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Ludington AJ, Hammond JM, Breen J, Deveson IW, Sanders KL. New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biol 2023; 21:284. [PMID: 38066641 PMCID: PMC10709897 DOI: 10.1186/s12915-023-01772-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Sea snakes underwent a complete transition from land to sea within the last ~ 15 million years, yet they remain a conspicuous gap in molecular studies of marine adaptation in vertebrates. RESULTS Here, we generate four new annotated sea snake genomes, three of these at chromosome-scale (Hydrophis major, H. ornatus and H. curtus), and perform detailed comparative genomic analyses of sea snakes and their closest terrestrial relatives. Phylogenomic analyses highlight the possibility of near-simultaneous speciation at the root of Hydrophis, and synteny maps show intra-chromosomal variations that will be important targets for future adaptation and speciation genomic studies of this system. We then used a strict screen for positive selection in sea snakes (against a background of seven terrestrial snake genomes) to identify genes over-represented in hypoxia adaptation, sensory perception, immune response and morphological development. CONCLUSIONS We provide the best reference genomes currently available for the prolific and medically important elapid snake radiation. Our analyses highlight the phylogenetic complexity and conserved genome structure within Hydrophis. Positively selected marine-associated genes provide promising candidates for future, functional studies linking genetic signatures to the marine phenotypes of sea snakes and other vertebrates.
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Affiliation(s)
- Alastair J Ludington
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia
- John Curtin School of Medical Research, College of Health & Medicine, Australian National University, Canberra, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- The South Australian Museum, Adelaide, Australia.
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2
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Sosiak C, Janovitz T, Perrichot V, Timonera JP, Barden P. Trait-Based Paleontological Niche Prediction Recovers Extinct Ecological Breadth of the Earliest Specialized Ant Predators. Am Nat 2023; 202:E147-E162. [PMID: 38033183 DOI: 10.1086/726739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractPaleoecological estimation is fundamental to the reconstruction of evolutionary and environmental histories. The ant fossil record preserves a range of species in three-dimensional fidelity and chronicles faunal turnover across the Cretaceous and Cenozoic; taxonomically rich and ecologically diverse, ants are an exemplar system to test new methods of paleoecological estimation in evaluating hypotheses. We apply a broad extant ecomorphological dataset to evaluate random forest machine learning classification in predicting the total ecological breadth of extinct and enigmatic hell ants. In contrast to previous hypotheses of extinction-prone arboreality, we find that hell ants were primarily leaf litter or ground-nesting and foraging predators, and by comparing ecospace occupations of hell ants and their extant analogs, we recover a signature of ecomorphological turnover across temporally and phylogenetically distinct lineages on opposing sides of the Cretaceous-Paleogene boundary. This paleoecological predictive framework is applicable across lineages and may provide new avenues for testing hypotheses over deep time.
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3
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Martin SB, De Silva MLI, Pathirana E, Rajapakse RPVJ. Polyphyly of the Dinurinae Looss, 1907 (Digenea: Hemiuridae) and resurrection of the Mecoderinae Skrjabin & Guschanskaja, 1954 based on novel collection of Tubulovesicula laticaudi Parukhin, 1969 from marine elapid snakes in Sri Lanka. Parasitol Int 2023; 97:102776. [PMID: 37437775 DOI: 10.1016/j.parint.2023.102776] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
With one exception, the only known hemiurid trematodes that do not use teleost fishes as definitive hosts instead occur in marine elapid snakes. These comprise six species across four genera and three subfamilies, and so presumably indicate at least three independent invasions of marine snakes from teleost fishes. Here, one of these taxa, Tubulovesicula laticaudi Parukhin, 1969 (= T. orientalis Chattopadhyaya, 1970 n. syn.) is reported from Sri Lanka, collected from Shaw's sea snake Hydrophis curtus (Shaw) (Elapidae: Hydrophiinae: Hydrophinii), the annulated sea snake H. cyanocinctus Daudin and the yellow sea snake H. spiralis (Shaw) off Nayaru in the Bay of Bengal, and from H. spiralis in Portugal Bay, Gulf of Mannar. Novel molecular data, for COI mtDNA and ITS2 and 28S rDNA, are the first for a species of Tubulovesicula Yamaguti, 1934. Nominally, Tubulovesicula belongs in the Dinurinae Looss, 1907, but in phylogenetic analyses based on 28S rDNA, our sequences for T. laticaudi resolved relatively distant from that for representatives of Dinurus Looss, 1907, the type-genus, rendering the subfamily polyphyletic. Tubulovesicula laticaudi resolved closest to data for the type-species of the Plerurinae Gibson & Bray, 1979, but that subfamily is also polyphyletic. These findings lead us to re-evaluate an alternative classification considered by Gibson & Bray (1979). We propose restricting the Dinurinae for forms with a permanent sinus-organ (Dinurus, Ectenurus Looss, 1907; Erilepturus Woolcock, 1935; Paradinurus Vigueras, 1958; Qadriana Bilqees, 1971) and resurrect the Mecoderinae Skrjabin & Guschanskaja, 1954 for forms with a temporary sinus-organ (Mecoderus Manter, 1940, Allostomachicola Yamaguti, 1958, Stomachicola Yamaguti, 1934 and Tubulovesicula).
