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Cachera M, Le Loc'h F. Assessing the relationships between phylogenetic and functional singularities in sharks (Chondrichthyes). Ecol Evol 2017; 7:6292-6303. [PMID: 28861233 PMCID: PMC5574805 DOI: 10.1002/ece3.2871] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/07/2017] [Accepted: 02/10/2017] [Indexed: 11/11/2022] Open
Abstract
The relationships between diversity and ecosystem functioning have become a major focus of science. A crucial issue is to estimate functional diversity, as it is intended to impact ecosystem dynamics and stability. However, depending on the ecosystem, it may be challenging or even impossible to directly measure ecological functions and thus functional diversity. Phylogenetic diversity was recently under consideration as a proxy for functional diversity. Phylogenetic diversity is indeed supposed to match functional diversity if functions are conservative traits along evolution. However, in case of adaptive radiation and/or evolutive convergence, a mismatch may appear between species phylogenetic and functional singularities. Using highly threatened taxa, sharks, this study aimed to explore the relationships between phylogenetic and functional diversities and singularities. Different statistical computations were used in order to test both methodological issue (phylogenetic reconstruction) and overall a theoretical questioning: the predictive power of phylogeny for function diversity. Despite these several methodological approaches, a mismatch between phylogeny and function was highlighted. This mismatch revealed that (i) functions are apparently nonconservative in shark species, and (ii) phylogenetic singularity is not a proxy for functional singularity. Functions appeared to be not conservative along the evolution of sharks, raising the conservational challenge to identify and protect both phylogenetic and functional singular species. Facing the current rate of species loss, it is indeed of major importance to target phylogenetically singular species to protect genetic diversity and also functionally singular species in order to maintain particular functions within ecosystem.
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Affiliation(s)
- Marie Cachera
- SHOMBrest Cedex 2France
- UMR LEMAR CNRS/UBO/IRD/Ifremer, IUEM, Rue Dumont d'Urville, Technopôle Brest IroisePlouzanéFrance
| | - François Le Loc'h
- UMR LEMAR CNRS/UBO/IRD/Ifremer, IUEM, Rue Dumont d'Urville, Technopôle Brest IroisePlouzanéFrance
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52
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Read TD, Petit RA, Joseph SJ, Alam MT, Weil MR, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb DH, Tan M, Dove ADM. Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828. BMC Genomics 2017; 18:532. [PMID: 28709399 PMCID: PMC5513125 DOI: 10.1186/s12864-017-3926-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. RESULTS We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. CONCLUSIONS This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.
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Affiliation(s)
- Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Robert A Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Sandeep J Joseph
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Md Tauqeer Alam
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - M Ryan Weil
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Maida Ahmad
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Ravila Bhimani
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Jocelyn S Vuong
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Chad P Haase
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - D Harry Webb
- , Georgia Aquarium, 225 Baker Street, Atlanta, GA, 30313, USA
| | - Milton Tan
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA. .,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
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53
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Trypanorhynch Assemblages Indicate Ecological and Phylogenetical Attributes of Their Elasmobranch Final Hosts. FISHES 2017. [DOI: 10.3390/fishes2020008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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54
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Kryukova NV. Functional analysis of the musculo-skeletal system of the gill apparatus in Heptranchias perlo (Chondrichthyes: Hexanchidae). J Morphol 2017; 278:1075-1090. [PMID: 28470783 DOI: 10.1002/jmor.20695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 03/15/2017] [Accepted: 04/13/2017] [Indexed: 11/09/2022]
Abstract
Musculo-skeletal morphology is an indispensable source for understanding functional adaptations. Analysis of morphology of the branchial apparatus of Hexanchiform sharks can provide insight into aspects of their respiration that are difficult to observe directly. In this study, I compare the structure of the musculo-skeletal system of the gill apparatus of Heptranchias perlo and Squalus acanthias in respect to their adaptation for one of two respiratory mechanisms known in sharks, namely, the active two-pump (oropharyngeal and parabranchial) ventilation and the ram-jet ventilation. In both species, the oropharyngeal pump possesses two sets of muscles, one for compression and the other for expansion. The parabranchial pump only has constrictors. Expansion of this pump occurs only due to passive elastic recoil of the extrabranchial cartilages. In Squalus acanthias the parabranchial chambers are large and equipped by powerful superficial constrictors. These muscles and the outer walls of the parabranchial chambers are much reduced in Heptranchias perlo, and thus it likely cannot use this pump. However, this reduction allows for vertical elongation of outer gill slits which, along with greater number of gill pouches, likely decreases branchial resistance and, at the same time, increases the gill surface area, and can be regarded as an adaptation for ram ventilation at lower speeds.
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Affiliation(s)
- Nadezhda V Kryukova
- Laboratory of morphological adaptations of vertebrates, Severtsov Institute of Ecology and Evolution, RAS, Moscow, 119071, Russia
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55
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Larouche O, Zelditch ML, Cloutier R. Fin modules: an evolutionary perspective on appendage disparity in basal vertebrates. BMC Biol 2017; 15:32. [PMID: 28449681 PMCID: PMC5406925 DOI: 10.1186/s12915-017-0370-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fishes are extremely speciose and also highly disparate in their fin configurations, more specifically in the number of fins present as well as their structure, shape, and size. How they achieved this remarkable disparity is difficult to explain in the absence of any comprehensive overview of the evolutionary history of fish appendages. Fin modularity could provide an explanation for both the observed disparity in fin configurations and the sequential appearance of new fins. Modularity is considered as an important prerequisite for the evolvability of living systems, enabling individual modules to be optimized without interfering with others. Similarities in developmental patterns between some of the fins already suggest that they form developmental modules during ontogeny. At a macroevolutionary scale, these developmental modules could act as evolutionary units of change and contribute to the disparity in fin configurations. This study addresses fin disparity in a phylogenetic perspective, while focusing on the presence/absence and number of each of the median and paired fins. RESULTS Patterns of fin morphological disparity were assessed by mapping fin characters on a new phylogenetic supertree of fish orders. Among agnathans, disparity in fin configurations results from the sequential appearance of novel fins forming various combinations. Both median and paired fins would have appeared first as elongated ribbon-like structures, which were the precursors for more constricted appendages. Among chondrichthyans, disparity in fin configurations relates mostly to median fin losses. Among actinopterygians, fin disparity involves fin losses, the addition of novel fins (e.g., the adipose fin), and coordinated duplications of the dorsal and anal fins. Furthermore, some pairs of fins, notably the dorsal/anal and pectoral/pelvic fins, show non-independence in their character distribution, supporting expectations based on developmental and morphological evidence that these fin pairs form evolutionary modules. CONCLUSIONS Our results suggest that the pectoral/pelvic fins and the dorsal/anal fins form two distinct evolutionary modules, and that the latter is nested within a more inclusive median fins module. Because the modularity hypotheses that we are testing are also supported by developmental and variational data, this constitutes a striking example linking developmental, variational, and evolutionary modules.
