sea is characterized by a sharper environmental gradient, ranging from extensive coral cover and warm temperatures in the southwest, to sparse coral cover, cooler temperatures, and seasonal upwelling in the northeast. Reef fish, however, are not confined to these seas, with some Red Sea fishes extending varying distances into the northern Arabian Sea, while their pelagic larvae are presumably capable of much greater dispersal. These species must therefore cope with a diversity of conditions that invoke the possibility of steep clines in natural selection. Here, we test for genetic structure in two widespread reef fish species (a butterflyfish and surgeonfish) and eight range-restricted butterflyfishes across the Red Sea and Arabian Sea using genome-wide single nucleotide polymorphisms. We performed multiple matrix regression with randomization analyses on genetic distances for all species, as well as reconstructed scenarios for population subdivision in the species with signatures of isolation. We found that (a) widespread species displayed more genetic subdivision than regional endemics and (b) this genetic structure was not correlated with contemporary environmental parameters but instead may reflect historical events. We propose that the endemic species may be adapted to a diversity of local conditions, but the widespread species are instead subject to ecological filtering where different combinations of genotypes persist under divergent ecological regimes.
Collapse
Affiliation(s)
- Joseph D. DiBattista
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Pablo Saenz‐Agudelo
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Instituto de Ciencias Ambientales y EvolutivasUniversidad Austral de ChileValdiviaChile
| | - Marek J. Piatek
- Computational Bioscience Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Edgar Fernando Cagua
- Centre for Integrative EcologySchool of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | | | - John Howard Choat
- School of Marine and Tropical BiologyJames Cook UniversityTownsvilleQldAustralia
| | - Luiz A. Rocha
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Michelle R. Gaither
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCAUSA
- Genomics and Bioinformatics ClusterDepartment of BiologyUniversity of Central FloridaOrlandoFLUSA
| | - Jean‐Paul A. Hobbs
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Tane H. Sinclair‐Taylor
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | | | - Mark A. Priest
- Marine Spatial Ecology LabSchool of Biological Sciences and ARC Centre of Excellence for Coral Reef StudiesUniversity of QueenslandSt. LuciaQldAustralia
| | - Camrin D. Braun
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Steven T. Kessel
- Daniel P. Haerther Center for Conservation and ResearchJohn G. Shedd AquariumChicagoILUSA
| | - Michael L. Berumen
- Division of Biological and Environmental Science and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| |
Collapse
|
56
|
Oliveira Carvalho C, Pires Marceniuk A, Oliveira C, Wosiacki WB. Integrative taxonomy of the species complex Haemulon steindachneri () (Eupercaria; Haemulidae) with a description of a new species from the western Atlantic. ZOOLOGY 2020; 141:125782. [PMID: 32502832 DOI: 10.1016/j.zool.2020.125782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 12/01/2022]
Abstract
Haemulon steindachneri (Jordan and Gilbert) (Haemulidae), popularly known as "cocoroca-de-boca-larga", "latin-grunt" or "latin-burro", represents a species complex found on the Atlantic western coast and on the Pacific eastern coast, condition confirmed recently by molecular phylogenies. In the present study, DNA barcoding analysis recognizes two distinct clusters; the first includes Brazil and Caribbean, and the second is composed of Pacific specimens, with genetic distance of 7.4%, differentiated by 35 base pairs. In addition to the molecular evidence, our results show morphological differences that distinguish the Atlantic lineage from that of the Pacific: anal fin, usually, with eight rays (vs. generally nine rays in Pacific); 13-15 scales below the lateral line, rarely 12 (vs. 12 scales below the lateral line, rarely 13 in Pacific), posterior margin of the maxilla robust with a slightly angled end (vs. smaller maxilla with moderately convex extremity), and presence of a spot on the pre-operculum, broad and robust, with no definite shape (vs. narrow spot, with anterior extremity tuned and posterior straight, resembling a triangle in Pacific). Therefore, based on both molecular and morphological evidences, H. steindachneri is redescribed for the Pacific coast while a new species is described for the Atlantic coast.
Collapse
Affiliation(s)
- Cintia Oliveira Carvalho
- Museu Paraense Emílio Goeldi, 66040-170, Belém, PA, Brazil; Programa de Pós-Graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, 66040-170, Belém, PA, Brazil.
| | | | - Claudio Oliveira
- Universidade Estadual Paulista - Campus Botucatu, 18618-689, Botucatu, SP, Brazil.
| | | |
Collapse
|
57
|
Yip ZT, Quek RZB, Huang D. Historical biogeography of the widespread macroalga Sargassum (Fucales, Phaeophyceae). JOURNAL OF PHYCOLOGY 2020; 56:300-309. [PMID: 31677168 PMCID: PMC7187439 DOI: 10.1111/jpy.12945] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 10/16/2019] [Indexed: 05/13/2023]
Abstract
Sargassum is a cosmopolitan brown algal genus spanning the three ocean basins of the Atlantic, Pacific and Indian Oceans, inhabiting temperate, subtropical and tropical habitats. Sargassum has been postulated to have originated in the Oligocene epoch approximately 30 mya according to a broad phylogenetic analysis of brown macroalgae, but its diversification to become one of the most widespread and speciose macroalgal genera remains unclear. Here, we present a Bayesian molecular clock study, which analyzed data from the order Fucales of the brown algal crown radiation (BACR) group to reconstruct a time-calibrated phylogeny of the Sargassum clade. Our phylogeny included a total of 120 taxa with 99 Sargassum species sampled for three molecular markers - ITS-2, cox3 and rbcLS - calibrated with an unambiguous Sargassaceae fossil from between the lower and middle Miocene. The analysis revealed a much later origin of Sargassum than expected at about 6.7 mya, with the genus diversifying since approximately 4.3 mya. Current geographic distributions of Sargassum species were then analyzed in conjunction with the time-calibrated phylogeny using the dispersal-extinction-cladogenesis (DEC) model to estimate ancestral ranges of clades in the genus. Results strongly support origination of Sargassum in the Central Indo-Pacific (CIP) region with subsequent independent dispersal events into other marine realms. The longer history of diversification in the ancestral CIP range could explain the much greater diversity there relative to other marine areas today. Analyses of these dynamic processes, when fine-tuned to a higher spatial resolution, enable the identification of evolutionary hotspots and provide insights into long-term dispersal patterns.
Collapse
Affiliation(s)
- Zhi Ting Yip
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
| | - Randolph Z. B. Quek
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore City117558Singapore
- Tropical Marine Science InstituteNational University of SingaporeSingapore City119227Singapore
| |
Collapse
|
58
|
Hopkinson BM, King AC, Owen DP, Johnson-Roberson M, Long MH, Bhandarkar SM. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One 2020; 15:e0230671. [PMID: 32208447 PMCID: PMC7093084 DOI: 10.1371/journal.pone.0230671] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/05/2020] [Indexed: 11/18/2022] Open
Abstract
Coral reefs are biologically diverse and structurally complex ecosystems, which
have been severally affected by human actions. Consequently, there is a need for
rapid ecological assessment of coral reefs, but current approaches require time
consuming manual analysis, either during a dive survey or on images collected
during a survey. Reef structural complexity is essential for ecological function
but is challenging to measure and often relegated to simple metrics such as
rugosity. Recent advances in computer vision and machine learning offer the
potential to alleviate some of these limitations. We developed an approach to
automatically classify 3D reconstructions of reef sections and assessed the
accuracy of this approach. 3D reconstructions of reef sections were generated
using commercial Structure-from-Motion software with images extracted from video
surveys. To generate a 3D classified map, locations on the 3D reconstruction
were mapped back into the original images to extract multiple views of the
location. Several approaches were tested to merge information from multiple
views of a point into a single classification, all of which used convolutional
neural networks to classify or extract features from the images, but differ in
the strategy employed for merging information. Approaches to merging information
entailed voting, probability averaging, and a learned neural-network layer. All
approaches performed similarly achieving overall classification accuracies of
~96% and >90% accuracy on most classes. With this high classification
accuracy, these approaches are suitable for many ecological applications.