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Affiliation(s)
- Storm Blas Martin
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia.
| | - M L I De Silva
- Divsion of Parasitology, Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Sri Lanka; Department of Aquatic Bioresources, Faculty of Urban and Aquatic Bioresources, University of Sri Jayawardenepura, Gangodawila, Nugegoda, Sri Lanka.
| | - Erandi Pathirana
- Department of Aquatic Bioresources, Faculty of Urban and Aquatic Bioresources, University of Sri Jayawardenepura, Gangodawila, Nugegoda, Sri Lanka
| | - R P V J Rajapakse
- Divsion of Parasitology, Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Sri Lanka
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4
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Loaiza-Lange A, Székely D, Torres-Carvajal O, Tinoco N, Salazar-Valenzuela D, Székely P. Feeding ecology of the Terciopelo pit viper snake ( Bothrops asper) in Ecuador. PeerJ 2023; 11:e14817. [PMID: 36785705 PMCID: PMC9921990 DOI: 10.7717/peerj.14817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/06/2023] [Indexed: 02/10/2023] Open
Abstract
Thoroughly documenting prey items and diet composition is crucial for understanding a predator's role in the ecosystem. In gape restricted predators, such as snakes, documenting and analyzing the type and size of the prey is important to interpret their ecological role. We describe the diet patterns of a species of venomous snake, the Terciopelo pit viper (Bothrops asper), from its Ecuadorian populations. Examining the gastrointestinal contents of museum specimens collected over an extensive area of the Pacific lowlands of Ecuador, we encountered 69 identifiable prey items from four major taxonomic groups (amphibians, centipedes, mammals, and reptiles). We evaluated the observed composition of prey to check for differences between sexes and size-classes. To complement our observations of the Terciopelo species complex throughout their distribution, we carried out a systematic literature review. Our data show an ontogenetic shift in diet, with a transition from more diverse diet in juveniles towards a mammal-specialized diet in adults, and distinct proportion of prey taxa between the sexes in the juvenile size class.
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Affiliation(s)
- Amaru Loaiza-Lange
- Museo de Zoología, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Diana Székely
- Museo de Zoología, Universidad Técnica Particular de Loja, Loja, Ecuador,Departamento de Ciencias Biológicas y Agropecuarias, Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Facultad de Ciencias Exactas y Naturales, Universidad Técnica Particular de Loja, Loja, Ecuador,Research Center of the Department of Natural Sciences, Faculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Constanţa, Romania
| | - Omar Torres-Carvajal
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Nicolás Tinoco
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias del Medio Ambiente, Universidad Indoamérica, Quito, Ecuador
| | - Paul Székely
- Museo de Zoología, Universidad Técnica Particular de Loja, Loja, Ecuador,Departamento de Ciencias Biológicas y Agropecuarias, Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Facultad de Ciencias Exactas y Naturales, Universidad Técnica Particular de Loja, Loja, Ecuador,Research Center of the Department of Natural Sciences, Faculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Constanţa, Romania
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5
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Sherratt E, Nash-Hahn T, Nankivell JH, Rasmussen AR, Hampton PM, Sanders KL. Macroevolution in axial morphospace: innovations accompanying the transition to marine environments in elapid snakes. ROYAL SOCIETY OPEN SCIENCE 2022; 9:221087. [PMID: 36569233 PMCID: PMC9768463 DOI: 10.1098/rsos.221087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Sea snakes in the Hydrophis-Microcephalophis clade (Elapidae) show exceptional body shape variation along a continuum from similar forebody and hindbody girths, to dramatically reduced girths of the forebody relative to hindbody. The latter is associated with specializations on burrowing prey. This variation underpins high sympatric diversity and species richness and is not shared by other marine (or terrestrial) snakes. Here, we examined a hypothesis that macroevolutionary changes in axial development contribute to the propensity, at clade level, for body shape change. We quantified variation in the number and size of vertebrae in two body regions (pre- and post-apex of the heart) for approximately 94 terrestrial and marine elapids. We found Hydrophis-Microcephalophis exhibit increased rates of vertebral evolution in the pre- versus post-apex regions compared to all other Australasian elapids. Unlike other marine and terrestrial elapids, axial elongation in Hydrophis-Microcephalophis occurs via the preferential addition of vertebrae pre-heart apex, which is the region that undergoes concomitant shifts in vertebral number and size during transitions along the relative fore- to hindbody girth axis. We suggest that this macroevolutionary developmental change has potentially acted as a key innovation in Hydrophis-Microcephalophis by facilitating novel (especially burrowing) prey specializations that are not shared with other marine snakes.
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Affiliation(s)
- Emma Sherratt
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Tamika Nash-Hahn
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - James H. Nankivell
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Arne R. Rasmussen
- The Royal Danish Academy, Institute of Conservation, 1435 Copenhagen, Denmark
| | - Paul M. Hampton
- Department of Biology, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Kate L. Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
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6
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Sinnott‐Armstrong MA, Deanna R, Pretz C, Liu S, Harris JC, Dunbar‐Wallis A, Smith SD, Wheeler LC. How to approach the study of syndromes in macroevolution and ecology. Ecol Evol 2022; 12:e8583. [PMID: 35342598 PMCID: PMC8928880 DOI: 10.1002/ece3.8583] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 11/12/2022] Open
Abstract
Syndromes, wherein multiple traits evolve convergently in response to a shared selective driver, form a central concept in ecology and evolution. Recent work has questioned the existence of some classic syndromes, such as pollination and seed dispersal syndromes. Here, we discuss some of the major issues that have afflicted research into syndromes in macroevolution and ecology. First, correlated evolution of traits and hypothesized selective drivers is often relied on as the only evidence for adaptation of those traits to those hypothesized drivers, without supporting evidence. Second, the selective driver is often inferred from a combination of traits without explicit testing. Third, researchers often measure traits that are easy for humans to observe rather than measuring traits that are suited to testing the hypothesis of adaptation. Finally, species are often chosen for study because of their striking phenotypes, which leads to the illusion of syndromes and divergence. We argue that these issues can be avoided by combining studies of trait variation across entire clades or communities with explicit tests of adaptive hypotheses and that taking this approach will lead to a better understanding of syndrome‐like evolution and its drivers.