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Affiliation(s)
- Olivier Larouche
- Laboratoire de Paléontologie et de Biologie évolutive, Université du Québec à Rimouski, Rimouski, Québec G5L 3A1 Canada
| | | | - Richard Cloutier
- Laboratoire de Paléontologie et de Biologie évolutive, Université du Québec à Rimouski, Rimouski, Québec G5L 3A1 Canada
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56
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Abstract
Thelodonts are an enigmatic group of Paleozoic jawless vertebrates that have been well studied from taxonomical, biostratigraphic and paleogeographic points of view, although our knowledge of their ecology and mode of life is still scant. Their bodies were covered by micrometric scales whose morphology, histology and the developmental process are extremely similar to those of extant sharks. Based on these similarities and on the well-recognized relationship between squamation and ecology in sharks, here we explore the ecological diversity and lifestyles of thelodonts. For this we use classic morphometrics and discriminant analysis to characterize the squamation patterns of a significant number of extant shark species whose ecology is well known. Multivariate analyses have defined a characteristic squamation pattern for each ecological group, thus establishing a comparative framework for inferring lifestyles in thelodonts. We then use this information to study the squamation of the currently described 147 species of thelodonts, known from both articulated and disarticulated remains. Discriminant analysis has allowed recognizing squamation patterns comparable to those of sharks and links them to specific ecological groups. Our results suggest a remarkable ecological diversity in thelodonts. A large number of them were probably demersal species inhabiting hard substrates, within caves and crevices in rocky environments or reefs, taking advantage of the flexibility provided by their micromeric squamations. Contrary to classical interpretations, only few thelodonts were placed among demersal species inhabiting sandy and muddy substrates. Schooling species with defensive scales against ectoparasites could be also abundant suggesting that social interactions and pressure of ectoparasites were present in vertebrates as early the Silurian. The presence of species showing scales suggestive of low to moderate speed and a lifestyle presumably associated with open water environments indicates adaptation of thelodonts to deep water habitats. Scale morphology suggests that some other thelodonts were strong-swimming pelagic species, most of them radiating during the Early Devonian in association with the Nekton Revolution.
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Affiliation(s)
- Humberto G. Ferrón
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Paterna, Valencia, Spain
| | - Héctor Botella
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Paterna, Valencia, Spain
- * E-mail:
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57
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Santaquiteria A, Nielsen J, Klemetsen T, Willassen NP, Præbel K. The complete mitochondrial genome of the long-lived Greenland shark (Somniosus microcephalus): characterization and phylogenetic position. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-016-0676-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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58
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Underwood C, Johanson Z, Smith MM. Cutting blade dentitions in squaliform sharks form by modification of inherited alternate tooth ordering patterns. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160385. [PMID: 28018617 PMCID: PMC5180115 DOI: 10.1098/rsos.160385] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/04/2016] [Indexed: 05/25/2023]
Abstract
The squaliform sharks represent one of the most speciose shark clades. Many adult squaliforms have blade-like teeth, either on both jaws or restricted to the lower jaw, forming a continuous, serrated blade along the jaw margin. These teeth are replaced as a single unit and successor teeth lack the alternate arrangement present in other elasmobranchs. Micro-CT scans of embryos of squaliforms and a related outgroup (Pristiophoridae) revealed that the squaliform dentition pattern represents a highly modified version of tooth replacement seen in other clades. Teeth of Squalus embryos are arranged in an alternate pattern, with successive tooth rows containing additional teeth added proximally. Asynchronous timing of tooth production along the jaw and tooth loss prior to birth cause teeth to align in oblique sets containing teeth from subsequent rows; these become parallel to the jaw margin during ontogeny, so that adult Squalus has functional tooth rows comprising obliquely stacked teeth of consecutive developmental rows. In more strongly heterodont squaliforms, initial embryonic lower teeth develop into the oblique functional sets seen in adult Squalus, with no requirement to form, and subsequently lose, teeth arranged in an initial alternate pattern.
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Affiliation(s)
- Charlie Underwood
- Department of Earth and Planetary Sciences, Birkbeck, University of London, London, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Zerina Johanson
- Department of Earth and Planetary Sciences, Birkbeck, University of London, London, UK
| | - Moya Meredith Smith
- Department of Earth and Planetary Sciences, Birkbeck, University of London, London, UK
- Dental Institute, Craniofacial Development, King's College London, London, UK
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59
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Ciezarek AG, Dunning LT, Jones CS, Noble LR, Humble E, Stefanni SS, Savolainen V. Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biol Evol 2016; 8:3011-3021. [PMID: 27614233 PMCID: PMC5630876 DOI: 10.1093/gbe/evw211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite 400–450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterized by centralization of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behavior. Here, we tested the hypothesis that their convergent evolution was driven by selection on a set of metabolic genes. We sequenced white muscle transcriptomes of six tuna, one mackerel, and three shark species, and supplemented this data set with previously published RNA-seq data. Using 26 species in total (including 7,032 tuna genes plus 1,719 shark genes), we constructed phylogenetic trees and carried out maximum-likelihood analyses of gene selection. We inferred several genes relating to metabolism to be under selection. We also found that the same one gene, glycogenin-1, evolved under positive selection independently in tunas and lamnid sharks, providing evidence of convergent selective pressures at gene level possibly underlying shared physiology.
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Affiliation(s)
- Adam G Ciezarek
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK
| | - Luke T Dunning
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK Present address: Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Catherine S Jones
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, Scotland, UK
| | - Leslie R Noble
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, Scotland, UK
| | - Emily Humble
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK Present address: Department of Animal Behaviour, University of Bielefeld, Postfach 100131, Bielefeld, Germany
| | | | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, UK
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60
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Díaz-Jaimes P, Uribe-Alcocer M, Adams DH, Rangel-Morales JM, Bayona-Vásquez NJ. Complete mitochondrial genome of the porbeagle shark, Lamna nasus (Chondrichthyes, Lamnidae). Mitochondrial DNA B Resour 2016; 1:730-731. [PMID: 33473607 PMCID: PMC7799682 DOI: 10.1080/23802359.2016.1233465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We report for the first time, the complete mitochondrial genome sequence of the porbeagle shark, Lamna nasus, from a specimen collected from offshore waters of New England, USA in the western North Atlantic Ocean. The genome structure of this species is similar to the other reported shark mitogenomes. The genome sequence has a total length of 16,697 bases; similar in size to the mtDNA genomes reported for other lamnid species. A Bayesian phylogenetic tree was reconstructed for the Lamnidae family using mitogenome sequences available in the Genbank.
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Affiliation(s)
- Píndaro Díaz-Jaimes
- Laboratorio de Genética de Organismos Acuáticos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, Ciudad de México, México
| | - Manuel Uribe-Alcocer
- Laboratorio de Genética de Organismos Acuáticos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, Ciudad de México, México
| | | | - Jose Miguel Rangel-Morales
- Posgrado en Ciencias del Mar y Limnología, Circuito exterior s/n, Ciudad Universitaria, Ciudad de México, México
| | - Natalia J Bayona-Vásquez
- Laboratorio de Genética de Organismos Acuáticos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito exterior s/n, Ciudad Universitaria, Ciudad de México, México
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61
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Mitterboeck TF, Chen AY, Zaheer OA, Ma EYT, Adamowicz SJ. Do saline taxa evolve faster? Comparing relative rates of molecular evolution between freshwater and marine eukaryotes. Evolution 2016; 70:1960-78. [PMID: 27402284 DOI: 10.1111/evo.13000] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 05/24/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022]
Abstract
The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline versus freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein-coding and noncoding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein-coding genes in freshwater taxa-the comparisons mainly involving bony fish-compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.