Collapse
Affiliation(s)
- Brian M. Hopkinson
- Department of Marine Sciences, University of Georgia, Athens, Georgia,
United States of America
- * E-mail:
| | - Andrew C. King
- Institute for Artificial Intelligence, University of Georgia, Athens,
Georgia, United States of America
| | - Daniel P. Owen
- Department of Marine Sciences, University of Georgia, Athens, Georgia,
United States of America
| | - Matthew Johnson-Roberson
- Department of Naval Architecture and Marine Engineering, University of
Michigan, Ann Arbor, Michigan, United States of America
| | - Matthew H. Long
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic
Institution, Woods Hole, Massachusetts, United States of
America
| | - Suchendra M. Bhandarkar
- Institute for Artificial Intelligence, University of Georgia, Athens,
Georgia, United States of America
- Department of Computer Science, University of Georgia, Athens, Georgia,
United States of America
| |
Collapse
|
59
|
Rodríguez‐Flores PC, Buckley D, Macpherson E, Corbari L, Machordom A. Deep‐sea squat lobster biogeography (Munidopsidae:
Leiogalathea
) unveils Tethyan vicariance and evolutionary patterns shared by shallow‐water relatives. ZOOL SCR 2020. [DOI: 10.1111/zsc.12414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paula C. Rodríguez‐Flores
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
- Centre d'Estudis Avançats de Blanes (CEAB‐CSIC) Blanes Spain
| | - David Buckley
- Departamento de Biología (Genética) Facultad de Biología Universidad Autónoma de Madrid Madrid Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM) Facultad de Biología Universidad Autónoma de Madrid Madrid Spain
| | | | - Laure Corbari
- Institut de Systématique Évolution Biodiversité (ISYEB, UMR 7205) Muséum national d'Histoire naturelle CNRS Sorbonne UniversitéEPHE Paris France
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
| |
Collapse
|
60
|
Tisthammer KH, Forsman ZH, Toonen RJ, Richmond RH. Genetic structure is stronger across human-impacted habitats than among islands in the coral Porites lobata. PeerJ 2020; 8:e8550. [PMID: 32110487 PMCID: PMC7034377 DOI: 10.7717/peerj.8550] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/12/2020] [Indexed: 11/26/2022] Open
Abstract
We examined genetic structure in the lobe coral Porites lobata among pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oahu and Maui, Hawaii. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVA F ST = 0.04∼0.19, P < 0.001), but no significant isolation by distance between islands. Strikingly, corals from the two nearshore sites with higher levels of environmental stressors on different islands over 100 km apart with similar environmentally stressful conditions were genetically closer (FST = 0.0, P = 0.73) than those within a single location less than 2 km apart (FST = 0.04∼0.08, P < 0.01). In contrast, a third site with a less impacted nearshore site (i.e., less pronounced environmental gradient) showed no significant structure from the offshore comparison. Our results show much stronger support for environment than distance separating these populations. Our finding suggests that ecological boundaries from human impacts may play a role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow might be explained by selective pressure across contrasting habitats.
Collapse
Affiliation(s)
- Kaho H. Tisthammer
- Kewalo Marine Laboratory, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Zac H. Forsman
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, United States of America
| | - Robert J. Toonen
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, United States of America
| | - Robert H. Richmond
- Kewalo Marine Laboratory, University of Hawaii at Manoa, Honolulu, HI, United States of America
| |
Collapse
|
61
|
Simmonds SE, Fritts‐Penniman AL, Cheng SH, Mahardika GN, Barber PH. Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836). Ecol Evol 2020; 10:1817-1837. [PMID: 32128119 PMCID: PMC7042750 DOI: 10.1002/ece3.5977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022] Open
Abstract
The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails' adaptation to their coral hosts. Genome-wide single nucleotide polymorphism (SNP) data from type II restriction site-associated DNA (2b-RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host-associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.
Collapse
Affiliation(s)
- Sara E. Simmonds
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| | | | - Samantha H. Cheng
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
- Center for Biodiversity and ConservationAmerican Museum of Natural HistoryNew YorkNYUSA
| | - Gusti Ngurah Mahardika
- Animal Biomedical and Molecular Biology LaboratoryFaculty of Veterinary MedicineUdayana University BaliDenpasarIndonesia
| | - Paul H. Barber
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCAUSA
| |
Collapse
|
62
|
Garcia E, Simison WB, Bernardi G. Patterns of Genomic Divergence and Signals of Selection in Sympatric and Allopatric Northeastern Pacific and Sea of Cortez Populations of the Sargo (Anisotremus davidsonii) and Longjaw Mudsucker (Gillichthys mirabilis). J Hered 2020; 111:57-69. [DOI: 10.1093/jhered/esz071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 11/14/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractStudying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.
Collapse
Affiliation(s)
- Eric Garcia
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
- Department of Biological Sciences, Old Dominion University, Norfolk, VA
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, CA
| | - Giacomo Bernardi
- Ecology and Evolutionary Biology Department, Long Marine Laboratory, University of California Santa Cruz, Santa Cruz, CA
| |
Collapse
|
63
|
Cryptic ecological and geographic diversification in coral-associated nudibranchs. Mol Phylogenet Evol 2019; 144:106698. [PMID: 31812568 DOI: 10.1016/j.ympev.2019.106698] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/03/2019] [Accepted: 11/30/2019] [Indexed: 12/18/2022]
Abstract
Coral reefs are among the most biologically diverse ecosystems of the world, yet little is known about the processes creating and maintaining their diversity. Ecologically, corallivory in nudibranchs resembles phytophagy in insects- a process that for decades has served as a model for ecological speciation via host shifting. This study uses extensive field collections, DNA sequencing, and phylogenetic analyses to reconstruct the evolutionary history of coral-associated nudibranchs and assess the relative roles that host shifting and geography may have played in their diversification. We find that the number of species is three times higher than the number previously known to science, with evidence for both allopatric and ecological divergence through host shifting and host specialization. Results contribute to growing support for the importance of ecological diversification in marine environments and provide evidence for new species in the genus Tenellia.
Collapse
|
64
|
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]
|
65
|
Wainwright BJ, Zahn GL, Zushi J, Lee NLY, Ooi JLS, Lee JN, Huang D. Seagrass-associated fungal communities show distance decay of similarity that has implications for seagrass management and restoration. Ecol Evol 2019; 9:11288-11297. [PMID: 31641473 PMCID: PMC6802368 DOI: 10.1002/ece3.5631] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 01/18/2023] Open
Abstract
Marine fungal biodiversity remains vastly understudied, and even less is known of their biogeography and the processes responsible for driving these distributions in marine environments. We investigated the fungal communities associated with the seagrass Enhalus acoroides collected from Singapore and Peninsular Malaysia to test the hypothesis that fungal communities are homogeneous throughout the study area. Seagrass samples were separated into different structures (leaves, roots, and rhizomes), and a sediment sample was collected next to each plant. Amplicon sequencing of the fungal internal transcribed spacer 1 and subsequent analysis revealed significant differences in fungal communities collected from different locations and different structures. We show a significant pattern of distance decay, with samples collected close to each other having more similar fungal communities in comparison with those that are more distant, indicating dispersal limitations and/or differences in habitat type are contributing to the observed biogeographic patterns. These results add to our understanding of the seagrass ecosystem in an understudied region of the world that is also the global epicenter of seagrass diversity. This work has implications for seagrass management and conservation initiatives, and we recommend that fungal community composition be a consideration for any seagrass transplant or restoration programme.