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Affiliation(s)
- Miranda A. Sinnott‐Armstrong
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
- Department of Chemistry University of Cambridge Cambridge UK
| | - Rocio Deanna
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
- Instituto Multidisciplinario de Biología Vegetal IMBIV (CONICET‐UNC) Córdoba Argentina
- Departamento de Ciencias Farmacéuticas Facultad de Ciencias Químicas (FCQ, UNC) Córdoba Argentina
| | - Chelsea Pretz
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
| | - Sukuan Liu
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
| | - Jesse C. Harris
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
| | - Amy Dunbar‐Wallis
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
| | - Stacey D. Smith
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
| | - Lucas C. Wheeler
- Department of Ecology and Evolutionary Biology University of Colorado‐Boulder Boulder Colorado USA
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7
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Fujishima K, Sasai T, Hibino Y, Nishizawa H. Morphology, Diet, and Reproduction of Coastal Hydrophis Sea Snakes (Elapidae: Hydrophiinae) at Their Northern Distribution Limit. Zoolog Sci 2021; 38:405-415. [PMID: 34664915 DOI: 10.2108/zs210010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/31/2021] [Indexed: 11/17/2022]
Abstract
The Ryukyu Archipelago represents the northern distribution limit for hydrophiine sea snakes, the largest group of marine reptiles. Ryukyuan sea snakes may have developed distinct local adaptations in morphology and ecology, but they have been poorly studied. We examined preserved specimens of 111 Hydrophismelanocephalusand 61 Hydrophis ornatusfrom the Ryukyu Archipelago to obtain data on morphology, diet, and reproduction. Sexual size dimorphism was detected in H. melanocephalus (mean ± standard deviation of adult snout-vent length: SVL, females 1062 ± 141 mm vs. males 959 ± 96 mm) but not in H. ornatus. Female H. melanocephalus had larger head widths and shorter tail lengths relative to SVL compared to males. Relative girth was low in neonates of both species (1.0-1.3), but increased in adults to about 1.7-2.6 in H. melanocephalus and 1.3-1.8 in female H. ornatus. Stomach contents of H. melanocephalus consisted of ophichthid and congrid eels, a sand diver, and gobies, whereas in H. ornatus, gobies and a goat fish were found. Litter size of three reproductive H. melanocephalus ranged from five to seven, and parturition seems to occur from August to October. Litter size of six H. ornatus ranged from two to seven, and was correlated with maternal SVL. Parturition in H. ornatus probably occurs around November. Different selective forces related to locomotion, feeding and predation risk, which influence the pregnant mother and neonates, may have resulted in having few, long but slender offspring that show positive allometric growth in hind-body girth.
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Affiliation(s)
- Kanta Fujishima
- Graduate School of Informatics, Kyoto University, Yoshida Hommachi, Kyoto 606-8501, Japan,
| | - Takahide Sasai
- Graduate School of Engineering and Science, University of the Ryukyus, Nishihara-cho, Okinawa 903-0213, Japan.,Okinawa Churashima Foundation, Motobu-cho, Okinawa 905-0206, Japan
| | - Yusuke Hibino
- Kitakyushu Museum of Natural History and Human History, Kitakyushu, Fukuoka 805-0071, Japan
| | - Hideaki Nishizawa
- Graduate School of Informatics, Kyoto University, Yoshida Hommachi, Kyoto 606-8501, Japan
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8
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Zhao HY, Sun Y, Du Y, Li JQ, Lv JG, Qu YF, Lin LH, Lin CX, Ji X, Gao JF. Venom of the Annulated Sea Snake Hydrophis cyanocinctus: A Biochemically Simple but Genetically Complex Weapon. Toxins (Basel) 2021; 13:548. [PMID: 34437419 PMCID: PMC8402435 DOI: 10.3390/toxins13080548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022] Open
Abstract
Given that the venom system in sea snakes has a role in enhancing their secondary adaption to the marine environment, it follows that elucidating the diversity and function of venom toxins will help to understand the adaptive radiation of sea snakes. We performed proteomic and de novo NGS analyses to explore the diversity of venom toxins in the annulated sea snake (Hydrophis cyanocinctus) and estimated the adaptive molecular evolution of the toxin-coding unigenes and the toxicity of the major components. We found three-finger toxins (3-FTxs), phospholipase A2 (PLA2) and cysteine-rich secretory protein (CRISP) in the venom proteome and 59 toxin-coding unigenes belonging to 24 protein families in the venom-gland transcriptome; 3-FTx and PLA2 were the most abundant families. Nearly half of the toxin-coding unigenes had undergone positive selection. The short- (i.p. 0.09 μg/g) and long-chain neurotoxin (i.p. 0.14 μg/g) presented fairly high toxicity, whereas both basic and acidic PLA2s expressed low toxicity. The toxicity of H. cyanocinctus venom was largely determined by the 3-FTxs. Our data show the venom is used by H. cyanocinctus as a biochemically simple but genetically complex weapon and venom evolution in H. cyanocinctus is presumably driven by natural selection to deal with fast-moving prey and enemies in the marine environment.
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Affiliation(s)
- Hong-Yan Zhao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
| | - Yan Sun
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
| | - Yu Du
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China; (Y.D.); (J.-G.L.)
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
| | - Jia-Qi Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
| | - Jin-Geng Lv
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China; (Y.D.); (J.-G.L.)
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
| | - Chi-Xian Lin
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya 572022, China; (Y.D.); (J.-G.L.)
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
| | - Xiang Ji
- MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya 572022, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (J.-Q.L.); (Y.-F.Q.)