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Affiliation(s)
- T Fatima Mitterboeck
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada. .,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| | - Alexander Y Chen
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Omar A Zaheer
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Eddie Y T Ma
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,School of Computer Science, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Sarah J Adamowicz
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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62
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Smith WL, Stern JH, Girard MG, Davis MP. Evolution of Venomous Cartilaginous and Ray-Finned Fishes. Integr Comp Biol 2016; 56:950-961. [DOI: 10.1093/icb/icw070] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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63
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Rodríguez C, Fernández B, Olivero J, Salmerón F, Torres-Prioris A, Sans-Coma V, Durán AC. The relative length of the cardiac bulbus arteriosus reflects phylogenetic relationships among elasmobranchs. ZOOL ANZ 2016. [DOI: 10.1016/j.jcz.2016.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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64
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Davis MP, Sparks JS, Smith WL. Repeated and Widespread Evolution of Bioluminescence in Marine Fishes. PLoS One 2016; 11:e0155154. [PMID: 27276229 PMCID: PMC4898709 DOI: 10.1371/journal.pone.0155154] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 04/25/2016] [Indexed: 11/20/2022] Open
Abstract
Bioluminescence is primarily a marine phenomenon with 80% of metazoan bioluminescent genera occurring in the world's oceans. Here we show that bioluminescence has evolved repeatedly and is phylogenetically widespread across ray-finned fishes. We recover 27 independent evolutionary events of bioluminescence, all among marine fish lineages. This finding indicates that bioluminescence has evolved many more times than previously hypothesized across fishes and the tree of life. Our exploration of the macroevolutionary patterns of bioluminescent lineages indicates that the present day diversity of some inshore and deep-sea bioluminescent fish lineages that use bioluminescence for communication, feeding, and reproduction exhibit exceptional species richness given clade age. We show that exceptional species richness occurs particularly in deep-sea fishes with intrinsic bioluminescent systems and both shallow water and deep-sea lineages with luminescent systems used for communication.
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Affiliation(s)
- Matthew P. Davis
- St. Cloud State University, St. Cloud, MN 56301, United States of America
| | - John S. Sparks
- American Museum of Natural History, New York, NY 10024, United States of America
| | - W. Leo Smith
- University of Kansas, Lawrence, KS 66045, United States of America
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65
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Gruber DF, Loew ER, Deheyn DD, Akkaynak D, Gaffney JP, Smith WL, Davis MP, Stern JH, Pieribone VA, Sparks JS. Biofluorescence in Catsharks (Scyliorhinidae): Fundamental Description and Relevance for Elasmobranch Visual Ecology. Sci Rep 2016; 6:24751. [PMID: 27109385 PMCID: PMC4843165 DOI: 10.1038/srep24751] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/05/2016] [Indexed: 01/01/2023] Open
Abstract
Biofluorescence has recently been found to be widespread in marine fishes, including sharks. Catsharks, such as the Swell Shark (Cephaloscyllium ventriosum) from the eastern Pacific and the Chain Catshark (Scyliorhinus retifer) from the western Atlantic, are known to exhibit bright green fluorescence. We examined the spectral sensitivity and visual characteristics of these reclusive sharks, while also considering the fluorescent properties of their skin. Spectral absorbance of the photoreceptor cells in these sharks revealed the presence of a single visual pigment in each species. Cephaloscyllium ventriosum exhibited a maximum absorbance of 484 ± 3 nm and an absorbance range at half maximum (λ1/2max) of 440-540 nm, whereas for S. retifer maximum absorbance was 488 ± 3 nm with the same absorbance range. Using the photoreceptor properties derived here, a "shark eye" camera was designed and developed that yielded contrast information on areas where fluorescence is anatomically distributed on the shark, as seen from other sharks' eyes of these two species. Phylogenetic investigations indicate that biofluorescence has evolved at least three times in cartilaginous fishes. The repeated evolution of biofluorescence in elasmobranchs, coupled with a visual adaptation to detect it; and evidence that biofluorescence creates greater luminosity contrast with the surrounding background, highlights the potential importance of biofluorescence in elasmobranch behavior and biology.
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Affiliation(s)
- David F. Gruber
- Baruch College, City University of New York, Department of Natural Sciences, New York, NY 10010, USA
- City University of New York, The Graduate Center, Program in Biology, New York, NY 10016, USA
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY 10024, USA
| | - Ellis R. Loew
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Dimitri D. Deheyn
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Derya Akkaynak
- University of Haifa, Charney School of Marine Sciences, Haifa, 3498838, Israel
- Interuniversity Institute of Marine Sciences, Eilat, 88103, Israel
| | - Jean P. Gaffney
- Baruch College, City University of New York, Department of Natural Sciences, New York, NY 10010, USA
| | - W. Leo Smith
- University of Kansas, Biodiversity Institute and Department of Ecology and Evolutionary Biology, Lawrence, KS 66049, USA
| | - Matthew P. Davis
- St. Cloud State University, Department of Biological Sciences, St. Cloud, MN 56301, USA
| | - Jennifer H. Stern
- University of Kansas, Biodiversity Institute and Department of Ecology and Evolutionary Biology, Lawrence, KS 66049, USA
| | - Vincent A. Pieribone
- The John B. Pierce Laboratory, Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - John S. Sparks
- American Museum of Natural History, Sackler Institute for Comparative Genomics, New York, NY 10024, USA
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Ichthyology, New York, NY 10024, USA
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Chen H, Yu J, Si R, Chen X, Ai W. Complete mitochondrial genome and the phylogenetic position of the graceful catshark Proscyllium habereri (Carcharhiniformes: Proscylliidae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:268-269. [PMID: 33473469 PMCID: PMC7799998 DOI: 10.1080/23802359.2016.1159934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this study, the complete mitogenome of Proscyllium habereri (Carcharhiniformes: Proscylliidae) is first determined. It is 16,708 bp in length, containing 37 genes with typical order to that of most other vertebrates. Its overall base composition of the H-strand is A 30.9%; C 23.7%; G 14.2%; T 31.2%. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) are found in the protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Cys, tRNA-Ser2) to 75 bp (tRNA-Leu1). The phylogenetic result showed that P. habereri was clustered to Pseudotriakis microdon.
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Affiliation(s)
- Hao Chen
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Junqi Yu
- Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, PR China
| | - Ranran Si
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xiao Chen
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Weiming Ai
- Department of Marine Biotechnology, School of Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
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Díaz-Jaimes P, Bayona-Vásquez NJ, Adams DH, Uribe-Alcocer M. Complete mitochondrial DNA genome of bonnethead shark, Sphyrna tiburo, and phylogenetic relationships among main superorders of modern elasmobranchs. Meta Gene 2016; 7:48-55. [PMID: 27014583 PMCID: PMC4794228 DOI: 10.1016/j.mgene.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 11/30/2022] Open
Abstract
Elasmobranchs are one of the most diverse groups in the marine realm represented by 18 orders, 55 families and about 1200 species reported, but also one of the most vulnerable to exploitation and to climate change. Phylogenetic relationships among main orders have been controversial since the emergence of the Hypnosqualean hypothesis by Shirai (1992) that considered batoids as a sister group of sharks. The use of the complete mitochondrial DNA (mtDNA) may shed light to further validate this hypothesis by increasing the number of informative characters. We report the mtDNA genome of the bonnethead shark Sphyrna tiburo, and compare it with mitogenomes of other 48 species to assess phylogenetic relationships. The mtDNA genome of S. tiburo, is quite similar in size to that of congeneric species but also similar to the reported mtDNA genome of other Carcharhinidae species. Like most vertebrate mitochondrial genomes, it contained 13 protein coding genes, two rRNA genes and 22 tRNA genes and the control region of 1086 bp (D-loop). The Bayesian analysis of the 49 mitogenomes supported the view that sharks and batoids are separate groups.
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Key Words
- ATP, Adenosine triphosphate
- Bonnethead
- CO, Cytochrome oxidase
- Cytb, Cytochrome B
- D-loop, Control region
- Hypnosqualea hypothesis
- ML, Maximum likelihood
- Mitogenome
- ND, Nicotine adenine dehydrogenase
- PCR, Polymerase chain reaction
- Phylogeny
- bp, Base pairs
- mt, Mitochondrial
- myr, Million years
- rRNA, Ribosomal RNA
- tRNA, Transference RNA
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Affiliation(s)
- Píndaro Díaz-Jaimes
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Natalia J. Bayona-Vásquez
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
| | - Douglas H. Adams
- Florida Fish and Wildlife Conservation Commission, Fish and
Wildlife Research Institute, 1220 Prospect Avenue, Suite 285, Melbourne, FL
32901, USA
| | - Manuel Uribe-Alcocer
- Laboratorio de Genética de Organismos Acuáticos, Instituto de
Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Apdo.
