1
|
Weber MD, Richards TM, Sutton TT, Carter JE, Eytan RI. Deep-pelagic fishes: Demographic instability in a stable environment. Ecol Evol 2024; 14:e11267. [PMID: 38638366 PMCID: PMC11024635 DOI: 10.1002/ece3.11267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/10/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
Demographic histories are frequently a product of the environment, as populations expand or contract in response to major environmental changes, often driven by changes in climate. Meso- and bathy-pelagic fishes inhabit some of the most temporally and spatially stable habitats on the planet. The stability of the deep-pelagic could make deep-pelagic fishes resistant to the demographic instability commonly reported in fish species inhabiting other marine habitats, however the demographic histories of deep-pelagic fishes are unknown. We reconstructed the historical demography of 11 species of deep-pelagic fishes using mitochondrial and nuclear DNA sequence data. We uncovered widespread evidence of population expansions in our study species, a counterintuitive result based on the nature of deep-pelagic ecosystems. Frequency-based methods detected potential demographic changes in nine species of fishes, while extended Bayesian skyline plots identified population expansions in four species. These results suggest that despite the relatively stable nature of the deep-pelagic environment, the fishes that reside here have likely been impacted by past changes in climate. Further investigation is necessary to better understand how deep-pelagic fishes, by far Earth's most abundant vertebrates, will respond to future climatic changes.
Collapse
Affiliation(s)
- Max D. Weber
- Texas A&M University at GalvestonGalvestonTexasUSA
| | | | | | | | - Ron I. Eytan
- Texas A&M University at GalvestonGalvestonTexasUSA
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisianaUSA
| |
Collapse
|
2
|
Carter JE, Sporre MA, Eytan RI. Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico. Mol Phylogenet Evol 2023; 189:107933. [PMID: 37769827 DOI: 10.1016/j.ympev.2023.107933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied. This genus is transatlantically distributed and comprises 11 species with a convoluted taxonomic history. In this study, relationships for ten Hypleurochilus species are resolved using multi-locus nuclear and mtDNA sequence data, morphological data, and mined COI barcode data. Mitochondrial and nuclear sequence data from 61 individuals collected from the western Atlantic and northern Gulf of Mexico (N. GoM) delimit seven species into a temperate clade, a tropical clade, and a third distinct lineage. This lineage, herein referred to as H. cf. aequipinnis, may represent a species of Hypleurochilus whose range has expanded into the N. GoM. Inclusion of publicly available COI sequence for an additional three species provides further phylogenetic resolution. H. bananensis forms a new eastern Atlantic clade with H. cf. aequipinnis, providing further evidence for a western Atlantic range expansion. Single marker COI delimitation was unable to elucidate the relationships between H. springeri/H. pseudoaequipinnis and between H. multifilis/H. caudovittatus due to incomplete lineage sorting. Mitochondrial data are also unable to accurately resolve the placement of H. bermudensis. However, a comprehensive approach using multi-locus phylogenetic and species delimitation methods was able to resolve these relationships. While mining publicly available sequence data allowed for the inclusion of an increased number of species in the analysis and a more comprehensive phylogeny, it was not without drawbacks, as a handful of sequences are potentially mis-identified. Overall, we find that the recent divergence of some species within this genus and potential introgression events confound the results of single locus delimitation methods, yet a combination of single and multi-locus analyses has allowed for insights into the biogeography of this genus and uncovered a potential transatlantic range expansion.