Collapse
Affiliation(s)
- Benjamin J. Wainwright
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | | | - Joshua Zushi
- Biology DepartmentUtah Valley UniversityOremUTUSA
| | - Nicole Li Ying Lee
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
| | - Jillian Lean Sim Ooi
- Department of GeographyFaculty of Arts and Social SciencesUniversity of MalayaKuala LumpurMalaysia
| | - Jen Nie Lee
- Faculty of Science and Marine EnvironmentUniversity Malaysia TerengganuTerengganuMalaysia
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingapore CitySingapore
- Tropical Marine Science InstituteNational University of SingaporeSingapore CitySingapore
| |
Collapse
|
66
|
Torquato F, Range P, Ben‐Hamadou R, Sigsgaard EE, Thomsen PF, Riera R, Berumen ML, Burt JA, Feary DA, Marshell A, D'Agostino D, DiBattista JD, Møller PR. Consequences of marine barriers for genetic diversity of the coral-specialist yellowbar angelfish from the Northwestern Indian Ocean. Ecol Evol 2019; 9:11215-11226. [PMID: 31641466 PMCID: PMC6802022 DOI: 10.1002/ece3.5622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Ocean circulation, geological history, geographic distance, and seascape heterogeneity play an important role in phylogeography of coral-dependent fishes. Here, we investigate potential genetic population structure within the yellowbar angelfish (Pomacanthus maculosus) across the Northwestern Indian Ocean (NIO). We then discuss our results with respect to the above abiotic features in order to understand the contemporary distribution of genetic diversity of the species. To do so, restriction site-associated DNA sequencing (RAD-seq) was utilized to carry out population genetic analyses on P. maculosus sampled throughout the species' distributional range. First, genetic data were correlated to geographic and environmental distances, and tested for isolation-by-distance and isolation-by-environment, respectively, by applying the Mantel test. Secondly, we used distance-based and model-based methods for clustering genetic data. Our results suggest the presence of two putative barriers to dispersal; one off the southern coast of the Arabian Peninsula and the other off northern Somalia, which together create three genetic subdivisions of P. maculosus within the NIO. Around the Arabian Peninsula, one genetic cluster was associated with the Red Sea and the adjacent Gulf of Aden in the west, and another cluster was associated with the Arabian Gulf and the Sea of Oman in the east. Individuals sampled in Kenya represented a third genetic cluster. The geographic locations of genetic discontinuities observed between genetic subdivisions coincide with the presence of substantial upwelling systems, as well as habitat discontinuity. Our findings shed light on the origin and maintenance of genetic patterns in a common coral reef fish inhabiting the NIO, and reinforce the hypothesis that the evolution of marine fish species in this region has likely been shaped by multiple vicariance events.
Collapse
Affiliation(s)
- Felipe Torquato
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Pedro Range
- Environmental Science CenterQatar UniversityDohaQatar
| | - Radhouane Ben‐Hamadou
- Department Biological and Environmental ScienceCollege of Arts and SciencesQatar UniversityDohaQatar
| | - Eva E. Sigsgaard
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Department of BioscienceUniversity of AarhusAarhusDenmark
| | | | - Rodrigo Riera
- Departamento de EcologíaFacultad de CienciasUniversidad Católica de la Santísima ConcepciónConcepciónChile
| | - Michael L. Berumen
- Division of Biological and Environmental Sciences and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - John A. Burt
- Center for Genomics and Systems BiologyNew York University Abu DhabiAbu DhabiUAE
| | | | - Alyssa Marshell
- Marine Ecology Lab OmanDepartment of Marine Science and FisheriesCollege of Agriculture and Marine ScienceSultan Qaboos UniversityMuscatOman
| | | | - Joseph D. DiBattista
- Division of Biological and Environmental Sciences and EngineeringRed Sea Research CenterKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- School of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
- Australian Museum Research InstituteAustralian MuseumSydneyNSWAustralia
| | - Peter R. Møller
- Section for Evolutionary GenomicsNatural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
67
|
Phuong MA, Alfaro ME, Mahardika GN, Marwoto RM, Prabowo RE, von Rintelen T, Vogt PWH, Hendricks JR, Puillandre N. Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails. Syst Biol 2019; 68:781-796. [PMID: 30816949 PMCID: PMC6934442 DOI: 10.1093/sysbio/syz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022] Open
Abstract
Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.
Collapse
Affiliation(s)
- Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Gusti N Mahardika
- Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University Bali, Jl Sesetan-Markisa 6, Denpasar, Bali 80225, Indonesia
| | - Ristiyanti M Marwoto
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, LIPI, Km.46, Jl. Raya Bogor, Cibinong, Bogor, West Java 16911, Indonesia
| | - Romanus Edy Prabowo
- Aquatic Biology Laboratory, Faculty of Biology, Universitas Jenderal Soedirman, Jalan dr. Suparno 63 Grendeng, Purwokerto, Indonesia, 53122
| | - Thomas von Rintelen
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Philipp W H Vogt
- Museum für Naturkunde—Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | | | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, 1259 Trumansburg Road, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| |
Collapse
|
68
|
Titus BM, Blischak PD, Daly M. Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria). Mol Ecol 2019; 28:3572-3586. [PMID: 31233641 DOI: 10.1111/mec.15157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 05/21/2019] [Accepted: 06/04/2019] [Indexed: 12/23/2022]
Abstract
Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
Collapse
Affiliation(s)
- Benjamin M Titus
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Paul D Blischak
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
69
|
Kerkhove TRH, Boyen J, De Backer A, Mol JH, Volckaert FAM, Leliaert F, De Troch M. Multilocus data reveal cryptic species in the Atlantic seabob shrimp Xiphopenaeus kroyeri (Crustacea: Decapoda). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz065] [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]
Abstract
AbstractThe recognition of cryptic biodiversity provides valuable insights for the management of exploited species. The Atlantic seabob shrimp (Xiphopenaeus kroyeri) is a commercially important fishery resource in the Guianan ecoregion, South America. Previous research in Brazil suggested the presence of cryptic species within the genus. Here, we confirm this presence and delimit the species by applying a multilocus approach based on two mitochondrial (COI and cytb) and two nuclear (PEPCK and NaK) genes. Species boundaries were tested using BPP, GMYC and bPTP delimitation algorithms. These analyses provided strong support for three clades within the genus Xiphopenaeus, including one undescribed clade, which occurs sympatrically with X. kroyeri in the Western Atlantic. Unexpectedly, this undescribed clade is more closely related to the Pacific Xiphopenaeus riveti than to their Atlantic congener. Our DNA-based species delimitation was further supported by new ecological information on habitat and morphology (colour). We also expand the known distribution range of the cryptic species, currently restricted to Brazil, to include French Guiana, Suriname and Colombia. Our findings have important consequences for the management of the species, in terms of both biodiversity management and fisheries management.
Collapse
Affiliation(s)
- Thomas R H Kerkhove
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Jens Boyen
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| | - Annelies De Backer
- Institute for Agricultural and Fisheries Research (ILVO), Animal Sciences, Bio-Environmental Research Group, Ankerstraat, Ostend, Belgium
| | - Jan H Mol
- Anton de Kom University of Suriname, Faculty of Mathematics and Natural Sciences, Department of Biology, Leysweg, Postbus, Paramaribo, Suriname
| | - Filip A M Volckaert
- University of Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Ch. Deberiotstraat, Leuven, Belgium
| | - Frederik Leliaert
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
- Meise Botanic Garden, Nieuwelaan, Meise, Belgium
| | - Marleen De Troch
- Ghent University, Department of Biology, Marine Biology Research Group, Campus Sterre S8, Krijgslaan, Ghent, Belgium
| |
Collapse
|
70
|
Parton KJ, Galloway TS, Godley BJ. Global review of shark and ray entanglement in anthropogenic marine debris. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00964] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
71
|
Miguel-Gordo M, Gegunde S, Calabro K, Jennings LK, Alfonso A, Genta-Jouve G, Vacelet J, Botana LM, Thomas OP. Bromotryptamine and Bromotyramine Derivatives from the Tropical Southwestern Pacific Sponge Narrabeena nigra. Mar Drugs 2019; 17:E319. [PMID: 31151240 PMCID: PMC6627171 DOI: 10.3390/md17060319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
So far, the Futuna Islands located in the Central Indo-Pacific Ocean have not been inventoried for their diversity in marine sponges and associated chemical diversity. As part of the Tara Pacific expedition, the first chemical investigation of the sponge Narrabeena nigra collected around the Futuna Islands yielded 18 brominated alkaloids: seven new bromotryptamine derivatives 1-7 and one new bromotyramine derivative 8 together with 10 known metabolites of both families 9-18. Their structures were deduced from extensive analyses of nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS) data. In silico metabolite anticipation using the online tool MetWork revealed the presence of a key and minor biosynthetic intermediates. These 18 compounds showed almost no cytotoxic effect up to 10 µM on human neuroblastoma SH-SY5Y and microglia BV2 cells, and some of them exhibited an interesting neuroprotective activity by reducing oxidative damage.