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Jian-Fang Gao
- Hangzhou Key Laboratory for Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; (H.-Y.Z.); (Y.S.); (L.-H.L.)
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9
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Cleuren SGC, Hocking DP, Evans AR. Fang evolution in venomous snakes: Adaptation of 3D tooth shape to the biomechanical properties of their prey. Evolution 2021; 75:1377-1394. [PMID: 33904594 DOI: 10.1111/evo.14239] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/27/2022]
Abstract
Venomous snakes are among the world's most specialized predators. During feeding, they use fangs to penetrate the body tissues of their prey, but the success of this penetration depends on the shape of these highly specialized teeth. Here, we examined the evolution of fang shape in a wide range of snakes using 3D geometric morphometrics (3DGM) and cross-sectional tooth sharpness measurements. We investigated the relationship of these variables with six diet categories based on the prey's biomechanical properties, and tested for evolutionary convergence using two methods. Our results show that slender elongate fangs with sharp tips are used by snakes that target soft-skinned prey (e.g., mammals), whereas fangs become more robust and blunter as the target's skin becomes scaly (e.g., fish and reptiles) and eventually hard-shelled (e.g., crustaceans), both with and without correction for evolutionary allometry. Convergence in fang shape is present, indicating that fangs of snakes with the same diet are more similar than those of closely related species with different diets. Establishing the relationship between fang morphology and diet helps to explain how snakes became adapted to different lifestyles, while also providing a proxy to infer diet in lesser known species or extinct snakes from the fossil record.
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Affiliation(s)
- Silke G C Cleuren
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - David P Hocking
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Clayton, Victoria, 3800, Australia.,Geosciences, Museums Victoria, Melbourne, Victoria, 3001, Australia
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10
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Ludington AJ, Sanders KL. Demographic analyses of marine and terrestrial snakes (Elapidae) using whole genome sequences. Mol Ecol 2020; 30:545-554. [PMID: 33170980 DOI: 10.1111/mec.15726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/13/2020] [Accepted: 11/03/2020] [Indexed: 11/27/2022]
Abstract
The question of whether spatial aspects of evolution differ in marine versus terrestrial realms has endured since Ernst Mayr's 1954 essay on marine speciation. Marine systems are often suggested to support larger and more highly connected populations, but quantitative comparisons with terrestrial systems have been lacking. Here, we compared the population histories of marine and terrestrial elapid snakes using the pairwise sequentially Markovian coalescent (PSMC) model to track historical fluctuations in species' effective population sizes (Ne ) from individual whole-genome sequences. To do this we generated a draft genome for the olive sea snake (Aiysurus laevis) and analysed this alongside six published elapid genomes and their sequence reads (marine species Hydrophis curtus, H. melanocephalus and Laticauda laticaudata; terrestrial species Pseudonaja textilis, Naja Naja and Notechis scutatus). Counter to the expectation that marine species should show higher overall Ne and less pronounced fluctuations in Ne , our analyses reveal demographic patterns that are highly variable among species and do not clearly correspond to major ecological divisions. At deeper time intervals, the four marine elapids appear to have experienced relatively stable Ne , while each terrestrial species shows a prominent upturn in Ne starting at ~4 million years ago (Ma) followed by an equally strong decline. However, over the last million years, all seven species show strong and divergent fluctuations. Estimates of Ne in the most recent intervals (~10 kya) are lowest in two of four marine species (H. melanocephalus and Laticauda), and do not correspond to contemporary range sizes in marine or terrestrial taxa.
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Affiliation(s)
- Alastair J Ludington
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kate L Sanders
- School of Biological Science, The University of Adelaide, Adelaide, South Australia, Australia
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11
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Population history and genomic admixture of sea snakes of the genus Laticauda in the West Pacific. Mol Phylogenet Evol 2020; 155:107005. [PMID: 33160037 DOI: 10.1016/j.ympev.2020.107005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 11/23/2022]
Abstract
Speciation in the open ocean has long been studied, but it remains largely elusive what factors promote or inhibit speciation in such an open environment. Marine amniotes, which evolved from terrestrial ancestors, provide valuable opportunities for studying speciation in the ocean because of their evident aquatic origins. Sea snakes are phylogenetically related to terrestrial elapid snakes and consist of two monophyletic groups (Hydrophiini and Laticaudini). These two groups migrated from land to water almost at the same time, but species diversities are remarkably different: there are approx. 60 species in 16 genera described for hydrophiins, whereas only eight species in the genus Laticauda are described for laticaudins. Here, we provide a high-quality reference genome assembly of a laticaudin L. colubrina with a scaffold N50 value of 40 Mbp, and focused on laticaudins to consider why they have seldom speciated. We performed whole-genome shotgun sequencing of several species of laticaudins sampled in their southmost (Vanuatu) and northmost (Ryukyu) habitats. Demographic histories of Vanuatu and Ryukyu populations suggest that populations of broadly distributed major species are geographically structured. Each species is genetically clearly distinguished, but there is a considerable amount of gene flow between two sibling species distributed sympatrically in Vanuatu. In addition, inter-species genomic admixture is ubiquitously observed among laticaudins even between phylogenetically distant species. Broad distribution of major species combined with such genetic mixability might have prevented laticaudins from genetic isolation and speciation.
