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Collins SB, Bracken-Grissom HD. The language of light: a review of bioluminescence in deep-sea decapod shrimps. Biol Rev Camb Philos Soc 2024. [PMID: 38706106 DOI: 10.1111/brv.13093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
In the dark, expansive habitat of the deep sea, the production of light through bioluminescence is commonly used among a wide range of taxa. In decapod crustaceans, bioluminescence is only known in shrimps (Dendrobranchiata and Caridea) and may occur in different modes, including luminous secretions that are used to deter predators and/or from specialised light organs called photophores that function by providing camouflage against downwelling light. Photophores exhibit an extensive amount of morphological variation across decapod families: they may be internal (of hepatic origin) or embedded in surface tissues (dermal), and may possess an external lens, suggesting independent origins and multiple functions. Within Dendrobranchiata, we report bioluminescence in Sergestidae, Aristeidae, and Solenoceridae, and speculate that it may also be found in Acetidae, Luciferidae, Sicyonellidae, Benthesicymidae, and Penaeidae. Within Caridea, we report bioluminescence in Acanthephyridae, Oplophoridae, Pandalidae, and new observations for Pasiphaeidae. This comprehensive review includes historic taxonomic literature and recent studies investigating bioluminescence in all midwater and deep benthic shrimp families. Overall, we report known or suspected bioluminescence in 157 species across 12 families of decapod shrimps, increasing previous records of bioluminescent species by 65%. Mounting evidence from personal observations and the literature allow us to speculate the presence of light organs in several families thought to lack bioluminescence, making this phenomenon much more common than previously reported. We provide a detailed discussion of light organ morphology and function within each group and indicate future directions that will contribute to a better understanding of how deep-sea decapods use the language of light.
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Affiliation(s)
- Stormie B Collins
- Department of Biological Sciences, Florida International University, Institute of Environment, 3000 NE 151st St, North Miami, FL, 33181, USA
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University, Institute of Environment, 3000 NE 151st St, North Miami, FL, 33181, USA
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, Washington, WA, 20013-7012, USA
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2
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Wolfe JM, Ballou L, Luque J, Watson-Zink VM, Ahyong ST, Barido-Sottani J, Chan TY, Chu KH, Crandall KA, Daniels SR, Felder DL, Mancke H, Martin JW, Ng PKL, Ortega-Hernández J, Palacios Theil E, Pentcheff ND, Robles R, Thoma BP, Tsang LM, Wetzer R, Windsor AM, Bracken-Grissom HD. Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments. Syst Biol 2023:syad066. [PMID: 37941464 DOI: 10.1093/sysbio/syad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Indexed: 11/10/2023] Open
Abstract
For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Lauren Ballou
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | | | - Shane T Ahyong
- Australian Museum, 1 William St, Sydney, NSW 2010, Australia
- School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Joëlle Barido-Sottani
- Institut de Biologie de l'École Normale Supérieure (IBENS), ENS, CNRS, INSERM, Université PSL (Paris Sciences & Lettres), Paris, France
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202301, Taiwan, ROC
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Darryl L Felder
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Harrison Mancke
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Joel W Martin
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Peter K L Ng
- Lee Kong Chian Natural History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore, Singapore
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA
| | - Emma Palacios Theil
- Department of Invertebrate Zoology and Hydrobiology, University of Łódź, ul. Banacha 12/16, 90237 Łódź, Poland
| | - N Dean Pentcheff
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Rafael Robles
- Department of Biology and Laboratory for Crustacean Research, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Campeche, San Francisco de Campeche, Campeche, México
| | - Brent P Thoma
- Department of Biology, Jackson State University, P.O. Box 18540, Jackson, MS 39217, USA
| | - Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Regina Wetzer
- Research and Collections, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA
| | - Amanda M Windsor
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- United States Food and Drug Administration, Office of Regulatory Science, 5001 Campus Dr. College Park, MD 20740, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, Biscayne Bay Campus, North Miami, FL 33181, USA
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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Schweikert LE, Bagge LE, Naughton LF, Bolin JR, Wheeler BR, Grace MS, Bracken-Grissom HD, Johnsen S. Dynamic light filtering over dermal opsin as a sensory feedback system in fish color change. Nat Commun 2023; 14:4642. [PMID: 37607908 PMCID: PMC10444757 DOI: 10.1038/s41467-023-40166-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
Dynamic color change has evolved multiple times, with a physiological basis that has been repeatedly linked to dermal photoreception via the study of excised skin preparations. Despite the widespread prevalence of dermal photoreception, both its physiology and its function in regulating color change remain poorly understood. By examining the morphology, physiology, and optics of dermal photoreception in hogfish (Lachnolaimus maximus), we describe a cellular mechanism in which chromatophore pigment activity (i.e., dispersion and aggregation) alters the transmitted light striking SWS1 receptors in the skin. When dispersed, chromatophore pigment selectively absorbs the short-wavelength light required to activate the skin's SWS1 opsin, which we localized to a morphologically specialized population of putative dermal photoreceptors. As SWS1 is nested beneath chromatophores and thus subject to light changes from pigment activity, one possible function of dermal photoreception in hogfish is to monitor chromatophores to detect information about color change performance. This framework of sensory feedback provides insight into the significance of dermal photoreception among color-changing animals.