Collapse
Affiliation(s)
- Maria Miguel-Gordo
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland.
| | - Sandra Gegunde
- Departamento de Farmacología, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
| | - Kevin Calabro
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland.
| | - Laurence K Jennings
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland.
| | - Amparo Alfonso
- Departamento de Farmacología, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
| | - Grégory Genta-Jouve
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire (C-TAC) UMR CNRS 8038 CiTCoM Université Paris-Descartes, 4, avenue de l'Observatoire, 75006 Paris, France.
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Universités, CNRS, 75005 Paris, France.
| | - Jean Vacelet
- Aix Marseille Université, CNRS, IRD, IMBE UMR 7263, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station Marine d'Endoume, Chemin de la Batterie des Lions, 13007 Marseille, France.
| | - Luis M Botana
- Departamento de Farmacología, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain.
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland.
| |
Collapse
|
72
|
Gabriela Arango B, T Pinheiro H, Rocha C, D Greene B, L Pyle R, M Copus J, Shepherd B, A Rocha L. Three new species of Chromis (Teleostei, Pomacentridae) from mesophotic coral ecosystems of the Philippines. Zookeys 2019; 835:1-15. [PMID: 31043847 PMCID: PMC6477865 DOI: 10.3897/zookeys.835.27528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 02/24/2019] [Indexed: 11/12/2022] Open
Abstract
Three new species of Chromis (Perciformes, Pomacentridae) from the Philippines, collected between 75–150 m depth, are described by a combination of morphological features and their coloration. Chromisguntingsp. n. was found in Batangas and Oriental Mindoro, and differs from its congeners in body depth (2.1–2.2 in SL), and color of adults, light brown, with a silver area on the anterior end and a bilateral black margin along the exterior side of the tail. It is most similar to C.scotochiloptera, with a 5.3% genetic divergence in COI. Chromishangganansp. n. was found around Lubang Island. Body depth (1.9–2.0 in SL) and adult coloration (yellowish with dark black outer margins on dorsal and anal fins) also separate this species from its congeners. It is most similar to C.pembae, with a 2.5% genetic divergence. Chromisbowesisp. n. was found in Batangas, and also differs from its congeners by the combination of body depth (1.5–1.6 in SL), and color of adults (brownish grey in the dorsal side to whitish on the ventral side, with alternating dark and light stripes in the sides of body). It is most similar to C.earina, with a 3.6% genetic divergence in COI.
Collapse
Affiliation(s)
- B Gabriela Arango
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| | - Hudson T Pinheiro
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| | - Claudia Rocha
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| | - Brian D Greene
- Bernice P. Bishop Museum, Honolulu, HI 96817, USA Bernice P. Bishop Museum Honolulu United States of America
| | - Richard L Pyle
- Bernice P. Bishop Museum, Honolulu, HI 96817, USA Bernice P. Bishop Museum Honolulu United States of America
| | - Joshua M Copus
- Department of Biology, University of Hawai'i at Mānoa, Hawai'i Institute of Marine Biology, Kãne'ohe, HI 96744, USA University of Hawai'i at Mānoa Kãne'ohe United States of America
| | - Bart Shepherd
- Steinhart Aquarium, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Steinhart Aquarium, California Academy of Sciences San Francisco United States of America
| | - Luiz A Rocha
- Department of Ichthyology, California Academy of Sciences, 55 Music Concourse Dr., San Francisco, CA 94118, USA Department of Ichthyology, California Academy of Sciences San Francisco United States of America
| |
Collapse
|
73
|
Moody KN, Wren JLK, Kobayashi DR, Blum MJ, Ptacek MB, Blob RW, Toonen RJ, Schoenfuss HL, Childress MJ. Evidence of local adaptation in a waterfall-climbing Hawaiian goby fish derived from coupled biophysical modeling of larval dispersal and post-settlement selection. BMC Evol Biol 2019; 19:88. [PMID: 30975077 PMCID: PMC6458715 DOI: 10.1186/s12862-019-1413-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background Local adaptation of marine and diadromous species is thought to be a product of larval dispersal, settlement mortality, and differential reproductive success, particularly in heterogeneous post-settlement habitats. We evaluated this premise with an oceanographic passive larval dispersal model coupled with individual-based models of post-settlement selection and reproduction to infer conditions that underlie local adaptation in Sicyopterus stimpsoni, an amphidromous Hawaiian goby known for its ability to climb waterfalls. Results Our model results demonstrated that larval dispersal is spatio-temporally asymmetric, with more larvae dispersed from the southeast (the Big Island) to northwest (Kaua‘i) along the archipelago, reflecting prevailing conditions such as El Niño/La Niña oscillations. Yet connectivity is nonetheless sufficient to result in homogenous populations across the archipelago. We also found, however, that ontogenetic shifts in habitat can give rise to adaptive morphological divergence when the strength of predation-driven post-settlement selection crosses a critical threshold. Notably, our simulations showed that larval dispersal is not the only factor determining the likelihood of morphological divergence. We found adaptive potential and evolutionary trajectories of S. stimpsoni were greater on islands with stronger environmental gradients and greater variance in larval cohort morphology due to fluctuating immigration. Conclusions Contrary to expectation, these findings indicate that immigration can act in concert with selection to favor local adaptation and divergence in species with marine larval dispersal. Further development of model simulations, parameterized to reflect additional empirical estimates of abiotic and biotic factors, will help advance our understanding of the proximate and ultimate mechanisms driving adaptive evolution, population resilience, and speciation in marine-associated species. Electronic supplementary material The online version of this article (10.1186/s12862-019-1413-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kristine N Moody
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN, 37996, USA. .,The ByWater Institute, Tulane University, New Orleans, LA, 70118, USA. .,Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA.
| | - Johanna L K Wren
- Department of Oceanography, School of Ocean and Earth Science and Technology (SOEST), University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Joint Institute of Marine and Atmospheric Research, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.,Pacific Islands Fisheries Science Center, NOAA/NMFS, NOAA IRC, Honolulu, HI, 96818, USA
| | - Donald R Kobayashi
- Pacific Islands Fisheries Science Center, NOAA/NMFS, NOAA IRC, Honolulu, HI, 96818, USA
| | - Michael J Blum
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN, 37996, USA.,The ByWater Institute, Tulane University, New Orleans, LA, 70118, USA
| | - Margaret B Ptacek
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Richard W Blob
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Heiko L Schoenfuss
- Aquatic Toxicology Laboratory, St. Cloud State University, St Cloud, MN, 56301, USA
| | - Michael J Childress
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| |
Collapse
|
74
|
Luque J, Feldmann RM, Vernygora O, Schweitzer CE, Cameron CB, Kerr KA, Vega FJ, Duque A, Strange M, Palmer AR, Jaramillo C. Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony. SCIENCE ADVANCES 2019; 5:eaav3875. [PMID: 31032408 PMCID: PMC6482010 DOI: 10.1126/sciadv.aav3875] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
Evolutionary origins of novel forms are often obscure because early and transitional fossils tend to be rare, poorly preserved, or lack proper phylogenetic contexts. We describe a new, exceptionally preserved enigmatic crab from the mid-Cretaceous of Colombia and the United States, whose completeness illuminates the early disparity of the group and the origins of novel forms. Its large and unprotected compound eyes, small fusiform body, and leg-like mouthparts suggest larval trait retention into adulthood via heterochronic development (pedomorphosis), while its large oar-like legs represent the earliest known adaptations in crabs for active swimming. Our phylogenetic analyses, including representatives of all major lineages of fossil and extant crabs, challenge conventional views of their evolution by revealing multiple convergent losses of a typical "crab-like" body plan since the Early Cretaceous. These parallel morphological transformations may be associated with repeated invasions of novel environments, including the pelagic/necto-benthic zone in this pedomorphic chimera crab.