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12
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Sosiak CE, Barden P. Multidimensional trait morphology predicts ecology across ant lineages. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13697] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christine E. Sosiak
- Federated Department of Biological Sciences New Jersey Institute of Technology Newark NJ USA
| | - Phillip Barden
- Federated Department of Biological Sciences New Jersey Institute of Technology Newark NJ USA
- Division of Invertebrate Zoology American Museum of Natural History New York NY USA
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13
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Simões BF, Gower DJ, Rasmussen AR, Sarker MAR, Fry GC, Casewell NR, Harrison RA, Hart NS, Partridge JC, Hunt DM, Chang BS, Pisani D, Sanders KL. Spectral Diversification and Trans-Species Allelic Polymorphism during the Land-to-Sea Transition in Snakes. Curr Biol 2020; 30:2608-2615.e4. [PMID: 32470360 DOI: 10.1016/j.cub.2020.04.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 11/16/2022]
Abstract
Snakes are descended from highly visual lizards [1] but have limited (probably dichromatic) color vision attributed to a dim-light lifestyle of early snakes [2-4]. The living species of front-fanged elapids, however, are ecologically very diverse, with ∼300 terrestrial species (cobras, taipans, etc.) and ∼60 fully marine sea snakes, plus eight independently marine, amphibious sea kraits [1]. Here, we investigate the evolution of spectral sensitivity in elapids by analyzing their opsin genes (which are responsible for sensitivity to UV and visible light), retinal photoreceptors, and ocular lenses. We found that sea snakes underwent rapid adaptive diversification of their visual pigments when compared with their terrestrial and amphibious relatives. The three opsins present in snakes (SWS1, LWS, and RH1) have evolved under positive selection in elapids, and in sea snakes they have undergone multiple shifts in spectral sensitivity toward the longer wavelengths that dominate below the sea surface. Several relatively distantly related Hydrophis sea snakes are polymorphic for shortwave sensitive visual pigment encoded by alleles of SWS1. This spectral site polymorphism is expected to confer expanded "UV-blue" spectral sensitivity and is estimated to have persisted twice as long as the predicted survival time for selectively neutral nuclear alleles. We suggest that this polymorphism is adaptively maintained across Hydrophis species via balancing selection, similarly to the LWS polymorphism that confers allelic trichromacy in some primates. Diving sea snakes thus appear to share parallel mechanisms of color vision diversification with fruit-eating primates.
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Affiliation(s)
- Bruno F Simões
- University of Plymouth, School of Biological and Marine Sciences, Drake Circus, Plymouth PL4 8AA, United Kingdom; University of Bristol, School of Biological Sciences and School of Earth Sciences, Tyndall Avenue, Bristol BS8 1TG, United Kingdom; The University of Adelaide, School of Biological Sciences, North Terrace, Adelaide, South Australia 5005, Australia.
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Arne R Rasmussen
- The Royal Danish Academy of Fine Arts, School of Architecture, Design and Conservation, Philip de Langes Allé, 1435 Copenhagen K, Denmark
| | - Mohammad A R Sarker
- University of Dhaka, Department of Zoology, Curzon Hall Campus, Dhaka 1000, Bangladesh
| | - Gary C Fry
- CSIRO Oceans and Atmosphere, Queensland Biosciences Precinct, St Lucia, Queensland 4072, Australia
| | - Nicholas R Casewell
- Liverpool School of Tropical Medicine, Centre for Snakebite Research & Interventions, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Robert A Harrison
- Liverpool School of Tropical Medicine, Centre for Snakebite Research & Interventions, Pembroke Place, Liverpool L3 5QA, United Kingdom
| | - Nathan S Hart
- Macquarie University, Department of Biological Sciences, North Ryde, Sydney, New South Wales 2109, Australia
| | - Julian C Partridge
- The University of Western Australia, Oceans Institute, Crawley, Perth, Western Australia 6009, Australia
| | - David M Hunt
- The University of Western Australia, School of Biological Sciences, Crawley, Perth, Western Australia 6009, Australia; The Lions Eye Institute, Centre for Ophthalmology and Visual Science, Nedlands, Perth, Western Australia 6009, Australia
| | - Belinda S Chang
- University of Toronto, Departments of Ecology & Evolutionary, Cell & Systems Biology, Willcocks Street, Toronto M5S 3G5, Canada
| | - Davide Pisani
- University of Bristol, School of Biological Sciences and School of Earth Sciences, Tyndall Avenue, Bristol BS8 1TG, United Kingdom
| | - Kate L Sanders
- The University of Adelaide, School of Biological Sciences, North Terrace, Adelaide, South Australia 5005, Australia; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
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14
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Goiran C, Shine R. The ability of damselfish to distinguish between dangerous and harmless sea snakes. Sci Rep 2020; 10:1377. [PMID: 31992782 PMCID: PMC6987208 DOI: 10.1038/s41598-020-58258-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/13/2020] [Indexed: 11/30/2022] Open
Abstract
In defence of their nests or territories, damselfish (Pomacentridae) attack even large and potentially dangerous intruders. The Indo-Pacific region contains many species of sea snakes, some of which eat damselfish whereas others do not. Can the fishes identify which sea snake taxa pose a threat? We recorded responses of damselfishes to natural encounters with five species of snakes in two shallow bays near Noumea, New Caledonia. Attacks by fishes were performed mostly by demersal territorial species of damselfish, and were non-random with respect to the species, size, sex and colouration of the snakes involved. The most common target of attack was Emydocephalus annulatus, a specialist egg-eater that poses no danger to adult fishes. Individuals of a generalist predator (Aipysurus duboisii) that were melanic (and thus resembled E. annulatus in colour) attracted more attacks than did paler individuals. Larger faster-swimming snake species (Aipysurus laevis, Laticauda saintgironsi) were watched but not attacked, or were actively avoided (Hydrophis major), even though only one of these species (A. laevis) eats pomacentrids. Attacks were more common towards female snakes rather than males, likely reflecting slower swimming speeds in females. In summary, damselfishes distinguish between sea snake species using cues such as size, colour and behaviour, but the fishes sometimes make mistakes.