Postal 70-305, México D.F. 04510, Mexico
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Fanti F, Minelli D, Conte GL, Miyashita T. An exceptionally preserved Eocene shark and the rise of modern predator-prey interactions in the coral reef food web. ZOOLOGICAL LETTERS 2016; 2:9. [PMID: 27042332 PMCID: PMC4818435 DOI: 10.1186/s40851-016-0045-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/22/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Following extreme climatic warming events, Eocene Lagerstätten document aquatic and terrestrial vertebrate faunas surprisingly similar to modern counterparts. This transition in marine systems is best documented in the earliest teleost-dominated coral reef assemblage of Pesciara di Bolca, northern Italy, from near the end of the Eocene Climatic Optimum. Its rich fauna shows similarities with that of the modern Great Barrier Reef in niche exploitation by and morphological disparity among teleost primary consumers. However, such paleoecological understanding has not transcended trophic levels above primary consumers, particularly in carcharhiniform sharks. RESULTS We report an exceptionally preserved fossil school shark (Galeorhinus cuvieri) from Pesciara di Bolca. In addition to the spectacular preservation of soft tissues, including brain, muscles, and claspers, this male juvenile shark has stomach contents clearly identifiable as a sphyraenid acanthomorph (barracuda). This association provides evidence that a predator-prey relationship between Galeorhinus and Sphyraena in the modern coral reefs has roots in the Eocene. A growth curve of the living species of Galeorhinus fitted to G. cuvieri suggests that all specimens of G. cuvieri from the lagoonal deposits of Bolca represent sexually and somatically immature juveniles. CONCLUSION The modern trophic association between higher-degree consumers (Galeorhinus and Sphyraena) has a counterpart in the Eocene Bolca, just as Bolca and the Great Barrier Reef show parallels among teleost primary consumers. Given the age of Bolca, trophic networks among consumers observed in modern coral reefs arose by the exit from the Climatic Optimum. The biased representation of juveniles suggests that the Bolca Lagerstätte served as a nursery habitat for G. cuvieri. Ultraviolet photography may be useful in probing for exceptional soft tissue preservation before common acid preparation methods.
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Affiliation(s)
- Federico Fanti
- />Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Alma Mater Studiorum, Università di Bologna, Via Zamboni 67, Bologna, 40126 Italy
- />Museo Geologico Giovanni Capellini, Alma Mater Studiorum, Università di Bologna, Via Zamboni 63, Bologna, 40126 Italy
| | - Daniela Minelli
- />Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Alma Mater Studiorum, Università di Bologna, Via Zamboni 67, Bologna, 40126 Italy
| | - Gabriele Larocca Conte
- />Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Alma Mater Studiorum, Università di Bologna, Via Zamboni 67, Bologna, 40126 Italy
| | - Tetsuto Miyashita
- />Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9 Canada
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69
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da Silva JPCB, Vaz DFB, de Carvalho MR. Systematic Implications of the Anterior Pectoral Basals in Squaliform Sharks (Chondrichthyes: Elasmobranchii). COPEIA 2015. [DOI: 10.1643/ci-14-138] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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70
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The shark panel: An InDel multiplex for shark species identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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71
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Bowden DL, Vargas-Caro C, Ovenden JR, Bennett MB, Bustamante C. The phylogenomic position of the grey nurse shark Carcharias taurus Rafinesque, 1810 (Lamniformes, Odontaspididae) inferred from the mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4328-4330. [PMID: 26462847 DOI: 10.3109/19401736.2015.1089486] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the grey nurse shark Carcharias taurus is described from 25 963 828 sequences obtained using Illumina NGS technology. Total length of the mitogenome is 16 715 bp, consisting of 2 rRNAs, 13 protein-coding regions, 22 tRNA and 2 non-coding regions thus updating the previously published mitogenome for this species. The phylogenomic reconstruction inferred from the mitogenome of 15 species of Lamniform and Carcharhiniform sharks supports the inclusion of C. taurus in a clade with the Lamnidae and Cetorhinidae. This complete mitogenome contributes to ongoing investigation into the monophyly of the Family Odontaspididae.
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Affiliation(s)
- Deborah L Bowden
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
| | - Carolina Vargas-Caro
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
| | - Jennifer R Ovenden
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
| | | | - Carlos Bustamante
- a Shark and Ray Research Group and.,b Molecular Fisheries Laboratory, School of Biomedical Sciences, the University of Queensland , Queensland , St Lucia , Australia
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72
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Veron S, Davies TJ, Cadotte MW, Clergeau P, Pavoine S. Predicting loss of evolutionary history: Where are we? Biol Rev Camb Philos Soc 2015; 92:271-291. [PMID: 26467982 DOI: 10.1111/brv.12228] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/29/2023]
Abstract
The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.
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Affiliation(s)
- Simon Veron
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - T Jonathan Davies
- Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, Quebec H3A 1B1, Canada.,African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Marc W Cadotte
- Department of Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Philippe Clergeau
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France.,Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, U.K
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73
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Wang J, Chen H, Lin L, Ai W, Chen X. Mitochondrial genome and phylogenetic position of the sliteye shark Loxodon macrorhinus. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4288-4289. [PMID: 26404413 DOI: 10.3109/19401736.2015.1082099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The sliteye shark Loxodon macrorhinus is the only member of the genus Loxodon in the family Carcharhinidae. In this study, we first present the complete mitochondrial genome of L. macrorhinus and determine its phylogenetic position within Carcharhinidae based on relative mitogenomes. The mitochondrial genome was 16 702 bp in length with the typical gene order in vertebrates. The overall base composition of the H-strand was 31.7% A, 25.8% C, 13.1% G, and 29.4% T. Two start codons (ATG and GTG) and three stop codons (TAG, AGG, and TAA/T) were found in the protein-coding genes. The tRNA genes ranged from 67 bp to 75 bp. Loxodon macrorhinus was placed as sister to the genus Scoliodon in the Bayesian tree.
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Affiliation(s)
- Junjie Wang
- a Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences , Guangzhou , Guangdong , PR China and
| | - Hao Chen
- b Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhu , Zhejiang , PR China
| | - Lingling Lin
- b Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhu , Zhejiang , PR China
| | - Weiming Ai
- b Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhu , Zhejiang , PR China
| | - Xiao Chen
- b Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhu , Zhejiang , PR China
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74
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Chen H, Kishino H. Global pattern of phylogenetic species composition of shark and its conservation priority. Ecol Evol 2015; 5:4455-65. [PMID: 26819704 PMCID: PMC4667821 DOI: 10.1002/ece3.1724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/28/2015] [Accepted: 08/22/2015] [Indexed: 11/21/2022] Open
Abstract
The diversity of marine communities is in striking contrast with the diversity of terrestrial communities. In all oceans, species richness is low in tropical areas and high at latitudes between 20 and 40°. While species richness is a primary metric used in conservation and management strategies, it is important to take into account the complex phylogenetic patterns of species compositions within communities. We measured the phylogenetic skew and diversity of shark communities throughout the world. We found that shark communities in tropical seas were highly phylogenetically skewed, whereas temperate sea communities had phylogenetically diversified species compositions. Interestingly, although geographically distant from one another, tropical sea communities were all highly skewed toward requiem sharks (Carcharhinidae), hammerhead sharks (Sphyrnidae), and whale sharks (Rhincodon typus). Worldwide, the greatest phylogenetic evenness in terms of clades was found in the North Sea and coastal regions of countries in temperate zones, such as the United Kingdom, Ireland, southern Australia, and Chile. This study is the first to examine patterns of phylogenetic diversity of shark communities on a global scale. Our findings suggest that when establishing conservation activities, it is important to take full account of phylogenetic patterns of species composition and not solely use species richness as a target. Protecting areas of high phylogenetic diversity in sharks, which were identified in this study, could form a broader strategy for protecting other threatened marine species.