Collapse
Affiliation(s)
- Joshua E Carter
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States.
| | - Megan A Sporre
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
| |
Collapse
|
3
|
Sporre MA, Eytan RI. The complete mitogenomes of the spinyhead blenny, Acanthemblemaria spinosa (chaenopsidae) and the lofty triplefin, Enneanectes altivelis (Tripterygiidae). Mitochondrial DNA B Resour 2022; 7:353-355. [PMID: 35174288 PMCID: PMC8843169 DOI: 10.1080/23802359.2022.2034542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The blennies, Acanthemblemaria spinosa (Chaenopsidae) and Enneanectes altivelis (Tripterygiidae) are representative members of two families spanning the deepest node of the Blennioidei tree. The mitogenomes of 16,507 bp for A. spinosa and 16,529 bp for E. altivelis each consisted of 37 genes and one control loop region. Phylogenetic analysis confirmed the placement of Chaenopsidae and Tripterygiidae within the Blenniiformes, however, there was instability in the placement of the triplefins between reconstruction methods, likely due to low taxon sampling. These mitogenomes represent an important milestone in uncovering relationships within Blenniiformes and Ovalentaria.
Collapse
Affiliation(s)
- Megan A. Sporre
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA
| | - Ron I. Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, USA
| |
Collapse
|
4
|
Warren DL, Eytan RI, Dornburg A, Iglesias TL, Brandley MC, Wainwright PC. Reevaluating claims of ecological speciation in Halichoeres bivittatus. Ecol Evol 2021; 11:11449-11456. [PMID: 34429932 PMCID: PMC8366890 DOI: 10.1002/ece3.7936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 07/07/2021] [Indexed: 11/11/2022] Open
Abstract
Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep divergence in a single mitochondrial locus between the northern and southern Gulf of Mexico, combined with a finding that these two haplotypes were associated with different habitat types ("tropical" vs. "subtropical") in the Florida Keys and Bermuda, where they overlap. Here, we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study. We find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations in the Keys. These results undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. Future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.
Collapse
Affiliation(s)
- Dan L. Warren
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Ron I. Eytan
- Department of Marine BiologyTexas A&M University at GalvestonGalvestonTexasUSA
| | - Alex Dornburg
- Department of Bioinformatics and GenomicsUniversity of North Carolina CharlotteCharlotteNorth CarolinaUSA
| | - Teresa L. Iglesias
- Animal Resources SectionOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Matthew C. Brandley
- Section of Amphibians and ReptilesCarnegie Museum of Natural HistoryPittsburghPAUSA
- Powdermill Nature ReserveCarnegie Museum of Natural HistoryRectorPennsylvaniaUSA
| | - Peter C. Wainwright
- Department of Evolution and EcologyUniversity of CaliforniaDavisCaliforniaUSA
| |
Collapse
|
5
|
Hastings PA, Eytan RI, Summers AP. Acanthemblemaria aceroi, a new species of tube blenny from the Caribbean coast of South America with notes on Acanthemblemaria johnsoni (Teleostei: Chaenopsidae). Zootaxa 2020; 4816:zootaxa.4816.2.5. [PMID: 33055705 DOI: 10.11646/zootaxa.4816.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/04/2022]
Abstract
Acanthemblemaria aceroi new species is described from the upwelling region of the Caribbean coasts of Venezuela and Colombia. It differs from its closest relative, Acanthemblemaria rivasi Stephens, 1970, known from Panama and Costa Rica, in the posterior extent of the infraorbitals, details of head spination, and unique COI sequences. The description of Acanthemblemaria johnsonsi Almany Baldwin, 1996, heretofore known only from Tobago, is expanded based on specimens from islands offshore of eastern Venezuela.
Collapse
Affiliation(s)
- Philip A Hastings
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0208, U.S.A..
| | | | | |
Collapse
|
6
|
Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Mol Phylogenet Evol 2017; 110:27-38. [PMID: 28254474 DOI: 10.1016/j.ympev.2017.02.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 02/22/2017] [Accepted: 02/25/2017] [Indexed: 11/17/2022]
Abstract
Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates.