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Affiliation(s)
- Lorian E Schweikert
- Institute of the Environment, Department of Biological Sciences, Florida International University, North Miami, FL, 33181, USA.
- Biology Department, Duke University, Durham, NC, 27708, USA.
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, 28403, USA.
| | - Laura E Bagge
- Torch Technologies, Shalimar, FL, 32579, USA
- Air Force Research Laboratory/RWTCA, Eglin Air Force Base, FL, 32542, USA
| | - Lydia F Naughton
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, 28403, USA
| | - Jacob R Bolin
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, 28403, USA
| | | | - Michael S Grace
- College of Engineering and Science, Florida Institute of Technology, Melbourne, FL, 32901, USA
| | - Heather D Bracken-Grissom
- Institute of the Environment, Department of Biological Sciences, Florida International University, North Miami, FL, 33181, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Sönke Johnsen
- Biology Department, Duke University, Durham, NC, 27708, USA
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Pérez-Moreno JL, Kozma MT, DeLeo DM, Bracken-Grissom HD, Durica DS, Mykles DL. CrusTome: A transcriptome database resource for large-scale analyses across Crustacea. G3 (Bethesda) 2023:7148141. [PMID: 37130083 DOI: 10.1093/g3journal/jkad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 05/03/2023]
Abstract
Transcriptomes from non-traditional model organisms often harbor a wealth of unexplored data. Examining these datasets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for non-traditional model organisms remains limited. Crustaceans, for example, being amongst the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multi-species, multi-tissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoan for phylogenetic context) as an evolving, and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and datasets. CrusTome is presented in BLAST and DIAMOND formats, providing robust datasets for sequence similarity searches, orthology assignments, phylogenetic inference, etc., and thus allowing for straight-forward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the Cryptochrome Photolyase Family of proteins across crustaceans.