Collapse
Affiliation(s)
- J. Luque
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Smithsonian Tropical Research Institute, Balboa-Ancón 0843-03092, Panamá, Panamá
- Department of Geology and Geophysics, Yale University, New Haven, CT 06520-8109, USA
| | - R. M. Feldmann
- Department of Geology, Kent State University, Kent, OH 44242, USA
| | - O. Vernygora
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - C. E. Schweitzer
- Department of Geology, Kent State University at Stark, 6000 Frank Ave. NW, North Canton, OH 44720, USA
| | - C. B. Cameron
- Département de Sciences Biologiques Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - K. A. Kerr
- Smithsonian Tropical Research Institute, Balboa-Ancón 0843-03092, Panamá, Panamá
- Canadian Parks and Wilderness Society (CPAWS) Northern Alberta, P.O. Box 52031, Edmonton, AB T6G 2T5, Canada
| | - F. J. Vega
- Instituto de Geología, Universidad Autónoma de México, Ciudad Universitaria, México, CDMX 04510, México
| | - A. Duque
- Computer Animation and Visual Effects, College of Communication and Design, Lynn University, 2601 North Military Trail, Boca Raton, FL 33431, USA
| | - M. Strange
- Department of Geoscience, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4010, USA
| | - A. R. Palmer
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - C. Jaramillo
- Smithsonian Tropical Research Institute, Balboa-Ancón 0843-03092, Panamá, Panamá
| |
Collapse
|
75
|
Santos MEA, Wirtz P, Montenegro J, Kise H, López C, Brown J, Reimer JD. Diversity of Saint Helena Island and zoogeography of zoantharians in the Atlantic Ocean: Jigsaw falling into place. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1572667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maria E. A. Santos
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Peter Wirtz
- Centro de Ciências do Mar, Universidade do Algarve, Faro, P-8005-139, Portugal
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Hiroki Kise
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
| | - Cataixa López
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n, La Laguna, Tenerife, 38206, Spain
| | - Judith Brown
- Marine Section, Environmental Management Division, Saint Helena Government
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Engineering and Science, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa, 903-0213, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| |
Collapse
|
76
|
Bernal MA, Dixon GB, Matz MV, Rocha LA. Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). PeerJ 2019; 7:e6541. [PMID: 30842908 PMCID: PMC6398375 DOI: 10.7717/peerj.6541] [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: 10/25/2018] [Accepted: 01/29/2019] [Indexed: 01/21/2023] Open
Abstract
Background Coral reefs are major hotspots of diversity for marine fishes, yet there is still ongoing debate on the mechanisms that promote divergence in these rich ecosystems. Our understanding of how diversity originates in this environment could be enhanced by investigating the evolutionary dynamics of closely related fishes with overlapping ranges. Here, we focus on grunts of the genus Haemulon, a group of coral reef fishes with 15 species in the Western Atlantic, 11 of which are syntopic. Methods Wild fish samples from three sympatric species of the Caribbean: Haemulon flavolineatum, H. carbonarium and H. macrostomum, were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise d N/d S) and patterns of gene expression between the three species. Results Pairwise d N/d S analyses showed evidence of positive selection for genes associated with immune response, cranial morphology and formation of the anterior-posterior axis. Analyses of gene expression revealed that despite their sympatric distribution, H. macrostomum showed upregulation of oxidation-reduction machinery, while there was evidence for activation of immune response in H. carbonarium. Discussion Overall, our analyses suggest closely related grunts show important differences in genes associated with body shape and feeding morphology, a result in-line with previous morphological studies in the group. Further, despite their overlapping distribution they interact with their environment in distinct fashions. This is the largest compendium of genomic information for grunts thus far, representing a valuable resource for future studies in this unique group of coral reef fishes.
Collapse
Affiliation(s)
- Moisés A Bernal
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Groves B Dixon
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mikhail V Matz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Luiz A Rocha
- Institute for Biodiversity, Science and Sustainability, California Academy of Sciences, San Francisco, CA, USA
| |
Collapse
|
77
|
Diversification of the genus Apogon (Lacepède, 1801) (Apogonidae: Perciformes) in the tropical eastern Pacific. Mol Phylogenet Evol 2019; 132:232-242. [DOI: 10.1016/j.ympev.2018.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 11/09/2018] [Accepted: 12/08/2018] [Indexed: 11/18/2022]
|
78
|
Teske PR, Sandoval-Castillo J, Golla TR, Emami-Khoyi A, Tine M, von der Heyden S, Beheregaray LB. Thermal selection as a driver of marine ecological speciation. Proc Biol Sci 2019; 286:20182023. [PMID: 30963923 PMCID: PMC6408613 DOI: 10.1098/rspb.2018.2023] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/11/2019] [Indexed: 12/19/2022] Open
Abstract
Intraspecific genetic structure in widely distributed marine species often mirrors the boundaries between temperature-defined bioregions. This suggests that the same thermal gradients that maintain distinct species assemblages also drive the evolution of new biodiversity. Ecological speciation scenarios are often invoked to explain such patterns, but the fact that adaptation is usually only identified when phylogenetic splits are already evident makes it impossible to rule out the alternative scenario of allopatric speciation with subsequent adaptation. We integrated large-scale genomic and environmental datasets along one of the world's best-defined marine thermal gradients (the South African coastline) to test the hypothesis that incipient ecological speciation is a result of divergence linked to the thermal environment. We identified temperature-associated gene regions in a coastal fish species that is spatially homogeneous throughout several temperature-defined biogeographic regions based on selectively neutral markers. Based on these gene regions, the species is divided into geographically distinct regional populations. Importantly, the ranges of these populations are delimited by the same ecological boundaries that define distinct infraspecific genetic lineages in co-distributed marine species, and biogeographic disjunctions in species assemblages. Our results indicate that temperature-mediated selection represents an early stage of marine ecological speciation in coastal regions that lack physical dispersal barriers.
Collapse
Affiliation(s)
- Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide 5001, Australia
| | - Tirupathi Rao Golla
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Mbaye Tine
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Lab, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
| | - Luciano B. Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide 5001, Australia
| |
Collapse
|
79
|
Čandek K, Agnarsson I, Binford GJ, Kuntner M. Biogeography of the Caribbean Cyrtognatha spiders. Sci Rep 2019; 9:397. [PMID: 30674906 PMCID: PMC6344596 DOI: 10.1038/s41598-018-36590-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/01/2018] [Indexed: 12/18/2022] Open
Abstract
Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genus Cyrtognatha (Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, examine its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test if Cyrtognatha biogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (COI) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses in BioGeoBEARS of over 100 originally sampled Cyrtognatha individuals, using models with and without a founder event parameter. Our results suggest a radiation of Caribbean Cyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Although biogeographic reconstructions cannot refute a vicariant origin of the Caribbean clade, possibly an artifact of sparse outgroup availability, they indicate timing of colonization that is much too recent for GAARlandia to have played a role. Instead, an overwater colonization to the Caribbean in mid-Miocene better explains the data. From Hispaniola, Cyrtognatha subsequently dispersed to, and diversified on, the other islands of the Greater, and Lesser Antilles. Within the constraints of our island system and data, a model that omits the founder event parameter from biogeographic analysis is less suitable than the equivalent model with a founder event.