Collapse
Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA.
| | - Jeffrey P Townsend
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Biostatistics, Yale University, New Haven, CT 06510, USA
| | - Willa Brooks
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Elizabeth Spriggs
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Ron I Eytan
- Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA
| | - Jon A Moore
- Florida Atlantic University, Wilkes Honors College, Jupiter, FL 33458, USA; Florida Atlantic University, Harbor Branch Oceanographic Institution, Fort Pierce, FL 34946, USA
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, Davis, CA 95616, USA
| | - Alan Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
7
|
Harrington RC, Faircloth BC, Eytan RI, Smith WL, Near TJ, Alfaro ME, Friedman M. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evol Biol 2016; 16:224. [PMID: 27769164 PMCID: PMC5073739 DOI: 10.1186/s12862-016-0786-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/30/2016] [Indexed: 11/26/2022] Open
Abstract
Background Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. Results We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years. Conclusions The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0786-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Richard C Harrington
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK. .,Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA.
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, 77553, USA
| | - W Leo Smith
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, 06520, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Matt Friedman
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK.,Museum of Paleontology and Department of Earth and Environmental Science, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA
| |
Collapse
|
8
|
O’Dea A, Lessios HA, Coates AG, Eytan RI, Restrepo-Moreno SA, Cione AL, Collins LS, de Queiroz A, Farris DW, Norris RD, Stallard RF, Woodburne MO, Aguilera O, Aubry MP, Berggren WA, Budd AF, Cozzuol MA, Coppard SE, Duque-Caro H, Finnegan S, Gasparini GM, Grossman EL, Johnson KG, Keigwin LD, Knowlton N, Leigh EG, Leonard-Pingel JS, Marko PB, Pyenson ND, Rachello-Dolmen PG, Soibelzon E, Soibelzon L, Todd JA, Vermeij GJ, Jackson JBC. Formation of the Isthmus of Panama. Sci Adv 2016; 2:e1600883. [PMID: 27540590 PMCID: PMC4988774 DOI: 10.1126/sciadv.1600883] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 07/18/2016] [Indexed: 05/22/2023]
Abstract
The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.
Collapse
Affiliation(s)
- Aaron O’Dea
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Harilaos A. Lessios
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Anthony G. Coates
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Ron I. Eytan
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX 77553, USA
| | - Sergio A. Restrepo-Moreno
- Departamento de Geociencias y Medio Ambiente Universidad Nacional de Colombia, Bogotá, Colombia
- Department of Geological Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Alberto L. Cione
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Laurel S. Collins
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- Department of Earth and Environment, and Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Alan de Queiroz
- Department of Biology, University of Nevada, Reno, NV 89557–0314, USA
| | - David W. Farris
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL 32306, USA
| | | | - Robert F. Stallard
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- U.S. Geological Survey, 3215 Marine Street (Suite E127), Boulder, CO 80303, USA
| | - Michael O. Woodburne
- Department of Geological Sciences, University of California, Riverside, Riverside, CA 92507, USA
| | - Orangel Aguilera
- Universidade Federal Fluminense, Instituto de Biologia, Campus do Valonguinho, Outeiro São João Batista, s/n°, cep. 24020-141, Niterói, Rio de Janeiro, Brazil
| | - Marie-Pierre Aubry
- Department of Earth and Planetary Sciences, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854–8066, USA
| | - William A. Berggren
- Department of Earth and Planetary Sciences, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854–8066, USA
| | - Ann F. Budd
- Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Mario A. Cozzuol
- Laboratório de Paleozoologia, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, cep. 31270 010, Belo Horizonte, MG, Brazil
| | - Simon E. Coppard
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
| | - Herman Duque-Caro
- Academia Colombiana de Ciencias Exactas, Físicas y Naturales, Bogotá, Colombia
| | - Seth Finnegan
- Department of Integrative Biology, University of California, Berkeley, 3040 Valley Life Science Building #3140, Berkeley, CA 94720–3140, USA
| | - Germán M. Gasparini
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Ethan L. Grossman
- Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kenneth G. Johnson
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | | | - Nancy Knowlton
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Egbert G. Leigh
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
| | - Jill S. Leonard-Pingel
- Department of Geology, Washington and Lee University, 204 West Washington Street, Lexington, VA 24450, USA