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Affiliation(s)
| | - Mihika T Kozma
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Danielle M DeLeo
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave NW, Washington, DC 20560, USA
| | - Heather D Bracken-Grissom
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave NW, Washington, DC 20560, USA
- Department of Biological Sciences and Institute of Environment, Florida International University, North Miami, FL 33181, USA
| | - David S Durica
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Donald L Mykles
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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5
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Colín A, Galván-Tirado C, Carreón-Palau L, Bracken-Grissom HD, Baeza JA. Mitochondrial genomes of the land hermit crab Coenobita clypeatus (Anomura: Paguroidea) and the mole crab Emerita talpoida (Anomura: Hippoidea) with insights into phylogenetic relationships in the Anomura (Crustacea: Decapoda). Gene X 2023; 849:146896. [DOI: 10.1016/j.gene.2022.146896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/31/2022] [Accepted: 09/12/2022] [Indexed: 11/28/2022] Open
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6
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Schweikert LE, Thomas KN, Moreno VM, Casaubon A, Golightly C, Bracken-Grissom HD. Ecological Predictors and Functional Implications of Eye Size in Deep-Sea Shrimps. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.787315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Constraints on energy resources and available light in the deep sea should place strong selection pressure on eye size, a fundamental determinant of visual ability. By examining eye size among 16 species (454 individuals) of deep-sea sergestid shrimps, we show significant differences in intraspecific eye growth rates and species eye-size averages that are correlated to different aspects of ecology and result in variable sighting distance thresholds of bioluminescence, one measure of visual performance. We used linear regressions modeling the lowest and highest bounds of phylogenetic signal to test for ecological correlates of relative and absolute eye size, which indicate the allocation of energetic resources toward eyes and an optical basis of visual capability, respectively. Of the ecological variables tested [mean depth, diel vertical migration (DVM) distance, habitat type, and light organ type], light organ type was the only significant correlate of both relative and absolute eye size, suggesting that bioluminescence plays a particularly important role in the evolution of sergestid vision and that these animals may be reliant on bioluminescent signaling. Our findings also suggest that the DVM imposes visual demands distinct from the average depths occupied by a species. While DVM distance correlated with relative eye size, mean depth correlated with absolute eye size, revealing that eye size increases with depth before 1,000 m, then decreases in bathypelagic (aphotic) zone. By applying measured eye sizes to models of visual performance, we estimated that sergestids can detect a bioluminescent point source from ≤3.77 m away, and that these sighting distance thresholds vary between species by a factor of three. In relative terms, however, all sergestids under the test conditions had a common detection threshold at ∼63.5 body lengths, suggesting that bioluminescence sighting distance is proportional among species and may be related to shared behaviors of swarming and copulation. By considering the effects of evolutionary history, light and nutrient availability, and the constraints of body size, our study reveals new patterns of deep-sea eye size evolution and provides new insights into the visual ecology of this diverse and important deep-sea group.
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7
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Timm LE, Jackson TL, Browder JA, Bracken-Grissom HD. Population Genomics of the Commercially Important Gulf of Mexico Pink Shrimp Farfantepenaeus duorarum (Burkenroad, 1939) Support Models of Juvenile Transport Around the Florida Peninsula. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.659134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Gulf of Mexico pink shrimp, Farfantepenaeus duorarum, supports large fisheries in the United States and Mexico, with nearly 7,000 tons harvested from the region in 2016. Given the commercial importance of this species, management is critical: in 1997, the southern Gulf of Mexico pink shrimp fishery was declared collapsed and mitigation strategies went into effect, with recovery efforts lasting over a decade. Fisheries management can be informed and improved through a better understanding of how factors associated with early life history impact genetic diversity and population structure in the recruited population. Farfantepenaeus duorarum are short-lived, but highly fecund, and display high variability in recruitment patterns. To date, modeling the impacts of ecological, physical, and behavioral factors on juvenile settlement has focused on recruitment of larval individuals of F. duorarum to nursery grounds in Florida Bay. Here, we articulate testable hypotheses stemming from a recent model of larval transport and evaluate support for each with a population genomics approach, generating reduced representation library sequencing data for F. duorarum collected from seven regions around the Florida Peninsula. Our research represents the first and most molecular data-rich study of population structure in F. duorarum in the Gulf and reveals evidence of a differentiated population in the Dry Tortugas. Our approach largely validates a model of larval transport, allowing us to make management-informative inferences about the impacts of spawning location and recruitment patterns on intraspecific genetic diversity. Such inferences improve our understanding of the roles of non-genetic factors in generating and maintaining genetic diversity in a commercially important penaeid shrimp species.