Collapse
Affiliation(s)
- Klemen Čandek
- Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia.
- Evolutionary Zoology Laboratory, Institute of Biology, Research Centre of the Slovenian Academy of the Sciences and Arts, Ljubljana, Slovenia.
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA
| | - Greta J Binford
- Department of Biology, Lewis and Clark College, Portland, OR, USA
| | - Matjaž Kuntner
- Evolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA
- College of Life Sciences, Hubei University, Wuhan, Hubei, China
- Evolutionary Zoology Laboratory, Institute of Biology, Research Centre of the Slovenian Academy of the Sciences and Arts, Ljubljana, Slovenia
| |
Collapse
|
80
|
|
81
|
Berumen ML, Roberts MB, Sinclair-Taylor TH, DiBattista JD, Saenz-Agudelo P, Isari S, He S, Khalil MT, Hardenstine RS, Tietbohl MD, Priest MA, Kattan A, Coker DJ. Fishes and Connectivity of Red Sea Coral Reefs. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
82
|
Wooster MK, Voigt O, Erpenbeck D, Wörheide G, Berumen ML. Sponges of the Red Sea. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
83
|
|
84
|
Rodríguez-Flores PC, Macpherson E, Buckley D, Machordom A. High morphological similarity coupled with high genetic differentiation in new sympatric species of coral-reef squat lobsters (Crustacea: Decapoda: Galatheidae). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Paula C Rodríguez-Flores
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, Madrid, Spain
- Centre d’Estudis Avançats de Blanes (CEAB-CSIC), C. d’Accés Cala Sant Francesc, Blanes, Spain
| | - Enrique Macpherson
- Centre d’Estudis Avançats de Blanes (CEAB-CSIC), C. d’Accés Cala Sant Francesc, Blanes, Spain
| | - David Buckley
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, Madrid, Spain
- Centre d’Estudis Avançats de Blanes (CEAB-CSIC), C. d’Accés Cala Sant Francesc, Blanes, Spain
| | - Annie Machordom
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal, Madrid, Spain
| |
Collapse
|
85
|
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
|
86
|
Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus). Heredity (Edinb) 2018; 122:759-769. [PMID: 30459340 DOI: 10.1038/s41437-018-0164-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of species is a dynamic process as they modify, expand, and contract their spatial distributions over time. Range expansions (REs) occur through a series of founder events that are followed by migration among neighboring demes. The process usually results in structured metapopulations and leaves a distinct signature in the genetic variability of species. Explicitly modeling the consequences of complex demographic events such as REs is computationally very intensive. Here we propose an an alternative approach that requires less computational effort than a comprehensive RE model, but that can recover the demography of species undergoing a RE, by combining spatially explicit modelling with simplified but realistic metapopulation models. We examine the demographic and colonization history of Carcharhinus melanopterus, an abundant reef-associated shark, as a test case. We first used a population genomics approach to statistically confirm the occurrence of a RE in C. melanopterus, and identify its origin in the Indo-Australian Archipelago. Spatial genetic modelling identified two waves of stepping-stone colonization: an eastward wave moving through the Pacific and a westward one moving through the Indian Ocean. We show that metapopulation models best describe the demographic history of this species and that not accounting for this may lead to incorrectly interpreting the observed genetic variation as signals of widespread population bottlenecks. Our study highlights insights that can be gained about demography by coupling metapopulation models with spatial modeling and underscores the need for cautious interpretation of population genetic data when advancing conservation priorities.
Collapse
|
87
|
DiBattista JD, Alfaro ME, Sorenson L, Choat JH, Hobbs JA, Sinclair‐Taylor TH, Rocha LA, Chang J, Luiz OJ, Cowman PF, Friedman M, Berumen ML. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot. Ecol Evol 2018; 8:10989-11008. [PMID: 30519422 PMCID: PMC6262737 DOI: 10.1002/ece3.4566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 08/19/2018] [Accepted: 08/29/2018] [Indexed: 01/19/2023] Open
Abstract
For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (<1.75 Ma). Even though deep reef environments were drastically reduced during the extreme low sea level stands of glacial ages, shallow reefs persisted, and as such there was no evidence supporting mass extirpation of fauna in this region.
Collapse
Affiliation(s)
- Joseph D. DiBattista
- Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
- Australian Museum Research Institute, Australian MuseumSydneyNew South WalesAustralia
- School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCalifornia
| | - Laurie Sorenson
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCalifornia
| | - John H. Choat
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Jean‐Paul A. Hobbs
- School of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Tane H. Sinclair‐Taylor
- Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Luiz A. Rocha
- Section of IchthyologyCalifornia Academy of SciencesSan FranciscoCalifornia
| | - Jonathan Chang
- Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesCalifornia
| | - Osmar J. Luiz
- Research Institute for the Environment and Livelihoods, Charles Darwin UniversityDarwinNorthern TerritoryAustralia
| | - Peter F. Cowman
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueenslandAustralia
| | - Matt Friedman
- Department of Earth SciencesUniversity of OxfordOxfordUK
- Museum of Paleontology and Department of Earth and Environmental SciencesUniversity of MichiganAnn ArborMichigan
| | - Michael L. Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| |
Collapse
|
88
|
Argolo LA, Ramos RT, Barreto SB, Bitencourt JA, Sampaio I, Schneider H, Affonso PR. The flounder next door: Closer evolutionary relationship between allopatric than sympatric Bothus (Rafinesque, 1810) species (Pleuronectiformes, Bothidae). ZOOL ANZ 2018. [DOI: 10.1016/j.jcz.2018.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
89
|
Miller EC, Hayashi KT, Song D, Wiens JJ. Explaining the ocean's richest biodiversity hotspot and global patterns of fish diversity. Proc Biol Sci 2018; 285:20181314. [PMID: 30305433 PMCID: PMC6191688 DOI: 10.1098/rspb.2018.1314] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023] Open
Abstract
For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3-34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.
Collapse
Affiliation(s)
| | - Kenji T Hayashi
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
- Division of Biology and Medicine, Program in Biology, Brown University, Providence, RI 02912, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dongyuan Song
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
- Department of Ecology and Evolutionary Biology, Fudan University, Shanghai 200438, China
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
| |
Collapse
|
90
|
Addison JA, Kim JH. Cryptic species diversity and reproductive isolation among sympatric lineages of Strongylocentrotus sea urchins in the northwest Atlantic. Facets (Ott) 2018. [DOI: 10.1139/facets-2017-0081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Distinguishing between intra- and inter-specific variation in genetic studies is critical to understanding evolution because the mechanisms driving change among populations are expected to be different than those that shape reproductive isolation among lineages. Genetic studies of north Atlantic green sea urchins Strongylocentrotus droebachiensis (Müller, 1776) have detected significant population substructure and asymmetric gene flow from Europe to Atlantic Canada and interspecific hybridization between S. droebachiensis and Strongylocentrotus pallidus (Sars, 1871). However, combined with patterns of divergence at mtDNA sequences, morphological divergence at gamete traits suggests that the European and North American lineages of S. droebachiensis may be cryptic species. Here, we use a combination of cytochrome c oxidase subunit I ( COI) sequences and single nucleotide polymorphisms (SNPs) to test for cryptic species within Strongylocentrotus sea urchins and hybrids between S. droebachiensis and S. pallidus populations. We detect striking patterns of habitat and reproductive isolation between two S. droebachiensis lineages, with offshore deep-water collections consisting of S. pallidus in addition to a cryptic lineage sharing genetic similarity with previously published sequences from eastern Atlantic S. droebachiensis. We detected only limited hybridization among all three lineages of sea urchins, suggesting that shared genetic differences previously reported may be a result of historical introgression or incomplete lineage sorting.