| | - Peter B. Marko
- Department of Biology, University of Hawai’i at Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Nicholas D. Pyenson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Paola G. Rachello-Dolmen
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843, USA
| | - Esteban Soibelzon
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Leopoldo Soibelzon
- División Paleontología Vertebrados, Museo de La Plata, B1900FWA La Plata, Buenos Aires, Argentina
| | - Jonathan A. Todd
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Geerat J. Vermeij
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeremy B. C. Jackson
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Republic of Panama
- Scripps Institution of Oceanography, La Jolla, CA 92093–0244, USA
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| |
Collapse
|
9
|
Dornburg A, Eytan RI, Federman S, Pennington JN, Stewart AL, Jones CD, Near TJ. Molecular data support the existence of two species of the Antarctic fish genus Cryodraco (Channichthyidae). Polar Biol 2015. [DOI: 10.1007/s00300-015-1859-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
Thacker CE, Satoh TP, Katayama E, Harrington RC, Eytan RI, Near TJ. Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei. Mol Phylogenet Evol 2015; 93:172-9. [DOI: 10.1016/j.ympev.2015.08.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/10/2015] [Accepted: 08/01/2015] [Indexed: 10/23/2022]
|
11
|
Eytan RI, Evans BR, Dornburg A, Lemmon AR, Lemmon EM, Wainwright PC, Near TJ. Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment. BMC Evol Biol 2015; 15:113. [PMID: 26071950 PMCID: PMC4465735 DOI: 10.1186/s12862-015-0415-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be. RESULTS After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree. CONCLUSIONS Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.
Collapse
Affiliation(s)
- Ron I Eytan
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, 77553, TX, USA.
| | - Benjamin R Evans
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| | - Alex Dornburg
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, 32306, FL, USA.
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, 32306, FL, USA.
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, One Shields Avenue, Davis, 95616, CA, USA.
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| |
Collapse
|
12
|
Dornburg A, Moore J, Beaulieu JM, Eytan RI, Near TJ. The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes). Evolution 2014; 69:146-61. [DOI: 10.1111/evo.12562] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/27/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History; Yale University; New Haven Connecticut
| | - Jon Moore
- Wilkes Honors College; Florida Atlantic University; Jupiter Florida
- Harbor Branch Oceanographic Institution; Florida Atlantic University; Fort Pierce Florida
| | - Jeremy M. Beaulieu
- National Institute of Mathematical and Biological Synthesis; University of Tennessee; Knoxville Tennessee
| | - Ron I. Eytan
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History; Yale University; New Haven Connecticut
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History; Yale University; New Haven Connecticut
| |
Collapse
|
13
|
Price SA, Schmitz L, Oufiero CE, Eytan RI, Dornburg A, Smith WL, Friedman M, Near TJ, Wainwright PC. Two waves of colonization straddling the K-Pg boundary formed the modern reef fish fauna. Proc Biol Sci 2014; 281:20140321. [PMID: 24695431 PMCID: PMC3996619 DOI: 10.1098/rspb.2014.0321] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Living reef fishes are one of the most diverse vertebrate assemblages on Earth. Despite its prominence and ecological importance, the origins and assembly of the reef fish fauna is poorly described. A patchy fossil record suggests that the major colonization of reef habitats must have occurred in the Late Cretaceous and early Palaeogene, with the earliest known modern fossil coral reef fish assemblage dated to 50 Ma. Using a phylogenetic approach, we analysed the early evolutionary dynamics of modern reef fishes. We find that reef lineages successively colonized reef habitats throughout the Late Cretaceous and early Palaeogene. Two waves of invasion were accompanied by increasing morphological convergence: one in the Late Cretaceous from 90 to 72 Ma and the other immediately following the end-Cretaceous mass extinction. The surge in reef invasions after the Cretaceous–Palaeogene boundary continued for 10 Myr, after which the pace of transitions to reef habitats slowed. Combined, these patterns match a classic niche-filling scenario: early transitions to reefs were made rapidly by morphologically distinct lineages and were followed by a decrease in the rate of invasions and eventual saturation of morphospace. Major alterations in reef composition, distribution and abundance, along with shifts in climate and oceanic currents, occurred during the Late Cretaceous and early Palaeogene interval. A causal mechanism between these changes and concurrent episodes of reef invasion remains obscure, but what is clear is that the broad framework of the modern reef fish fauna was in place within 10 Myr of the end-Cretaceous extinction.