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8
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DeLeo DM, Bracken-Grissom HD. Lighting the way: Forces driving the diversification of bioluminescent signalling in sea fireflies. Mol Ecol 2021; 30:1747-1750. [PMID: 33709451 DOI: 10.1111/mec.15880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 11/29/2022]
Abstract
Understanding the drivers of diversification and processes that maintain biodiversity remains a central theme of evolutionary biology. However, these efforts are often impeded due to disparities across species and environments and the genetic complexity underlying many traits. The factors driving biodiversity can be more readily understood by focusing on the genetics of diversification, of one or few genes shared across species, with large influence over an organism's phenotype (Templeton, 1981; Wright, 1984). In this pursuit, previous studies often focus on the selective pressures that impact phenotypic diversity (Brawand et al., 2014; Yokoyama et al., 2015), often overlooking the contribution of neutral processes (i.e., genetic drift). In this issue of Molecular Ecology, Hensley et al. (2020) use an integrative approach, including RNA sequencing, in vitro protein expression and spectral measurements, to explore the drivers behind the diversification of bioluminescent signalling in cypridinid ostracods (Figure 1). Typical bioluminescent reactions primarily include an enzyme (luciferase) and substrate (luciferin). By focusing on a single gene, this study traces the molecular evolution of (c)luciferase in sea fireflies, elucidating diverse signatures of selection, drift and constraint to decipher the link between genotype and phenotype of their bioluminescent emissions.
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Affiliation(s)
- Danielle M DeLeo
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Institute of Environment, Florida International University, North Miami, FL, USA
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9
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Wolfe JM, Luque J, Bracken-Grissom HD. How to become a crab: Phenotypic constraints on a recurring body plan. Bioessays 2021; 43:e2100020. [PMID: 33751651 DOI: 10.1002/bies.202100020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022]
Abstract
A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as "carcinization." The repeated loss of this body plan has been identified as "decarcinization." In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.
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Affiliation(s)
- Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Javier Luque
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Smithsonian Tropical Research Institute, Balboa-Ancon, Panama.,Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, USA
| | - Heather D Bracken-Grissom
- Institute of Environment and Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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10
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Feller KD, Sharkey CR, McDuffee-Altekruse A, Bracken-Grissom HD, Lord NP, Porter ML, Schweikert LE. Surf and turf vision: Patterns and predictors of visual acuity in compound eye evolution. Arthropod Struct Dev 2021; 60:101002. [PMID: 33191145 DOI: 10.1016/j.asd.2020.101002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 06/11/2023]
Abstract
Eyes have the flexibility to evolve to meet the ecological demands of their users. Relative to camera-type eyes, the fundamental limits of optical diffraction in arthropod compound eyes restrict the ability to resolve fine detail (visual acuity) to much lower degrees. We tested the capacity of several ecological factors to predict arthropod visual acuity, while simultaneously controlling for shared phylogenetic history. In this study, we have generated the most comprehensive review of compound eye visual acuity measurements to date, containing 385 species that span six of the major arthropod classes. An arthropod phylogeny, made custom to this database, was used to develop a phylogenetically-corrected generalized least squares (PGLS) linear model to evaluate four ecological factors predicted to underlie compound eye visual acuity: environmental light intensity, foraging strategy (predator vs. non-predator), horizontal structure of the visual scene, and environmental medium (air vs. water). To account for optical constraints on acuity related to animal size, body length was also included, but this did not show a significant effect in any of our models. Rather, the PGLS analysis revealed that the strongest predictors of compound eye acuity are described by a combination of environmental medium, foraging strategy, and environmental light intensity.
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Affiliation(s)
- Kathryn D Feller
- Union College, Department of Biological Sciences, 807 Union St., Schenectady, NY, 12308, USA.
| | - Camilla R Sharkey
- University of Minnesota, Ecology Evolution and Behavior Department, Saint Paul, MN, USA
| | | | - Heather D Bracken-Grissom
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
| | - Nathan P Lord
- Louisiana State University, Entomology Department, Baton Rouge, LA, USA
| | - Megan L Porter
- University of Hawai'i at Mānoa, Department of Biology, Honolulu, HI, USA
| | - Lorian E Schweikert
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, FL 33181, USA
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11
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DeLeo DM, Bracken-Grissom HD. Illuminating the impact of diel vertical migration on visual gene expression in deep-sea shrimp. Mol Ecol 2020; 29:3494-3510. [PMID: 32748474 DOI: 10.1111/mec.15570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/19/2022]
Abstract
Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism's visual capabilities. Among deep-sea migrators are oplophorid shrimp that vertically migrate hundreds of metres to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid in camouflage. The organs have recently been shown to contain visual proteins (opsins) and genes that infer light sensitivity. Knowledge regarding the impacts of vertical migratory behaviour, and fluctuating environmental conditions, on sensory system evolution is unknown. In this study, the oplophorid Systellaspis debilis was either collected during the day from deep waters or at night from relatively shallow waters to ensure sampling across the vertical distributional range. De novo transcriptomes of light-sensitive tissues (eyes/photophores) from the day/night specimens were sequenced and analysed to characterize opsin diversity and visual/light interaction genes. Gene expression analyses were also conducted to quantify expression differences associated with DVM. Our results revealed an expanded opsin repertoire among the shrimp and differential opsin expression that may be linked to spectral tuning during the migratory process. This study sheds light on the sensory systems of a bioluminescent invertebrate and provides additional evidence for extraocular light sensitivity. Our findings further suggest opsin co-expression and subsequent fluctuations in opsin expression may play an important role in diversifying the visual responses of vertical migrators.