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Affiliation(s)
- Claire Goiran
- LabEx Corail & ISEA, Université de la Nouvelle-Calédonie, BP R4, 98851, Nouméa cedex, New Caledonia
| | - Richard Shine
- Department of Biological Sciences, Macquarie University, NSW, 2109, Sydney, Australia. .,School of Life and Environmental Sciences, University of Sydney, NSW, 2006, Sydney, Australia.
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15
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Sherratt E, Sanders KL. Patterns of intracolumnar size variation inform the heterochronic mechanisms underlying extreme body shape divergence in microcephalic sea snakes. Evol Dev 2019; 22:283-290. [PMID: 31730744 DOI: 10.1111/ede.12328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sea snakes (Hydrophiinae) that specialize on burrowing eel prey have repeatedly evolved tiny heads and reduced forebody relative to hindbody girths. Previous research has found that these "microcephalic" forms have higher counts of precaudal vertebrae, and postnatal ontogenetic changes cause their hindbodies to reach greater girths relative to their forebodies. We examine variation in vertebral size along the precaudal axis of neonates and adults of three species. In the nonmicrocephalic Hydrophis curtus, these intracolumnar patterns take the form of symmetrical curved profiles, with longer vertebrae in the midbody (50% of body length) relative to distal regions. In contrast, intracolumnar profiles in the microcephalic H. macdowelli and H. obscurus are strongly asymmetrical curves (negative skewness) due to the presence of numerous, smaller-sized vertebrate in the forebody (anterior to the heart). Neonate and adult H. macdowelli and H. obscurus specimens all exhibit this pattern, implying an onset of fore- versus hindbody decoupling in the embryo stage. Based on this, we suggest plausible developmental mechanisms involving the presence and positioning of Hox boundaries and heterochronic changes in segmentation. Tests of our hypotheses would give new insights into the drivers of rapid convergent shifts in evolution, but will ultimately require studies of gene expression in the embryos of relevant taxa.
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Affiliation(s)
- Emma Sherratt
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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16
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Chapuis L, Kerr CC, Collin SP, Hart NS, Sanders KL. Underwater hearing in sea snakes (Hydrophiinae): first evidence of auditory evoked potential thresholds. ACTA ACUST UNITED AC 2019; 222:222/14/jeb198184. [PMID: 31345949 DOI: 10.1242/jeb.198184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/01/2019] [Indexed: 11/20/2022]
Abstract
The viviparous sea snakes (Hydrophiinae) are a secondarily aquatic radiation of more than 60 species that possess many phenotypic adaptations to marine life. However, virtually nothing is known of the role and sensitivity of hearing in sea snakes. This study investigated the hearing sensitivity of the fully marine sea snake Hydrophis stokesii by measuring auditory evoked potential (AEP) audiograms for two individuals. AEPs were recorded from 40 Hz (the lowest frequency tested) up to 600 Hz, with a peak in sensitivity identified at 60 Hz (163.5 dB re. 1 µPa or 123 dB re. 1 µm s-2). Our data suggest that sea snakes are sensitive to low-frequency sounds but have relatively low sensitivity compared with bony fishes and marine turtles. Additional studies are required to understand the role of sound in sea snake life history and further assess these species' vulnerability to anthropogenic noise.
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Affiliation(s)
- Lucille Chapuis
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK .,Oceans Graduate School and the UWA Oceans Institute, The University of Western Australia, Perth, WA 6009, Australia
| | - Caroline C Kerr
- Oceans Graduate School and the UWA Oceans Institute, The University of Western Australia, Perth, WA 6009, Australia
| | - Shaun P Collin
- Oceans Graduate School and the UWA Oceans Institute, The University of Western Australia, Perth, WA 6009, Australia.,School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Nathan S Hart
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Kate L Sanders
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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17
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Sherratt E, Sanders KL, Watson A, Hutchinson MN, Lee MSY, Palci A. Heterochronic Shifts Mediate Ecomorphological Convergence in Skull Shape of Microcephalic Sea Snakes. Integr Comp Biol 2019; 59:616-624. [DOI: 10.1093/icb/icz033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Abstract
Morphological variation among the viviparous sea snakes (Hydrophiinae), a clade of fully aquatic elapid snakes, includes an extreme “microcephalic” ecomorph that has a very small head atop a narrow forebody, while the hind body is much thicker (up to three times the forebody girth). Previous research has demonstrated that this morphology has evolved at least nine times as a consequence of dietary specialization on burrowing eels, and has also examined morphological changes to the vertebral column underlying this body shape. The question addressed in this study is what happens to the skull during this extreme evolutionary change? Here we use X-ray micro-computed tomography and geometric morphometric methods to characterize cranial shape variation in 30 species of sea snakes. We investigate ontogenetic and evolutionary patterns of cranial shape diversity to understand whether cranial shape is predicted by dietary specialization, and examine whether cranial shape of microcephalic species may be a result of heterochronic processes. We show that the diminutive cranial size of microcephalic species has a convergent shape that is correlated with trophic specialization to burrowing prey. Furthermore, their cranial shape is predictable for their size and very similar to that of juvenile individuals of closely related but non-microcephalic sea snakes. Our findings suggest that heterochronic changes (resulting in pedomorphosis) have driven cranial shape convergence in response to dietary specializations in sea snakes.