Collapse
Affiliation(s)
- S A Price
- Department of Evolution and Ecology, University of California, , Davis, CA 95618, USA, W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, , 925 North Mills Avenue, Claremont, CA 91711, USA, Department of Biological Science, Towson University, , Towson, MD 21252, USA, Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, , New Haven, CT, USA, Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, , Lawrence, KS 66045, USA, Department of Earth Sciences, University of Oxford, , Oxford OX1 3AN, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Friedman M, Keck BP, Dornburg A, Eytan RI, Martin CH, Hulsey CD, Wainwright PC, Near TJ. Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proc Biol Sci 2013; 280:20131733. [PMID: 24048155 PMCID: PMC3779330 DOI: 10.1098/rspb.2013.1733] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/29/2013] [Indexed: 11/21/2022] Open
Abstract
Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (ca 65-57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography.
Collapse
Affiliation(s)
- Matt Friedman
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Alex Dornburg
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Ron I. Eytan
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | | | - C. Darrin Hulsey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Peter C. Wainwright
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
15
|
Ilves KL, Quattrini AM, Westneat MW, Eytan RI, Chaplin GW, Hertler H, Lundberg JG. Detection of Shifts in Coral Reef Fish Assemblage Structure Over 50 Years at Reefs of New Providence Island, the Bahamas Highlight the Value of the Academy of Natural Sciences' Collections in a Changing World. Proceedings of the Academy of Natural Sciences of Philadelphia 2013. [DOI: 10.1635/053.162.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
16
|
Wainwright PC, Smith WL, Price SA, Tang KL, Sparks JS, Ferry LA, Kuhn KL, Eytan RI, Near TJ. The evolution of pharyngognathy: a phylogenetic and functional appraisal of the pharyngeal jaw key innovation in labroid fishes and beyond. Syst Biol 2012; 61:1001-27. [PMID: 22744773 DOI: 10.1093/sysbio/sys060] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The perciform group Labroidei includes approximately 2600 species and comprises some of the most diverse and successful lineages of teleost fishes. Composed of four major clades, Cichlidae, Labridae (wrasses, parrotfishes, and weed whitings), Pomacentridae (damselfishes), and Embiotocidae (surfperches); labroids have been an icon for studies of biodiversity, adaptive radiation, and sexual selection. The success and diversification of labroids have been largely attributed to the presence of a major innovation in the pharyngeal jaw apparatus, pharyngognathy, which is hypothesized to increase feeding capacity and versatility. We present results of large-scale phylogenetic analyses and a survey of pharyngeal jaw functional morphology that allow us to examine the evolution of pharyngognathy in a historical context. Phylogenetic analyses were based on a sample of 188 acanthomorph (spiny-rayed fish) species, primarily percomorphs (perch-like fishes), and DNA sequence data collected from 10 nuclear loci that have been previously used to resolve higher level ray-finned fish relationships. Phylogenies inferred from this dataset using maximum likelihood, Bayesian, and species tree analyses indicate polyphyly of the traditional Labroidei and clearly separate Labridae from the remainder of the traditional labroid lineages (Cichlidae, Embiotocidae, and Pomacentridae). These three "chromide" families grouped within a newly discovered clade of 40 families and more than 4800 species (>27% of percomorphs and >16% of all ray-finned fishes), which we name Ovalentaria for its characteristic demersal, adhesive eggs with chorionic filaments. This fantastically diverse clade includes some of the most species-rich lineages of marine and freshwater fishes, including all representatives of the