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Affiliation(s)
- Danielle M DeLeo
- Institute of Environment, Department of Biology, Florida International University, North Miami, FL, USA.,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Heather D Bracken-Grissom
- Institute of Environment, Department of Biology, Florida International University, North Miami, FL, USA
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12
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Papastamatiou YP, Verbeck D, Hutchinson M, Bracken-Grissom HD, Chapman D. An encounter between a pelagic shark and giant cephalopod. J Fish Biol 2020; 97:588-589. [PMID: 32492182 DOI: 10.1111/jfb.14415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/27/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
An oceanic whitetip shark (Carcharhinus longimanus) was observed off the coast of Kona, Hawaii, with scars caused by the tentacles of a large cephalopod. While the exact species could not be confirmed, candidate species include the giant squid (Architeuthis dux) or species from the genera Thysanoteuthis (flying squids) and Megalocranchia (glass squids). Telemetry shows C. longimanus will dive within the mesopelagic zone and may interact with or even forage for large cephalopods.
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Affiliation(s)
- Yannis P Papastamatiou
- Department of Biological Sciences, Florida International University, North Miami, Florida
| | | | - Melanie Hutchinson
- Joint Institute for Marine and Atmospheric Research, Pacific Islands Fisheries Science Center, Honolulu, Hawaii
| | | | - Demian Chapman
- Department of Biological Sciences, Florida International University, North Miami, Florida
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Wolfe JM, Breinholt JW, Crandall KA, Lemmon AR, Lemmon EM, Timm LE, Siddall ME, Bracken-Grissom HD. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Proc Biol Sci 2020; 286:20190079. [PMID: 31014217 DOI: 10.1098/rspb.2019.0079] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
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Affiliation(s)
- Joanna M Wolfe
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA.,2 Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology , Cambridge, MA 02139 , USA.,3 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
| | - Jesse W Breinholt
- 4 Florida Museum of Natural History, University of Florida , Gainesville, FL 32611 , USA.,5 RAPiD Genomics , Gainesville, FL 32601 , USA
| | - Keith A Crandall
- 6 Computational Biology Institute, The George Washington University , Ashburn, VA 20147 , USA.,7 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution , Washington, DC 20012 , USA
| | - Alan R Lemmon
- 8 Department of Scientific Computing, Florida State University , Dirac Science Library, Tallahassee, FL 32306 , USA
| | - Emily Moriarty Lemmon
- 9 Department of Biological Science, Florida State University , Tallahassee, FL 32306 , USA
| | - Laura E Timm
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
| | - Mark E Siddall
- 1 Division of Invertebrate Zoology and Sackler Institute of Comparative Genomics, American Museum of Natural History , New York, NY 10024 , USA
| | - Heather D Bracken-Grissom
- 10 Department of Biological Sciences, Florida International University , North Miami, FL 33181 , USA
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14
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Bracken-Grissom HD, DeLeo DM, Porter ML, Iwanicki T, Sickles J, Frank TM. Light organ photosensitivity in deep-sea shrimp may suggest a novel role in counterillumination. Sci Rep 2020; 10:4485. [PMID: 32161283 PMCID: PMC7066151 DOI: 10.1038/s41598-020-61284-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/30/2020] [Indexed: 12/31/2022] Open
Abstract
Extraocular photoreception, the ability to detect and respond to light outside of the eye, has not been previously described in deep-sea invertebrates. Here, we investigate photosensitivity in the bioluminescent light organs (photophores) of deep-sea shrimp, an autogenic system in which the organism possesses the substrates and enzymes to produce light. Through the integration of transcriptomics, in situ hybridization and immunohistochemistry we find evidence for the expression of opsins and phototransduction genes known to play a role in light detection in most animals. Subsequent shipboard light exposure experiments showed ultrastructural changes in the photophore similar to those seen in crustacean eyes, providing further evidence that photophores are light sensitive. In many deep-sea species, it has long been documented that photophores emit light to aid in counterillumination - a dynamic form of camouflage that requires adjusting the organ's light intensity to "hide" their silhouettes from predators below. However, it remains a mystery how animals fine-tune their photophore luminescence to match the intensity of downwelling light. Photophore photosensitivity allows us to reconsider the organ's role in counterillumination - not only in light emission but also light detection and regulation.