Collapse
Affiliation(s)
- Jason A. Addison
- Department of Biology, University of New Brunswick, P.O. Box 4400, Fredericton, NB E3B 5A3, Canada
| | - Jin-Hong Kim
- Department of Biology, University of New Brunswick, P.O. Box 4400, Fredericton, NB E3B 5A3, Canada
| |
Collapse
|
91
|
Otwoma LM, Diemel V, Reuter H, Kochzius M, Meyer A. Genetic population structure of the convict surgeonfish Acanthurus triostegus: a phylogeographic reassessment across its range. JOURNAL OF FISH BIOLOGY 2018; 93:597-608. [PMID: 29956317 DOI: 10.1111/jfb.13686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
This study investigates the genetic population structure and connectivity of Acanthurus triostegus in five Indo-Pacific biogeographic regions (western and eastern Indian Ocean, western, central and eastern Pacific Ocean), using a mitochondrial DNA marker spanning the ATPase8 and ATPase6 gene regions. In order to assess the phylogeography and genetic population structure of A. triostegus across its range, 35 individuals were sampled from five localities in the western Indian Ocean and complemented with 227 sequences from two previous studies. Results from the overall analysis of molecular variance (AMOVA) without a priori grouping showed evidence of significant differentiation in the Indo-Pacific, with 25 (8.3%) out of 300 pairwise ΦST comparisons being significant. However, the hierarchical AMOVA grouping of Indian and Pacific Ocean populations failed to support the vicariance hypothesis, showing a lack of a genetic break between the two ocean basins. Instead, the correlation between pairwise ΦST values and geographic distance showed that dispersal of A. triostegus in the Indo-Pacific Ocean follows an isolation-by-distance model. Three haplogroups could be deduced from the haplotype network and phylogenetic tree, with haplogroup 1 and 2 dominating the Indian and the Pacific Ocean, respectively, while haplogroup 3 exclusively occurring in the Hawaiian Archipelago of the central Pacific Ocean.
Collapse
Affiliation(s)
- Levy M Otwoma
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Kenya Marine and Fisheries Research Institute (KMFRI), Mombasa, Kenya
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Valeska Diemel
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Hauke Reuter
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- Faculty Biology and Chemistry, University of Bremen, Bremen, Germany
| | | | - Achim Meyer
- Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| |
Collapse
|
92
|
He Z, Li X, Yang M, Wang X, Zhong C, Duke NC, Wu CI, Shi S. Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. Natl Sci Rev 2018; 6:275-288. [PMID: 31258952 PMCID: PMC6599600 DOI: 10.1093/nsr/nwy078] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca, narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn (m > 1) species after n cycles.
Collapse
Affiliation(s)
- Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ming Yang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xinfeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve Administration, Haikou 571129, China
| | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville 4811, Australia
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Department of Ecology and Evolution, University of Chicago, Chicago IL 60637, USA
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| |
Collapse
|
93
|
Mizuyama M, Masucci GD, Reimer JD. Speciation among sympatric lineages in the genus Palythoa (Cnidaria: Anthozoa: Zoantharia) revealed by morphological comparison, phylogenetic analyses and investigation of spawning period. PeerJ 2018; 6:e5132. [PMID: 30013833 PMCID: PMC6035721 DOI: 10.7717/peerj.5132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 06/06/2018] [Indexed: 11/20/2022] Open
Abstract
Zoantharians are sessile marine invertebrates and colonial organisms possessing sexual and asexual reproductive ability. The zooxanthellate zoantharian genus Palythoa is widely distributed in coral reef ecosystems. In the Ryukyu Archipelago, Japan, sympatric Palythoa tuberculosa and P. mutuki are the dominant species of this genus in the intertidal zone. Previous phylogenetic analyses have shown that these two species are closely related, and additionally revealed a putative sympatric hybrid species (designated as Palythoa sp. yoron). In this study, we attempted to delineate Palythoa species boundaries and to clarify the relationships among these three groups plus another additional putative sympatric species (P. aff. mutuki) by multiple independent criteria. The morphology of these four lineages was clearly different; for example the number of tentacles was significantly different for each species group in all pairwise comparisons. From observations of gonadal development conducted in 2010 and 2011, P. sp. yoron and P. aff. mutuki appear to be reproductively isolated from P. tuberculosa. In the phylogenetic tree resulting from maximum likelihood analyses of the ITS-rDNA sequence alignment, P. tuberculosa and P. sp. yoron formed a very well supported monophyletic clade (NJ = 100%, ML = 95%, Bayes = 0.99). This study demonstrates that despite clear morphological and/or reproductive differences, P. tuberculosa and P. sp. yoron are phylogenetically entangled and closely related to each other, as are P. mutuki and P. aff. mutuki. Additionally, no single molecular marker was able to divide these four lineages into monophyletic clades by themselves, and a marker that has enough resolution to solve this molecular phylogenetic species complex is required. In summary, the morphological and reproductive results suggest these lineages are four separate species, and that incomplete genetic lineage sorting may prevent the accurate phylogenetic detection of distinct species with the DNA markers utilized in this study, demonstrating the value of morphological and reproductive data when examining closely related lineages.
Collapse
Affiliation(s)
- Masaru Mizuyama
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Giovanni D Masucci
- Molecular Invertebrate Systematics and Ecology Laboratory, Graduate School of Marine Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - James D Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Marine Sciences, Chemistry and Biology, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan.,Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| |
Collapse
|
94
|
Goto R, Harrison TA, Ó Foighil D. Within-host speciation events in yoyo clams, obligate commensals with mantis shrimps, including one that involves a change in microhabitat and a loss of specialized traits. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Ryutaro Goto
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Nishimuro, Wakayama, Japan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Teal A Harrison
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Diarmaid Ó Foighil
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
95
|
Brustolin MC, Nagelkerken I, Fonseca G. Large-scale distribution patterns of mangrove nematodes: A global meta-analysis. Ecol Evol 2018; 8:4734-4742. [PMID: 29876053 PMCID: PMC5980601 DOI: 10.1002/ece3.3982] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/10/2017] [Accepted: 02/09/2018] [Indexed: 11/09/2022] Open
Abstract
Mangroves harbor diverse invertebrate communities, suggesting that macroecological distribution patterns of habitat-forming foundation species drive the associated faunal distribution. Whether these are driven by mangrove biogeography is still ambiguous. For small-bodied taxa, local factors and landscape metrics might be as important as macroecology. We performed a meta-analysis to address the following questions: (1) can richness of mangrove trees explain macroecological patterns of nematode richness? and (2) do local landscape attributes have equal or higher importance than biogeography in structuring nematode richness? Mangrove areas of Caribbean-Southwest Atlantic, Western Indian, Central Indo-Pacific, and Southwest Pacific biogeographic regions. We used random-effects meta-analyses based on natural logarithm of the response ratio (lnRR) to assess the importance of macroecology (i.e., biogeographic regions, latitude, longitude), local factors (i.e., aboveground mangrove biomass and tree richness), and landscape metrics (forest area and shape) in structuring nematode richness from 34 mangroves sites around the world. Latitude, mangrove forest area, and forest shape index explained 19% of the heterogeneity across studies. Richness was higher at low latitudes, closer to the equator. At local scales, richness increased slightly with landscape complexity and decreased with forest shape index. Our results contrast with biogeographic diversity patterns of mangrove-associated taxa. Global-scale nematode diversity may have evolved independently of mangrove tree richness, and diversity of small-bodied metazoans is probably more closely driven by latitude and associated climates, rather than local, landscape, or global biogeographic patterns.