Cichlidae, Embiotocidae, Pomacentridae, Ambassidae, Gobiesocidae, Grammatidae, Mugilidae, Opistognathidae, Pholidichthyidae, Plesiopidae (including Notograptus), Polycentridae, Pseudochromidae, Atherinomorpha, and Blennioidei. Beyond the discovery of Ovalentaria, this study provides a surprising, but well-supported, hypothesis for a convict-blenny (Pholidichthys) sister group to the charismatic cichlids and new insights into the evolution of pharyngognathy. Bayesian stochastic mapping ancestral state reconstructions indicate that pharyngognathy has evolved at least six times in percomorphs, including four separate origins in members of the former Labroidei, one origin in the Centrogenyidae, and one origin within Beloniformes. Our analyses indicate that all pharyngognathous fishes have a mechanically efficient biting mechanism enabled by the muscular sling and a single lower jaw element. However, a major distinction exists between Labridae, which lacks the widespread, generalized percomorph pharyngeal biting mechanism, and all other pharyngognathous clades, which possess this generalized biting mechanism in addition to pharyngognathy. Our results reveal a remarkable history of pharyngognathy: far from a single origin, it appears to have evolved at least six times, and its status as a major evolutionary innovation is reinforced by it being a synapomorphy for several independent major radiations, including some of the most species rich and ecologically diverse percomorph clades of coral reef and tropical freshwater fishes, Labridae and Cichlidae. [Acanthomorpha; Beloniformes; Centrogenyidae; key innovation; Labroidei; Ovalentaria; pharyngeal jaws; Perciformes.].
Collapse
Affiliation(s)
- Peter C Wainwright
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Eytan RI, Hastings PA, Holland BR, Hellberg ME. Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria). Mol Phylogenet Evol 2011; 62:159-73. [PMID: 22040767 DOI: 10.1016/j.ympev.2011.09.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/18/2011] [Accepted: 09/19/2011] [Indexed: 10/16/2022]
Abstract
Neotropical reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three rocky and coral reef fish families largely endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich and is characterized by elaborate spinous processes on the skull. Here we construct a species tree using five nuclear markers and compare the results to those from Bayesian and parsimony phylogenetic analyses of 60 morphological characters. The sequence-based species tree conflicted with the morphological phylogenies for Acanthemblemaria, primarily due to the convergence of a suite of characters describing the distribution of spines on the head. However, we were able to resolve some of these conflicts by performing phylogenetic analyses on suites of characters not associated with head spines. By using the species tree as a guide, we used a quantitative method to identify suites of correlated morphological characters that, together, produce the distinctive skull phenotypes found in these fishes. A time calibrated phylogeny with nearly complete taxon sampling provided divergence time estimates that recovered a mid-Miocene origin for the genus, with a temporally and geographically complex pattern of speciation both before and after the closure of the Isthmus of Panama. Some sister taxa are broadly sympatric, but many occur in allopatry. The ability to infer the geography of speciation in Acanthemblemaria is complicated by extinctions, incomplete knowledge of their present geographic ranges and by wide-spread taxa that likely represent cryptic species complexes.
Collapse
Affiliation(s)
- Ron I Eytan
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | | | | |
Collapse
|
18
|
Eytan RI, Hellberg ME. Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes. Evolution 2011; 64:3380-97. [PMID: 20584072 DOI: 10.1111/j.1558-5646.2010.01071.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species' Caribbean ranges. Although both species shared a similar pattern of genetic subdivision, A. spinosa had 20-25 times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fish.