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Affiliation(s)
| | - Danielle M DeLeo
- Department of Biology, Florida International University, North Miami, FL, 33181, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Tom Iwanicki
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Jamie Sickles
- Department of Biology, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Tamara M Frank
- Department of Biology, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
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15
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Ditter RE, Erdman RB, Goebel AM, Bracken-Grissom HD. Widespread phenotypic hypervariation in the enigmatic anchialine shrimp Barbouria cubensis (Decapoda: Barbouriidae). Zootaxa 2019; 4648:zootaxa.4648.1.1. [PMID: 31716957 DOI: 10.11646/zootaxa.4648.1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Indexed: 11/04/2022]
Abstract
Classification and evolutionary relationships among anchialine shrimp from the family Barbouriidae Christoffersen, 1987, has long been a topic of debate amongst crustacean taxonomists. To date, no study has examined morphological or molecular variation among populations of these enigmatic shrimp. The present study documents and analyzes patterns of widespread morphological variation within populations of Barbouria cubensis von Martens, 1872, from anchialine pools on three Bahamian islands. Such extensive morphological variation confounds identification using classic taxonomical methods. Phenotypic variation is by no means a new topic, but studies of decapods are typically limited to isolated individuals or few morphological characters. Moreover, past studies of B. cubensis do not report extensive morphological variation, however we find that upwards of 90% of individuals are affected. Anomalous phenotypes are described in 54 morphological characters with no detectable pattern associated with geographic distribution. The term phenotypic hypervariation (PhyV) is used to describe morphological variation that greatly deviates from any previous taxonomic descriptions. Analysis of partial sequences of the 16S and COI mitochondrial genes confirm the identity of morphologically variable specimens as B. cubensis without population structure across the tropical western Atlantic. A test for cryptic diversity within B. cubensis suggests PhyV is not correlated with cryptic diversity. Morphological variation at this scale likely depends on recent changes either to their environment or genetic diversity.
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16
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Sanchez JL, Bracken-Grissom HD, Trexler JC. Freshwater-to-marine transitions may explain the evolution of herbivory in the subgenus Mollienesia (genus Poecilia, mollies and guppies). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The ability of organisms to cross ecosystem boundaries is an important catalyst of evolutionary diversification. The genus Poecilia (mollies and guppies) is an excellent system for studying ecosystem transitions because species display a range of salinity and dietary preferences, with herbivory concentrated in the subgenus Mollienesia. We reconstructed ancestral habitats and diets across a phylogeny of the genus Poecilia, evaluated diversification rates and used phylogenetically independent contrasts to determine whether diet evolved in response to habitat transition in this group. The results suggest that ancestors of subgenus Mollienesia were exclusively herbivorous, whereas ancestral diets of other Poecilia included animals. We found that transitions across euryhaline boundaries occurred at least once in this group, probably after the divergence of the subgenus Mollienesia. Furthermore, increased salinity affiliation explained 24% of the decrease in animals in the gut, and jaw morphology was associated with the percentage of animals in the gut, but not with the percentage of species occupying saline habitats. These findings suggest that in the genus Poecilia, herbivory evolved in association with transitions from fresh to euryhaline habitats, and jaw morphology evolved in response to the appearance of herbivory. These results provide a rare example of increased diet diversification associated with the transition from freshwater to euryhaline habitats.