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Affiliation(s)
- Hungyen Chen
- National Research Institute of Fisheries ScienceFisheries Research AgencyKanagawa236-8648Japan; Graduate School of Agricultural and Life SciencesThe University of TokyoTokyo113-8657Japan
| | - Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences The University of Tokyo Tokyo 113-8657 Japan
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75
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Straube N, Li C, Claes JM, Corrigan S, Naylor GJP. Molecular phylogeny of Squaliformes and first occurrence of bioluminescence in sharks. BMC Evol Biol 2015; 15:162. [PMID: 26277575 PMCID: PMC4537554 DOI: 10.1186/s12862-015-0446-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/04/2015] [Indexed: 11/25/2022] Open
Abstract
Background Squaliform sharks represent approximately 27 % of extant shark diversity, comprising more than 130 species with a predominantly deep-dwelling lifestyle. Many Squaliform species are highly specialized, including some that are bioluminescent, a character that is reported exclusively from Squaliform sharks within Chondrichthyes. The interfamiliar relationships within the order are still not satisfactorily resolved. Herein we estimate the phylogenetic interrelationships of a generic level sampling of “squaloid” sharks and closely related taxa using aligned sequences derived from a targeted gene capture approach. The resulting phylogenetic estimate is further used to evaluate the age of first occurrence of bioluminescence in Squaliformes. Results Our dataset comprised 172 putative ortholog exon sequences. Phylogenetic estimates result in a fully resolved tree supporting a monophyletic lineage of Squaliformes excluding Echinorhinus. Non-luminous Squalidae are inferred to be the sister to a clade comprising all remaining Squaliform families. Our results suggest that the origin of photophores is coincident with an elevated diversification rate and the splitting of families Dalatiidae, Etmopteridae, Oxynotidae and Somniosidae at the transition of the Lower to the Upper Cretaceous. The presence of luminous organs was confirmed for the Sleeper shark genus Zameus. These results indicate that bioluminescence in sharks is not restricted solely to the families Etmopteridae and Dalatiidae as previously believed. Conclusions The sister-clade to non-luminous Squalidae comprises five families. The presence of photophores is reported for extant members of three out of these five families based on results of this study, i.e. Lantern sharks (Etmopteridae), Kitefin sharks (Dalatiidae) and Sleeper sharks (Somniosidae). Our results suggest that the origin of luminous organs arose during the rapid diversification event that gave rise to the extant Squaliform families. These inferences are consistent with the idea of diversification of Squaliform sharks being associated with the emergence of new deep-sea habitats in the Lower Cretaceous, which may have been facilitated by the evolution of bioluminescence. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0446-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas Straube
- Friedrich Schiller Universität Jena, Leutragraben 1, 07743, Jena, Germany. .,Hollings Marine Laboratory, 331 Fort Johnson Rd, Charleston, SC, 29412, USA. .,Bavarian State Collection of Zoology, Münchhausenstraße 21, 81247, Munich, Germany.
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306, China.
| | - Julien M Claes
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, Kellner building, 3 Place Croix du Sud - bte L7.06.04, 1348, Louvain-la-Neuve, Belgium.
| | - Shannon Corrigan
- Hollings Marine Laboratory, 331 Fort Johnson Rd, Charleston, SC, 29412, USA.
| | - Gavin J P Naylor
- Hollings Marine Laboratory, 331 Fort Johnson Rd, Charleston, SC, 29412, USA.
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76
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Chen H, Lin L, Chen X, Ai W, Chen S. Complete mitochondrial genome and the phylogenetic position of the Blotchy swell shark Cephaloscyllium umbratile. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3045-7. [PMID: 26258506 DOI: 10.3109/19401736.2015.1063127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, the complete mitochondrial genome of the Blotchy swell shark Cephaloscyllium umbratile was determined. It was a circle molecular (16 698 bp), contained 37 genes with typical order to that of most other vertebrates. The nucleotide composition was 31.0% A, 24.0% C, 14.0% G, and 31.3% T. There were 26 bp short intergenic spaces located in 11 gene junctions and 28 bp overlaps located in 7 gene junctions in the whole mitogenome. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The phylogenetic result showed that C. umbratile was clustered with Scyliorhinus canicula and formed the Scyliorhinidae clade, which was the most basal clade within Carcharhiniformes, and Carcharhinidae is not monophyletic.
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Affiliation(s)
- Hao Chen
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and
| | - Lingling Lin
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and
| | - Xiao Chen
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , Zhejiang , PR China
| | - Weiming Ai
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , Zhejiang , PR China
| | - Shaobo Chen
- a Department of Marine Biotechnology , School of Life Science, Wenzhou Medical University , Wenzhou , Zhejiang , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , Zhejiang , PR China
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77
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Newton KC, Wraith J, Dickson KA. Digestive enzyme activities are higher in the shortfin mako shark, Isurus oxyrinchus, than in ectothermic sharks as a result of visceral endothermy. FISH PHYSIOLOGY AND BIOCHEMISTRY 2015; 41:887-898. [PMID: 25893905 DOI: 10.1007/s10695-015-0055-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Lamnid sharks are regionally endothermic fishes that maintain visceral temperatures elevated above the ambient water temperature. Visceral endothermy is thought to increase rates of digestion and food processing and allow thermal niche expansion. We tested the hypothesis that, at in vivo temperatures, the endothermic shortfin mako shark, Isurus oxyrinchus, has higher specific activities of three digestive enzymes-gastric pepsin and pancreatic trypsin and lipase-than the thresher shark, Alopias vulpinus, and the blue shark, Prionace glauca, neither of which can maintain elevated visceral temperatures. Homogenized stomach or pancreas tissue obtained from sharks collected by pelagic longline was incubated at both 15 and 25 °C, at saturating substrate concentrations, to quantify tissue enzymatic activity. The mako had significantly higher enzyme activities at 25 °C than did the thresher and blue sharks at 15 °C. This difference was not a simple temperature effect, because at 25 °C the mako had higher trypsin activity than the blue shark and higher activities for all enzymes than the thresher shark. We also hypothesized that the thermal coefficient, or Q 10 value, would be higher for the mako shark than for the thresher and blue sharks because of its more stable visceral temperature. However, the mako and thresher sharks had similar Q 10 values for all enzymes, perhaps because of their closer phylogenetic relationship. The higher in vivo digestive enzyme activities in the mako shark should result in higher rates of food processing and may represent a selective advantage of regional visceral endothermy.