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Affiliation(s)
- Emma Sherratt
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kate L Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Amy Watson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mark N Hutchinson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Michael S Y Lee
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
| | - Alessandro Palci
- South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia
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18
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Sherratt E, Coutts FJ, Rasmussen AR, Sanders KL. Vertebral evolution and ontogenetic allometry: The developmental basis of extreme body shape divergence in microcephalic sea snakes. Evol Dev 2019; 21:135-144. [DOI: 10.1111/ede.12284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Emma Sherratt
- Department of Ecology and Evolutionary Biology School of Biological Sciences, The University of Adelaide Adelaide South Australia Australia
| | - Felicity J. Coutts
- Department of Ecology and Evolutionary Biology School of Biological Sciences, The University of Adelaide Adelaide South Australia Australia
- Earth Sciences Section, South Australian Museum Adelaide South Australia Australia
| | - Arne R. Rasmussen
- The Royal Danish Academy of Fine Arts, Schools of Architecture, Design and Conservation Copenhagen Denmark
| | - Kate L. Sanders
- Department of Ecology and Evolutionary Biology School of Biological Sciences, The University of Adelaide Adelaide South Australia Australia
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19
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Moon BR, Penning DA, Segall M, Herrel A. Feeding in Snakes: Form, Function, and Evolution of the Feeding System. FEEDING IN VERTEBRATES 2019. [DOI: 10.1007/978-3-030-13739-7_14] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Suntrarachun S, Chanhome L, Sumontha M. Identification of sea snake meat adulteration in meat products using PCR-RFLP of mitochondrial DNA. FOOD SCIENCE AND HUMAN WELLNESS 2018. [DOI: 10.1016/j.fshw.2018.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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21
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Sherratt E, Rasmussen AR, Sanders KL. Trophic specialization drives morphological evolution in sea snakes. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172141. [PMID: 29657807 PMCID: PMC5882731 DOI: 10.1098/rsos.172141] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/26/2018] [Indexed: 05/19/2023]
Abstract
Viviparous sea snakes are the most rapidly speciating reptiles known, yet the ecological factors underlying this radiation are poorly understood. Here, we reconstructed dated trees for 75% of sea snake species and quantified body shape (forebody relative to hindbody girth), maximum body length and trophic diversity to examine how dietary specialization has influenced morphological diversification in this rapid radiation. We show that sea snake body shape and size are strongly correlated with the proportion of burrowing prey in the diet. Specialist predators of burrowing eels have convergently evolved a 'microcephalic' morphotype with dramatically reduced forebody relative to hindbody girth and intermediate body length. By comparison, snakes that predominantly feed on burrowing gobies are generally short-bodied and small-headed, but there is no evidence of convergent evolution. The eel specialists also exhibit faster rates of size and shape evolution compared to all other sea snakes, including those that feed on gobies. Our results suggest that trophic specialization to particular burrowing prey (eels) has invoked strong selective pressures that manifest as predictable and rapid morphological changes. Further studies are needed to examine the genetic and developmental mechanisms underlying these dramatic morphological changes and assess their role in sea snake speciation.
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Affiliation(s)
- Emma Sherratt
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Arne R. Rasmussen
- The Royal Danish Academy of Fine Arts, Schools of Architecture, Design and Conservation, Copenhagen K, Denmark
| | - Kate L. Sanders
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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22
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Heatwole H, Grech A, Marsh H. Paleoclimatology, Paleogeography, and the Evolution and Distribution of Sea Kraits (Serpentes; Elapidae;Laticauda). HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Harold Heatwole
- School of Earth and Environmental Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Alana Grech
- Department of Environmental Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Helene Marsh
- College of Marine and Environmental Sciences, Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, Queensland 4811, Australia
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23
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Bever GS, Norell MA. A new rhynchocephalian (Reptilia: Lepidosauria) from the Late Jurassic of Solnhofen (Germany) and the origin of the marine Pleurosauridae. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170570. [PMID: 29291055 PMCID: PMC5717629 DOI: 10.1098/rsos.170570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
A new rhynchocephalian is described based on a recently discovered and well-preserved specimen from the Late Jurassic (Kimmeridgian) marine limestones of Solnhofen, Bavaria. Phylogenetic analysis recovers the new taxon as the sister group to Pleurosauridae, a small radiation of rhynchocephalians representing the oldest marine invasion of crown-clade Lepidosauria. The relatively strong evidence for this taxonomically exclusive lineage, within a generally volatile rhynchocephalian tree, places the new taxon in a position to inform the early history of the pleurosaur transition to the sea. The early steps in this transition are distributed throughout the skeleton and appear to increase hydrodynamic efficiency for both swimming and aquatic feeding. This early history may also have included a global truncation of plesiomorphic ontogenetic trajectories that left a number of skeletal features with reduced levels of ossification/fusion. The exact degree to which Vadasaurus had adopted an aquatic ecology remains unclear, but the insight it provides into the origin of the enigmatic pleurosaurs exemplifies the potential of Rhynchocephalia for generating and informing broad-based questions regarding the interplay of development, morphology, ecology and macroevolutionary patterns.