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Affiliation(s)
| | | | - Joel C Trexler
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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17
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Timm L, Browder JA, Simon S, Jackson TL, Zink IC, Bracken-Grissom HD. A tree money grows on: the first inclusive molecular phylogeny of the economically important pink shrimp (Decapoda : Farfantepenaeus) reveals cryptic diversity. INVERTEBR SYST 2019. [DOI: 10.1071/is18044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Species of Farfantepenaeus support economically important shrimp fisheries throughout the Western Hemisphere, necessitating proper fisheries management. To be effective, species management should be informed of the potential presence of cryptic species and of the evolutionary forces driving biodiversity. This is best accomplished through a robust phylogenetic framework and evidence-based species delimitation. This study represents the first comprehensive molecular phylogeny and species delimitation analyses of shrimps belonging to the genus Farfantepenaeus. Targeting three mitochondrial genes (12S, 16S, and COI), gene trees and a phylogeny for the genus were inferred using maximum likelihood and Bayesian approaches. In general, the phylogenetic relationships inferred here largely agree with those recovered from morphological data, including the most recent designation of F. isabelae as sister to F. subtilis. Molecular divergence was found between northern and southern populations of F. brasiliensis, suggesting the existence of unrecognised subspecies. However, previous recognition of F. duorarum and F. notialis as two distinct species was not supported by this study. The phylogeny inferred here also uncovers a phylogeographic signal of latitudinal speciation in the genus. The study presented here provides valuable insight into the evolutionary history of Farfantepenaeus, improving our ability to effectively manage these economically important species.
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18
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DeLeo DM, Pérez-Moreno JL, Vázquez-Miranda H, Bracken-Grissom HD. RNA profile diversity across arthropoda: guidelines, methodological artifacts, and expected outcomes. Biol Methods Protoc 2018; 3:bpy012. [PMID: 32161805 PMCID: PMC6994094 DOI: 10.1093/biomethods/bpy012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 12/19/2022] Open
Abstract
High-quality RNA is an important precursor for high-throughput RNA sequencing (RNAseq) and subsequent analyses. However, the primary metric used to assess RNA quality, the RNA Integrity Number (RIN), was developed based on model bacterial and vertebrate organisms. Though the phenomenon is not widely recognized, invertebrate 28S ribosomal RNA (rRNA) is highly prone to a form of denaturation known as gap deletion, in which the subunit collapses into two smaller fragments. In many nonmodel invertebrates, this collapse of the 28S subunit appears as a single band similar in size to the 18S rRNA subunit. This phenomenon is hypothesized to be commonplace among arthropods and is often misinterpreted as a "degraded" rRNA profile. The limited characterization of gap deletion in arthropods, a highly diverse group, as well as other nonmodel invertebrates, often biases RNA quality assessments. To test whether the collapse of 28S is a general pattern or a methodological artifact, we sampled more than half of the major lineages within Arthropoda. We found that the 28S collapse is present in ∼90% of the species sampled. Nevertheless, RNA profiles exhibit considerable diversity with a range of banding patterns. High-throughput RNAseq and subsequent assembly of high-quality transcriptomes from select arthropod species exhibiting collapsed 28S subunits further illustrates the limitations of current RIN proxies in accurately characterizing RNA quality in nonmodel organisms. Furthermore, we show that this form of 28S denaturation, which is often mistaken for true "degradation," can occur at relatively low temperatures.