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Affiliation(s)
- Kyle C Newton
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd, Fullerton, CA, 92834, USA
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78
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Molecular phylogenetic convergence within Elasmobranchii revealed by cytochrome oxidase subunits. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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79
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Mu X, Wang X, Liu Y, Song H, Liu C, Gu D, Wei H, Luo J, Hu Y. An unusual mitochondrial genome structure of the tonguefish, Cynoglossus trigrammus: Control region translocation and a long additional non-coding region inversion. Gene 2015; 573:216-24. [PMID: 26187073 DOI: 10.1016/j.gene.2015.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/06/2015] [Accepted: 07/13/2015] [Indexed: 10/23/2022]
Abstract
Flatfishes (Pleuronectiformes) exhibit different types of large-scale gene rearrangements. In the present study, the mitochondrial (mt) genome (18,369bp) of a tonguefish, Cynoglossus trigrammus, was determined using de novo mitochondrion genome sequencing. Compared with other flatfishes, the mt genome of C. trigrammus revealed distinct mitogenome architectures that primarily included two striking findings: 1) insertion of an additional long non-coding region (1647bp) making it the second largest genome length among Pleuronectiformes and 2) the translocation of the control region. The reconstructed phylogenetic tree based on 13 mt protein-coding gene sequences recovered the monophyletic suborder Pleuronectoidei and the family Cynoglossidae. These data provide useful information for a better understanding of the mitogenomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xuejie Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yi Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Liu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Dangen Gu
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Hui Wei
- Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jianren Luo
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application Cultivation, Ministry of Agriculture Guangzhou, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of the Conservation and Ecological Restoration of Fishery Resource in Pearl River, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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80
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Guinot G, Cavin L. 'Fish' (Actinopterygii and Elasmobranchii) diversification patterns through deep time. Biol Rev Camb Philos Soc 2015; 91:950-981. [PMID: 26105527 DOI: 10.1111/brv.12203] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022]
Abstract
Actinopterygii (ray-finned fishes) and Elasmobranchii (sharks, skates and rays) represent more than half of today's vertebrate taxic diversity (approximately 33000 species) and form the largest component of vertebrate diversity in extant aquatic ecosystems. Yet, patterns of 'fish' evolutionary history remain insufficiently understood and previous studies generally treated each group independently mainly because of their contrasting fossil record composition and corresponding sampling strategies. Because direct reading of palaeodiversity curves is affected by several biases affecting the fossil record, analytical approaches are needed to correct for these biases. In this review, we propose a comprehensive analysis based on comparison of large data sets related to competing phylogenies (including all Recent and fossil taxa) and the fossil record for both groups during the Mesozoic-Cainozoic interval. This approach provides information on the 'fish' fossil record quality and on the corrected 'fish' deep-time phylogenetic palaeodiversity signals, with special emphasis on diversification events. Because taxonomic information is preserved after analytical treatment, identified palaeodiversity events are considered both quantitatively and qualitatively and put within corresponding palaeoenvironmental and biological settings. Results indicate a better fossil record quality for elasmobranchs due to their microfossil-like fossil distribution and their very low diversity in freshwater systems, whereas freshwater actinopterygians are diverse in this realm with lower preservation potential. Several important diversification events are identified at familial and generic levels for elasmobranchs, and marine and freshwater actinopterygians, namely in the Early-Middle Jurassic (elasmobranchs), Late Jurassic (actinopterygians), Early Cretaceous (elasmobranchs, freshwater actinopterygians), Cenomanian (all groups) and the Paleocene-Eocene interval (all groups), the latter two representing the two most exceptional radiations among vertebrates. For each of these events along with the Cretaceous-Paleogene extinction, we provide an in-depth review of the taxa involved and factors that may have influenced the diversity patterns observed. Among these, palaeotemperatures, sea-levels, ocean circulation and productivity as well as continent fragmentation and environment heterogeneity (reef environments) are parameters that largely impacted on 'fish' evolutionary history, along with other biotic constraints.
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Affiliation(s)
- Guillaume Guinot
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, Route de Malagnou 1, CP 6434, CH-1211, Geneva 6, Switzerland
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81
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Comparative analyses of animal-tracking data reveal ecological significance of endothermy in fishes. Proc Natl Acad Sci U S A 2015; 112:6104-9. [PMID: 25902489 DOI: 10.1073/pnas.1500316112] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite long evolutionary separations, several sharks and tunas share the ability to maintain slow-twitch, aerobic red muscle (RM) warmer than ambient water. Proximate causes of RM endothermy are well understood, but ultimate causes are unclear. Two advantages often proposed are thermal niche expansion and elevated cruising speeds. The thermal niche hypothesis is generally supported, because fishes with RM endothermy often exhibit greater tolerance to broad temperature ranges. In contrast, whether fishes with RM endothermy cruise faster, and achieve any ecological benefits from doing so, remains unclear. Here, we compiled data recorded by modern animal-tracking tools for a variety of free-swimming marine vertebrates. Using phylogenetically informed allometry, we show that both cruising speeds and maximum annual migration ranges of fishes with RM endothermy are 2-3 times greater than fishes without it, and comparable to nonfish endotherms (i.e., penguins and marine mammals). The estimated cost of transport of fishes with RM endothermy is twice that of fishes without it. We suggest that the high energetic cost of RM endothermy in fishes is offset by the benefit of elevated cruising speeds, which not only increase prey encounter rates, but also enable larger-scale annual migrations and potentially greater access to seasonally available resources.
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82
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Underwood CJ, Johanson Z, Welten M, Metscher B, Rasch LJ, Fraser GJ, Smith MM. Development and evolution of dentition pattern and tooth order in the skates and rays (batoidea; chondrichthyes). PLoS One 2015; 10:e0122553. [PMID: 25874547 PMCID: PMC4398376 DOI: 10.1371/journal.pone.0122553] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Shark and ray (elasmobranch) dentitions are well known for their multiple generations of teeth, with isolated teeth being common in the fossil record. However, how the diverse dentitions characteristic of elasmobranchs form is still poorly understood. Data on the development and maintenance of the dental patterning in this major vertebrate group will allow comparisons to other morphologically diverse taxa, including the bony fishes, in order to identify shared pattern characters for the vertebrate dentition as a whole. Data is especially lacking from the Batoidea (skates and rays), hence our objective is to compile data on embryonic and adult batoid tooth development contributing to ordering of the dentition, from cleared and stained specimens and micro-CT scans, with 3D rendered models. We selected species (adult and embryonic) spanning phylogenetically significant batoid clades, such that our observations may raise questions about relationships within the batoids, particularly with respect to current molecular-based analyses. We include developmental data from embryos of recent model organisms Leucoraja erinacea and Raja clavata to evaluate the earliest establishment of the dentition. Characters of the batoid dentition investigated include alternate addition of teeth as offset successional tooth rows (versus single separate files), presence of a symphyseal initiator region (symphyseal tooth present, or absent, but with two parasymphyseal teeth) and a restriction to tooth addition along each jaw reducing the number of tooth families, relative to addition of successor teeth within each family. Our ultimate aim is to understand the shared characters of the batoids, and whether or not these dental characters are shared more broadly within elasmobranchs, by comparing these to dentitions in shark outgroups. These developmental morphological analyses will provide a solid basis to better understand dental evolution in these important vertebrate groups as well as the general plesiomorphic vertebrate dental condition.
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Affiliation(s)
- Charlie J. Underwood
- Department of Earth and Planetary Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, United Kingdom
- * E-mail:
| | - Zerina Johanson
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Monique Welten
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Brian Metscher
- Department of Theoretical Biology, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Liam J. Rasch
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Gareth J. Fraser
- Department of Animal and Plant Sciences, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Moya Meredith Smith
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
- King's College London, Dental Institute, Craniofacial Development, London SE1 9RT, United Kingdom
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83
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Ferguson AR, Huber DR, Lajeunesse MJ, Motta PJ. Feeding performance of king Mackerel, Scomberomorus cavalla. ACTA ACUST UNITED AC 2015; 323:399-413. [PMID: 25845956 DOI: 10.1002/jez.1933] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 11/09/2022]
Abstract
Feeding performance is an organism's ability to capture and handle prey. Although bite force is a commonly used metric of feeding performance, other factors such as bite pressure and strike speed are also likely to affect prey capture. Therefore, this study investigated static bite force, dynamic speeds, and predator and prey forces resulting from ram strikes, as well as bite pressure of the king mackerel, Scomberomorus cavalla, in order to examine their relative contributions to overall feeding performance. Theoretical posterior bite force ranged from 14.0-318.7 N. Ram speed, recorded with a rod and reel incorporated with a line counter and video camera, ranged from 3.3-15.8B L/s. Impact forces on the prey ranged from 0.1-1.9 N. Bite pressure, estimated using theoretical bite forces at three gape angles and tooth cross-sectional areas, ranged from 1.7-56.9 MPa. Mass-specific bite force for king mackerel is relatively low in comparison with other bony fishes and sharks, with relatively little impact force applied to the prey during the strike. This suggests that king mackerel rely on high velocity chases and high bite pressure generated via sharp, laterally compressed teeth to maximize feeding performance.