Collapse
Affiliation(s)
- Ron I Eytan
- Department of Biological Sciences, 107 Life Sciences Building, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
| | | |
Collapse
|
19
|
Xue Q, Hellberg ME, Schey KL, Itoh N, Eytan RI, Cooper RK, La Peyre JF. A new lysozyme from the eastern oyster, Crassostrea virginica, and a possible evolutionary pathway for i-type lysozymes in bivalves from host defense to digestion. BMC Evol Biol 2010; 10:213. [PMID: 20633278 PMCID: PMC3020801 DOI: 10.1186/1471-2148-10-213] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 07/15/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Lysozymes are enzymes that lyse bacterial cell walls, an activity widely used for host defense but also modified in some instances for digestion. The biochemical and evolutionary changes between these different functional forms has been well-studied in the c-type lysozymes of vertebrates, but less so in the i-type lysozymes prevalent in most invertebrate animals. Some bivalve molluscs possess both defensive and digestive lysozymes. RESULTS We report a third lysozyme from the oyster Crassostrea virginica, cv-lysozyme 3. The chemical properties of cv-lysozyme 3 (including molecular weight, isoelectric point, basic amino acid residue number, and predicted protease cutting sites) suggest it represents a transitional form between lysozymes used for digestion and immunity. The cv-lysozyme 3 protein inhibited the growth of bacteria (consistent with a defensive function), but semi-quantitative RT-PCR suggested the gene was expressed mainly in digestive glands. Purified cv-lysozyme 3 expressed maximum muramidase activity within a range of pH (7.0 and 8.0) and ionic strength (I = 0.005-0.01) unfavorable for either cv-lysozyme 1 or cv-lysozyme 2 activities. The topology of a phylogenetic analysis of cv-lysozyme 3 cDNA (full length 663 bp, encoding an open reading frame of 187 amino acids) is also consistent with a transitional condition, as cv-lysozyme 3 falls at the base of a monophyletic clade of bivalve lysozymes identified from digestive glands. Rates of nonsynonymous substitution are significantly high at the base of this clade, consistent with an episode of positive selection associated with the functional transition from defense to digestion. CONCLUSION The pattern of molecular evolution accompanying the shift from defensive to digestive function in the i-type lysozymes of bivalves parallels those seen for c-type lysozymes in mammals and suggests that the lysozyme paralogs that enhance the range of physiological conditions for lysozyme activity may provide stepping stones between defensive and digestive forms.
Collapse
Affiliation(s)
- Qinggang Xue
- Department of Veterinary Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70830, USA
| | - Michael E Hellberg
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kevin L Schey
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston, SC 29425, USA
- Mass Spectrometry Center, Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Naoki Itoh
- Department of Veterinary Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70830, USA
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiya-machi, Aoba-ku, Sendai 981-8555 Miyagi, Japan
| | - Ron I Eytan
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Richard K Cooper
- Department of Veterinary Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70830, USA
| | - Jerome F La Peyre
- Department of Veterinary Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70830, USA
| |
Collapse
|
20
|
Hayes ML, Eytan RI, Hellberg ME. High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2). BMC Evol Biol 2010; 10:150. [PMID: 20482872 PMCID: PMC2880987 DOI: 10.1186/1471-2148-10-150] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 05/19/2010] [Indexed: 12/22/2022] Open
Abstract
Background Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef. Here, we examine variation in and selection on a putative innate immunity gene from Oculina, a coral genus previously used as a model for studies of coral disease and bleaching. Results In a survey of 244 Oculina alleles, we find high nonsynonymous variation and a signature of positive selection, consistent with a putative role in immunity. Using computational protein structure prediction, we generate a structural model of the Oculina protein that closely matches the known structure of tachylectin-2 from the Japanese horseshoe crab (Tachypleus tridentatus), a protein with demonstrated function in microbial recognition and agglutination. We also demonstrate that at least three other genera of anthozoan cnidarians (Acropora, Montastrea and Nematostella) possess proteins structurally similar to tachylectin-2. Conclusions Taken together, the evidence of high amino acid diversity, positive selection and structural correspondence to the horseshoe crab tachylectin-2 suggests that this protein is 1) part of Oculina's innate immunity repertoire, and 2) evolving adaptively, possibly under selective pressure from coral-associated microorganisms. Tachylectin-2 may serve as a candidate locus to screen coral populations for their capacity to respond adaptively to future environmental change.
Collapse
Affiliation(s)
- Marshall L Hayes
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | | | | |
Collapse
|