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Affiliation(s)
- Gabriel S. Bever
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Mark A. Norell
- Division of Paleontology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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24
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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25
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Park J, Kim IH, Koo KS, Park D. First Record of Laticauda semifasciata (Reptilia: Squamata: Elapidae: Laticaudinae) from Korea. ANIMAL SYSTEMATICS, EVOLUTION AND DIVERSITY 2016. [DOI: 10.5635/ased.2016.32.2.148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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26
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Lu L, Ge D, Chesters D, Ho SYW, Ma Y, Li G, Wen Z, Wu Y, Wang J, Xia L, Liu J, Guo T, Zhang X, Zhu C, Yang Q, Liu Q. Molecular phylogeny and the underestimated species diversity of the endemic white-bellied rat (Rodentia: Muridae:Niviventer) in Southeast Asia and China. ZOOL SCR 2015. [DOI: 10.1111/zsc.12117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Simon Y. W. Ho
- School of Biological Sciences; University of Sydney; Sydney NSW 2006 Australia
| | - Ying Ma
- Qinghai Institute for Endemic Disease Prevention and Control; Qinghai 811602 China
| | - Guichang Li
- State Key Laboratory for Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Yongjie Wu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Jun Wang
- State Key Laboratory for Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Jingli Liu
- State Key Laboratory for Infectious Disease Prevention and Control; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
| | - Tianyu Guo
- Institute of Health Quarantine; Chinese Academy of Inspection and Quarantine; Beijing 100020 China
| | - Xiaolong Zhang
- Institute of Health Quarantine; Chinese Academy of Inspection and Quarantine; Beijing 100020 China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
| | - Qiyong Liu
- State Key Laboratory for Infectious Disease Prevention and Control; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; National Institute for Communicable Disease Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing 102206 China
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Lillywhite HB, Heatwole H, Sheehy CM. Dehydration and drinking behavior in true sea snakes (Elapidae: Hydrophiinae: Hydrophiini). J Zool (1987) 2015. [DOI: 10.1111/jzo.12239] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. B. Lillywhite
- Earth and Environmental Sciences; James Cook University; Townsville Qld Australia
- Department of Biology; University of Florida; Gainesville FL USA
| | - H. Heatwole
- Earth and Environmental Sciences; James Cook University; Townsville Qld Australia
- Department of Biology; North Carolina State University; Raleigh NC USA
- Department of Zoology; The University of New England; Armidale NSW Australia
| | - C. M. Sheehy
- Earth and Environmental Sciences; James Cook University; Townsville Qld Australia
- Department of Biology; University of Florida; Gainesville FL USA
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Ukuwela KDB, de Silva A, Mumpuni, Fry BG, Sanders KL. Multilocus phylogeography of the sea snakeHydrophis curtusreveals historical vicariance and cryptic lineage diversity. ZOOL SCR 2014. [DOI: 10.1111/zsc.12070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kanishka D. B. Ukuwela
- School of Earth and Environmental Sciences; University of Adelaide; Darling Building Adelaide SA 5005 Australia
| | - Anslem de Silva
- Amphibia and Reptile research Organization of Sri Lanka; 15/1, Dolosbage Rd. Gampola Sri Lanka
| | - Mumpuni
- Museum of Zoology Bogor; Puslit Biology-LIPI; Cibinong Indonesia
| | - Bryan G. Fry
- Venom Evolution Laboratory; School of Biological Sciences; University of Queensland; Brisbane QLD 4072 Australia
| | - Kate L. Sanders
- School of Earth and Environmental Sciences; University of Adelaide; Darling Building Adelaide SA 5005 Australia
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Keck BP, Hulsey CD. Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens. Mol Phylogenet Evol 2014; 73:53-9. [PMID: 24472673 DOI: 10.1016/j.ympev.2014.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 01/15/2014] [Accepted: 01/18/2014] [Indexed: 11/19/2022]
Abstract
The incredibly species-rich cichlid fish faunas of both the Neotropics and Africa are generally thought to be reciprocally monophyletic. However, the phylogenetic affinity of the African cichlid Heterochromis multidens is ambiguous, and this distinct lineage could make African cichlids paraphyletic. In past studies, Heterochromis has been variously suggested to be one of the earliest diverging lineages within either the Neotropical or the African cichlid radiations, and it has even been hypothesized to be the sister lineage to a clade containing all Neotropical and African cichlids. We examined the phylogenetic relationships among a representative sample of cichlids with a dataset of 29 nuclear loci to assess the support for the different hypotheses of the phylogenetic position of Heterochromis. Although individual gene trees in some instances supported alternative relationships, a majority of gene trees, integration of genes into species trees, and hypothesis testing of putative topologies all supported Heterochromis as belonging to the clade of African cichlids.
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Affiliation(s)
- Benjamin P Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996, USA.
| | - C Darrin Hulsey
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996, USA.
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Ceccarelli DM, McKinnon AD, Andréfouët S, Allain V, Young J, Gledhill DC, Flynn A, Bax NJ, Beaman R, Borsa P, Brinkman R, Bustamante RH, Campbell R, Cappo M, Cravatte S, D'Agata S, Dichmont CM, Dunstan PK, Dupouy C, Edgar G, Farman R, Furnas M, Garrigue C, Hutton T, Kulbicki M, Letourneur Y, Lindsay D, Menkes C, Mouillot D, Parravicini V, Payri C, Pelletier B, Richer de Forges B, Ridgway K, Rodier M, Samadi S, Schoeman D, Skewes T, Swearer S, Vigliola L, Wantiez L, Williams A, Williams A, Richardson AJ. The coral sea: physical environment, ecosystem status and biodiversity assets. ADVANCES IN MARINE BIOLOGY 2013; 66:213-290. [PMID: 24182902 DOI: 10.1016/b978-0-12-408096-6.00004-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Coral Sea, located at the southwestern rim of the Pacific Ocean, is the only tropical marginal sea where human impacts remain relatively minor. Patterns and processes identified within the region have global relevance as a baseline for understanding impacts in more disturbed tropical locations. Despite 70 years of documented research, the Coral Sea has been relatively neglected, with a slower rate of increase in publications over the past 20 years than total marine research globally. We review current knowledge of the Coral Sea to provide an overview of regional geology, oceanography, ecology and fisheries. Interactions between physical features and biological assemblages influence ecological processes and the direction and strength of connectivity among Coral Sea ecosystems. To inform management effectively, we will need to fill some major knowledge gaps, including geographic gaps in sampling and a lack of integration of research themes, which hinder the understanding of most ecosystem processes.
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