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Affiliation(s)
- Amber R Ferguson
- Department of Integrative Biology, University of South Florida, Tampa, Florida
| | - Daniel R Huber
- Department of Biology, University of Tampa, Tampa, Florida
| | - Marc J Lajeunesse
- Department of Integrative Biology, University of South Florida, Tampa, Florida
| | - Philip J Motta
- Department of Integrative Biology, University of South Florida, Tampa, Florida
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84
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Mara KR, Motta PJ, Martin AP, Hueter RE. Constructional morphology within the head of hammerhead sharks (sphyrnidae). J Morphol 2015; 276:526-39. [PMID: 25684106 DOI: 10.1002/jmor.20362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/24/2014] [Accepted: 12/02/2014] [Indexed: 01/11/2023]
Abstract
The study of functional trade-offs is important if a structure, such as the cranium, serves multiple biological roles, and is, therefore, shaped by multiple selective pressures. The sphyrnid cephalofoil presents an excellent model for investigating potential trade-offs among sensory, neural, and feeding structures. In this study, hammerhead shark species were chosen to represent differences in head form through phylogeny. A combination of surface-based geometric morphometrics, computed tomography (CT) volumetric analysis, and phylogenetic analyses were utilized to investigate potential trade-offs within the head. Hammerhead sharks display a diversity of cranial morphologies where the position of the eyes and nares vary among species, with only minor changes in shape, position, and volume of the feeding apparatus through phylogeny. The basal winghead shark, Eusphyra blochii, has small anteriorly positioned eyes. Through phylogeny, the relative size and position of the eyes change, such that derived species have larger, more medially positioned eyes. The lateral position of the external nares is highly variable, showing no phylogenetic trend. Mouth size and position are conserved, remaining relatively unchanged. Volumetric CT analyses reveal no trade-offs between the feeding apparatus and the remaining cranial structures. The few trade-offs were isolated to the nasal capsule volume's inverse correlation with braincase, chondrocranial, and total cephalofoil volume. Eye volume also decreased as cephalofoil width increased. These data indicate that despite considerable changes in head shape, much of the head is morphologically conserved through sphyrnid phylogeny, particularly the jaw cartilages and their associated feeding muscles, with shape change and morphological trade-offs being primarily confined to the lateral wings of the cephalofoil and their associated sensory structures.
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Affiliation(s)
- Kyle R Mara
- Department of Integrative Biology, University of South Florida, Tampa, Florida, 33620
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85
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Mu X, Liu Y, Lai M, Song H, Wang X, Hu Y, Luo J. Characterization of the Macropodus opercularis complete mitochondrial genome and family Channidae taxonomy using Illumina-based de novo transcriptome sequencing. Gene 2015; 559:189-95. [PMID: 25639355 DOI: 10.1016/j.gene.2015.01.056] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/19/2015] [Accepted: 01/28/2015] [Indexed: 11/16/2022]
Abstract
In this study, the complete mitochondrial genome of Macropodus opercularis was sequenced using Illumina-based de novo transcriptome technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,496bp in length and contained two ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes, and the control region. The gene composition and order were similar to suborder Anabantoidei. Phylogenetic analyses using concatenated amino acid and nucleotide sequences of the 13 protein-coding genes with two different methods (Neighbor-joining and Bayesian analysis) both highly supported the close relationship of M. opercularis to M. ocellatus, consistent with previous classifications based on morphological and molecular studies. Furthermore, family Channidae and Parachanna insignis were clustered in the same clade. Our results supported the inclusion of family Channidae in suborder Channoidei. The complete mitochondrial genome of M. opercularis will provide genetic markers for better understanding species identification, population genetics and phylogeographics of freshwater fishes.
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Affiliation(s)
- Xidong Mu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
| | - Yi Liu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
| | - Mingxin Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
| | - Hongmei Song
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
| | - Xuejie Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
| | - Yinchang Hu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China
| | - Jianren Luo
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Guangzhou 510380, China.
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86
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Characterization of testicular morphology and spermatogenesis in the nurse sharks Ginglymostoma cirratum (Bonnaterre, 1788). ZOOMORPHOLOGY 2014. [DOI: 10.1007/s00435-014-0240-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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87
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Molecular phylogeny of the bamboo sharks (Chiloscyllium spp.). BIOMED RESEARCH INTERNATIONAL 2014; 2014:213896. [PMID: 25013766 PMCID: PMC4071782 DOI: 10.1155/2014/213896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/01/2014] [Accepted: 05/16/2014] [Indexed: 12/03/2022]
Abstract
Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species.
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88
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Grady JM, Enquist BJ, Dettweiler-Robinson E, Wright NA, Smith FA. Dinosaur physiology. Evidence for mesothermy in dinosaurs. Science 2014; 344:1268-72. [PMID: 24926017 DOI: 10.1126/science.1253143] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Were dinosaurs ectotherms or fast-metabolizing endotherms whose activities were unconstrained by temperature? To date, some of the strongest evidence for endothermy comes from the rapid growth rates derived from the analysis of fossil bones. However, these studies are constrained by a lack of comparative data and an appropriate energetic framework. Here we compile data on ontogenetic growth for extant and fossil vertebrates, including all major dinosaur clades. Using a metabolic scaling approach, we find that growth and metabolic rates follow theoretical predictions across clades, although some groups deviate. Moreover, when the effects of size and temperature are considered, dinosaur metabolic rates were intermediate to those of endotherms and ectotherms and closest to those of extant mesotherms. Our results suggest that the modern dichotomy of endothermic versus ectothermic is overly simplistic.
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Affiliation(s)
- John M Grady
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. The Santa Fe Institute, USA, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | | | - Natalie A Wright
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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89
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Boeger W, Kritsky D, Domingues M, Bueno-Silva M. The phylogenetic position of the Loimoidae Price, 1936 (Monogenoidea: Monocotylidea) based on analyses of partial rDNA sequences and morphological data. Parasitol Int 2014; 63:492-9. [DOI: 10.1016/j.parint.2014.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/21/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
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90
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Sorenson L, Santini F, Alfaro ME. The effect of habitat on modern shark diversification. J Evol Biol 2014; 27:1536-48. [DOI: 10.1111/jeb.12405] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 03/24/2014] [Indexed: 02/06/2023]
Affiliation(s)
- L. Sorenson
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
| | - F. Santini
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
| | - M. E. Alfaro
- Department of Ecology and Evolutionary Biology; University of California; Los Angeles CA USA
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91
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The complete mitochondrial genome sequence of the world's largest fish, the whale shark (Rhincodon typus), and its comparison with those of related shark species. Gene 2014; 539:44-9. [DOI: 10.1016/j.gene.2014.01.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/16/2014] [Accepted: 01/26/2014] [Indexed: 11/22/2022]
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92
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Liu SYV, Chan CLC, Lin O, Hu CS, Chen CA. DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan. PLoS One 2013; 8:e79373. [PMID: 24260209 PMCID: PMC3832526 DOI: 10.1371/journal.pone.0079373] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 09/29/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan's fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits. METHODS In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan. RESULTS Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias. CONCLUSION DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.