Collapse
Affiliation(s)
- Marco C. Brustolin
- Centre of Sea StudiesFederal University of ParanáPontal do ParanáBrazil
- Department of Marine SciencesFederal University of São PauloSantosBrazil
| | - Ivan Nagelkerken
- Southern Seas Ecology LaboratoriesSchool of Biological Sciences and The Environment InstituteThe University of AdelaideAdelaideSAAustralia
| | - Gustavo Fonseca
- Department of Marine SciencesFederal University of São PauloSantosBrazil
| |
Collapse
|
96
|
Maas DL, Prost S, Bi K, Smith LL, Armstrong EE, Aji LP, Toha AHA, Gillespie RG, Becking LE. Rapid divergence of mussel populations despite incomplete barriers to dispersal. Mol Ecol 2018; 27:1556-1571. [DOI: 10.1111/mec.14556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Diede L. Maas
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
| | - Stefan Prost
- Department of Biology; Stanford University; Stanford CA USA
- Department of Integrative Biology; Center for Theoretical Evolutionary Genomics; University of California; Berkeley CA USA
| | - Ke Bi
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
- Computational Genomics Resource Laboratory; California Institute for Quantitative Biosciences; University of California; Berkley CA USA
| | - Lydia L. Smith
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
| | | | - Ludi P. Aji
- Research Centre for Oceanography; Indonesian Institute of Sciences; Jakarta Indonesia
| | | | - Rosemary G. Gillespie
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
| | - Leontine E. Becking
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
- Wageningen Marine Research; Den Helder The Netherlands
| |
Collapse
|
97
|
Di Martino E, Jackson JBC, Taylor PD, Johnson KG. Differences in extinction rates drove modern biogeographic patterns of tropical marine biodiversity. SCIENCE ADVANCES 2018; 4:eaaq1508. [PMID: 29740611 PMCID: PMC5938229 DOI: 10.1126/sciadv.aaq1508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/15/2018] [Indexed: 05/26/2023]
Abstract
Marine biodiversity in the Coral Triangle is several times higher than anywhere else, but why this is true is unknown because of poor historical data. To address this, we compared the first available record of fossil cheilostome bryozoans from Indonesia with the previously sampled excellent record from the Caribbean. These two regions differ several-fold in species richness today, but cheilostome diversity was strikingly similar until the end of the Miocene 5.3 million years ago so that the modern disparity must have developed more recently. However, the Miocene faunas were ecologically very different, with a greater proportion of erect and free-living species in the Caribbean compared to the less well-known Coral Triangle. Our results support the hypothesis that modern differences in diversity arose primarily from differential extinction of Caribbean erect and free-living species concomitant with oceanographic changes due to the uplift of the Isthmus of Panama, rather than exceptional rates of diversification in the Indo-Pacific.
Collapse
Affiliation(s)
- Emanuela Di Martino
- Department of Earth Sciences, Natural History Museum, Cromwell Road, SW7 5BD London, UK
| | - Jeremy B. C. Jackson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013–7012, USA
| | - Paul D. Taylor
- Department of Earth Sciences, Natural History Museum, Cromwell Road, SW7 5BD London, UK
| | - Kenneth G. Johnson
- Department of Earth Sciences, Natural History Museum, Cromwell Road, SW7 5BD London, UK
| |
Collapse
|
98
|
Whitney JL, Bowen BW, Karl SA. Flickers of speciation: Sympatric colour morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence with gene flow. Mol Ecol 2018; 27:1479-1493. [PMID: 29420860 DOI: 10.1111/mec.14527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/01/2023]
Abstract
One of the primary challenges of evolutionary research is to identify ecological factors that favour reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive colour polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few metres apart. To test whether ecological barriers have reduced gene flow among dark and light phenotypes, we evaluated genetic variation at 30 microsatellite loci and a nuclear exon (Mc1r) associated with melanistic coloration. We report low, but significant microsatellite differentiation among colour morphs and stronger divergence in the coding region of Mc1r indicating signatures of selection. Critically, we observed greater genetic divergence between colour morphs on the same reefs than that between the same morphs in different geographic locations. We hypothesize that adaptation to the contrasting microhabitats is overriding gene flow and is responsible for the partial reproductive isolation observed between sympatric colour morphs. Combined with complementary studies of hawkfish ecology and behaviour, these genetic results indicate an ecological barrier to gene flow initiated by habitat selection and enhanced by assortative mating. Hence, the arc-eye hawkfish fulfil theoretical expectations for the earliest phase of speciation with gene flow.
Collapse
Affiliation(s)
- Jonathan L Whitney
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| | - Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, USA
| |
Collapse
|
99
|
Dudoit 'A, Iacchei M, Coleman RR, Gaither MR, Browne WE, Bowen BW, Toonen RJ. The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages. PeerJ 2018. [PMID: 29527409 PMCID: PMC5844259 DOI: 10.7717/peerj.4409] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.
Collapse
Affiliation(s)
- 'Ale'alani Dudoit
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Matthew Iacchei
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America.,Department of Natural Science, Hawai'i Pacific University, Kāne'ohe, HI, United States of America
| | - Richard R Coleman
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Zoology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Michelle R Gaither
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Current affiliation: Department of Biology, University of Central Florida, Orlando, FL, United States of America
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
| | - Brian W Bowen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, HI, United States of America.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States of America
| |
Collapse
|
100
|
Pinheiro HT, Rocha LA, Macieira RM, Carvalho-Filho A, Anderson AB, Bender MG, Di Dario F, Ferreira CEL, Figueiredo-Filho J, Francini-Filho R, Gasparini JL, Joyeux JC, Luiz OJ, Mincarone MM, Moura RL, Nunes JDACC, Quimbayo JP, Rosa RS, Sampaio CLS, Sazima I, Simon T, Vila-Nova DA, Floeter SR. South-western Atlantic reef fishes: Zoogeographical patterns and ecological drivers reveal a secondary biodiversity centre in the Atlantic Ocean. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12729] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Hudson T. Pinheiro
- California Academy of Sciences; San Francisco CA USA
- Ecology and Evolutionary Biology Department; University of California Santa Cruz; Santa Cruz CA USA
- Associação Ambiental Voz da Natureza; Vitória ES Brazil
| | - Luiz A. Rocha
- California Academy of Sciences; San Francisco CA USA
- Ecology and Evolutionary Biology Department; University of California Santa Cruz; Santa Cruz CA USA
| | - Raphael M. Macieira
- Laboratório de Ecologia Marinha; Universidade Vila Velha; Vila Velha ES Brazil
| | | | - Antônio B. Anderson
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Mariana G. Bender
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Fabio Di Dario
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé; Universidade Federal do Rio de Janeiro; Macaé RJ Brazil
| | | | - Jessé Figueiredo-Filho
- Centro de Ciências Exatas e da Natureza; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Ronaldo Francini-Filho
- Departamento de Engenharia e Meio Ambiente; Universidade Federal da Paraíba; Rio Tinto PB Brazil
| | - João L. Gasparini
- Departamento de Oceanografia e Ecologia; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Jean-Christophe Joyeux
- Departamento de Oceanografia e Ecologia; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Osmar J. Luiz
- Department of Biological Sciences; Macquarie University; Sydney NSW Australia
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin NT Australia
| | - Michael M. Mincarone
- Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé; Universidade Federal do Rio de Janeiro; Macaé RJ Brazil
| | - Rodrigo L. Moura
- Instituto de Biologia and SAGE/COPPE; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ Brazil
| | | | - Juan P. Quimbayo
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Ricardo S. Rosa
- Centro de Ciências Exatas e da Natureza; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Cláudio L. S. Sampaio
- Laboratório de Ictiologia e Conservação; Universidade Federal de Alagoas; Penedo AL Brazil
| | - Ivan Sazima
- Museu de Zoologia; Universidade Estadual de Campinas; Campinas SP Brazil
| | - Thiony Simon
- Associação Ambiental Voz da Natureza; Vitória ES Brazil
- Departamento de Oceanografia e Ecologia; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Daniele A. Vila-Nova
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| | - Sergio R. Floeter
- Laboratório de Biogeografia e Macroecologia Marinha; Universidade Federal de Santa Catarina; Florianópolis SC Brazil
| |
Collapse
|