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Affiliation(s)
- Shang-Yin Vanson Liu
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei, Taiwan
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, United States of America
| | | | - Oceana Lin
- The Society of Wilderness, Taipei, Taiwan
| | | | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei, Taiwan
- Taiwan International Graduate Program-Biodiversity, Academia Sinica, Nangang, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- * E-mail:
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93
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Evolutionary relations of Hexanchiformes deep-sea sharks elucidated by whole mitochondrial genome sequences. BIOMED RESEARCH INTERNATIONAL 2013; 2013:147064. [PMID: 24089661 PMCID: PMC3780621 DOI: 10.1155/2013/147064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 07/26/2013] [Indexed: 11/23/2022]
Abstract
Hexanchiformes is regarded as a monophyletic taxon, but the morphological and genetic relationships between the five extant species within the order are still uncertain. In this study, we determined the whole mitochondrial DNA (mtDNA) sequences of seven sharks including representatives of the five Hexanchiformes, one squaliform, and one carcharhiniform and inferred the phylogenetic relationships among those species and 12 other Chondrichthyes (cartilaginous fishes) species for which the complete mitogenome is available. The monophyly of Hexanchiformes and its close relation with all other Squaliformes sharks were strongly supported by likelihood and Bayesian phylogenetic analysis of 13,749 aligned nucleotides of 13 protein coding genes and two rRNA genes that were derived from the whole mDNA sequences of the 19 species. The phylogeny suggested that Hexanchiformes is in the superorder Squalomorphi, Chlamydoselachus anguineus (frilled shark) is the sister species to all other Hexanchiformes, and the relations within Hexanchiformes are well resolved as Chlamydoselachus, (Notorynchus, (Heptranchias, (Hexanchus griseus, H. nakamurai))). Based on our phylogeny, we discussed evolutionary scenarios of the jaw suspension mechanism and gill slit numbers that are significant features in the sharks.
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94
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Body wall development in lamprey and a new perspective on the origin of vertebrate paired fins. Proc Natl Acad Sci U S A 2013; 110:11899-904. [PMID: 23818600 DOI: 10.1073/pnas.1304210110] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Classical hypotheses regarding the evolutionary origin of paired appendages propose transformation of precursor structures (gill arches and lateral fin folds) into paired fins. During development, gnathostome paired appendages form as outgrowths of body wall somatopleure, a tissue composed of somatic lateral plate mesoderm (LPM) and overlying ectoderm. In amniotes, LPM contributes connective tissue to abaxial musculature and forms ventrolateral dermis of the interlimb body wall. The phylogenetic distribution of this character is uncertain because lineage analyses of LPM have not been generated in anamniotes. We focus on the evolutionary history of the somatopleure to gain insight into the tissue context in which paired fins first appeared. Lampreys diverged from other vertebrates before the acquisition of paired fins and provide a model for investigating the preappendicular condition. We present vital dye fate maps that suggest the somatopleure is eliminated in lamprey as the LPM is separated from the ectoderm and sequestered to the coelomic linings during myotome extension. We also examine the distribution of postcranial mesoderm in catshark and axolotl. In contrast to lamprey, our findings support an LPM contribution to the trunk body wall of these taxa, which is similar to published data for amniotes. Collectively, these data lead us to hypothesize that a persistent somatopleure in the lateral body wall is a gnathostome synapomorphy, and the redistribution of LPM was a key step in generating the novel developmental module that ultimately produced paired fins. These embryological criteria can refocus arguments on paired fin origins and generate hypotheses testable by comparative studies on the source, sequence, and extent of genetic redeployment.
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95
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Renz AJ, Meyer A, Kuraku S. Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes. PLoS One 2013; 8:e66400. [PMID: 23825540 PMCID: PMC3692497 DOI: 10.1371/journal.pone.0066400] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 05/06/2013] [Indexed: 02/06/2023] Open
Abstract
Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.
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Affiliation(s)
- Adina J. Renz
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Shigehiro Kuraku
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
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96
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Soylemez O, Kondrashov FA. Estimating the rate of irreversibility in protein evolution. Genome Biol Evol 2013; 4:1213-22. [PMID: 23132897 PMCID: PMC3542581 DOI: 10.1093/gbe/evs096] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this question has
not been comprehensively addressed at the molecular level. Here, we use data from 221
human genes with known pathogenic mutations to estimate the rate of irreversibility in
protein evolution. For these genes, we reconstruct ancestral amino acid sequences along
the mammalian phylogeny and identify ancestral amino acid states that match known
pathogenic mutations. Such cases represent inherent evolutionary irreversibility because,
at the present moment, reversals to these ancestral amino acid states are impossible for
the human lineage. We estimate that approximately 10% of all amino acid
substitutions along the mammalian phylogeny are irreversible, such that a return to the
ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes
with high rates of irreversibility, as much as 40% of all amino acid evolution was
estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral
phenotypes, the molecular nature of the high rate of irreversibility in proteins is best
explained by evolution with a high prevalence of compensatory, epistatic interactions
between amino acid sites. Under such mode of protein evolution, once an amino acid
substitution is fixed, the probability of its reversal declines as the protein sequence
accumulates changes that affect the phenotypic manifestation of the ancestral state. The
prevalence of epistasis in evolution indicates that the observed high rate of
irreversibility in protein evolution is an inherent property of protein structure and
function.
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Affiliation(s)
- Onuralp Soylemez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
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97
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Primary cell culture from the nose of a marine organism, the banded houndshark, Triakis scyllium. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0494-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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98
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Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA. Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes 2012; 5:574. [PMID: 23088596 PMCID: PMC3583491 DOI: 10.1186/1756-0500-5-574] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 08/24/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use. FINDINGS Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree. CONCLUSIONS The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating which kinds of data and metadata are most important for a re-useable phylogenetic record.
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Affiliation(s)
- Arlin Stoltzfus
- Biochemical Science Division, NIST, 100 Bureau Drive, Gaithersburg, MD, USA
| | - Brian O'Meara
- Department of Ecology & Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA
| | - Jamie Whitacre
- NMNH, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Ross Mounce
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Sudhir Kumar
- Center for Evolutionary Medicine and Informatics, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5301, USA
| | - Dan F Rosauer
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Rutger A Vos
- NCB Naturalis, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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99
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Guinot G, Adnet S, Cappetta H. An analytical approach for estimating fossil record and diversification events in sharks, skates and rays. PLoS One 2012; 7:e44632. [PMID: 22957091 PMCID: PMC3434181 DOI: 10.1371/journal.pone.0044632] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/06/2012] [Indexed: 11/19/2022] Open
Abstract
Background Modern selachians and their supposed sister group (hybodont sharks) have a long and successful evolutionary history. Yet, although selachian remains are considered relatively common in the fossil record in comparison with other marine vertebrates, little is known about the quality of their fossil record. Similarly, only a few works based on specific time intervals have attempted to identify major events that marked the evolutionary history of this group. Methodology/Principal Findings Phylogenetic hypotheses concerning modern selachians’ interrelationships are numerous but differ significantly and no consensus has been found. The aim of the present study is to take advantage of the range of recent phylogenetic hypotheses in order to assess the fit of the selachian fossil record to phylogenies, according to two different branching methods. Compilation of these data allowed the inference of an estimated range of diversity through time and evolutionary events that marked this group over the past 300 Ma are identified. Results indicate that with the exception of high taxonomic ranks (orders), the selachian fossil record is by far imperfect, particularly for generic and post-Triassic data. Timing and amplitude of the various identified events that marked the selachian evolutionary history are discussed. Conclusion/Significance Some identified diversity events were mentioned in previous works using alternative methods (Early Jurassic, mid-Cretaceous, K/T boundary and late Paleogene diversity drops), thus reinforcing the efficiency of the methodology presented here in inferring evolutionary events. Other events (Permian/Triassic, Early and Late Cretaceous diversifications; Triassic/Jurassic extinction) are newly identified. Relationships between these events and paleoenvironmental characteristics and other groups’ evolutionary history are proposed.
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Affiliation(s)
- Guillaume Guinot
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier 2, Montpellier, France.
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100
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Shark species more diverse than thought. Nature 2012. [DOI: 10.1038/nature.2012.10879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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