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Affiliation(s)
- Danielle M DeLeo
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
| | - Jorge L Pérez-Moreno
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
| | - Hernán Vázquez-Miranda
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA
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19
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Pérez-Moreno JL, Balázs G, Bracken-Grissom HD. Transcriptomic Insights into the Loss of Vision in Molnár János Cave’s Crustaceans. Integr Comp Biol 2018; 58:452-464. [DOI: 10.1093/icb/icy071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jorge L Pérez-Moreno
- Department of Biological Sciences, Florida International University—Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University—Biscayne Bay Campus, North Miami, FL 33181, USA
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20
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Pérez-Moreno JL, Balázs G, Wilkins B, Herczeg G, Bracken-Grissom HD. The role of isolation on contrasting phylogeographic patterns in two cave crustaceans. BMC Evol Biol 2017; 17:247. [PMID: 29216829 PMCID: PMC5721366 DOI: 10.1186/s12862-017-1094-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 11/24/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The underlying mechanisms and processes that prompt the colonisation of extreme environments, such as caves, constitute major research themes of evolutionary biology and biospeleology. The special adaptations required to survive in subterranean environments (low food availability, hypoxic waters, permanent darkness), and the geographical isolation of caves, nominate cave biodiversity as ideal subjects to answer long-standing questions concerning the interplay amongst adaptation, biogeography, and evolution. The present project aims to examine the phylogeographic patterns exhibited by two sympatric species of surface and cave-dwelling peracarid crustaceans (Asellus aquaticus and Niphargus hrabei), and in doing so elucidate the possible roles of isolation and exaptation in the colonisation and successful adaptation to the cave environment. RESULTS Specimens of both species were sampled from freshwater hypogean (cave) and epigean (surface) habitats in Hungary, and additional data from neighbouring countries were sourced from Genbank. Sequencing of mitochondrial and nuclear loci revealed, through haplotype network reconstruction (TCS) and phylogenetic inference, the genetic structure, phylogeographic patterns, and divergence-time estimates of A. aquaticus and N. hrabei surface and cave populations. Contrasting phylogeographic patterns were found between species, with A. aquaticus showing strong genetic differentiation between cave and surface populations and N. hrabei lacking any evidence of genetic structure mediated by the cave environment. Furthermore, N. hrabei populations show very low levels of genetic differentiation throughout their range, which suggests the possibility of recent expansion events over the last few thousand years. CONCLUSIONS Isolation by cave environment, rather than distance, is likely to drive the genetic structuring observed between immediately adjacent cave and surface populations of A. aquaticus, a predominantly surface species with only moderate exaptations to subterranean life. For N. hrabei, in which populations exhibit a fully 'cave-adapted' (troglomorphic) phenotype, the lack of genetic structure suggests that subterranean environments do not pose a dispersal barrier for this surface-cave species.
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Affiliation(s)
- Jorge L. Pérez-Moreno
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, H-1117 Hungary
| | - Blake Wilkins
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
| | - Gábor Herczeg
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, H-1117 Hungary
| | - Heather D. Bracken-Grissom
- Department of Biological Sciences, Florida International University - Biscayne Bay Campus, 3000 NE 151 St., North Miami, FL 33181 USA
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21
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Robalino J, Wilkins B, Bracken-Grissom HD, Chan TY, O’Leary MA. The Origin of Large-Bodied Shrimp that Dominate Modern Global Aquaculture. PLoS One 2016; 11:e0158840. [PMID: 27415002 PMCID: PMC4945062 DOI: 10.1371/journal.pone.0158840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/22/2016] [Indexed: 11/18/2022] Open
Abstract
Several shrimp species from the clade Penaeidae are farmed industrially for human consumption, and this farming has turned shrimp into the largest seafood commodity in the world. The species that are in demand for farming are an anomaly within their clade because they grow to much larger sizes than other members of Penaeidae. Here we trace the evolutionary history of the anomalous farmed shrimp using combined data phylogenetic analysis of living and fossil species. We show that exquisitely preserved fossils of †Antrimpos speciosus from the Late Jurassic Solnhofen limestone belong to the same clade as the species that dominate modern farming, dating the origin of this clade to at least 145 mya. This finding contradicts a much younger Late Cretaceous age (ca. 95 mya) previously estimated for this clade using molecular clocks. The species in the farmed shrimp clade defy a widespread tendency, by reaching relatively large body sizes despite their warm water lifestyles. Small body sizes have been shown to be physiologically favored in warm aquatic environments because satisfying oxygen demands is difficult for large organisms breathing in warm water. Our analysis shows that large-bodied, farmed shrimp have more gills than their smaller-bodied shallow-water relatives, suggesting that extra gills may have been key to the clade's ability to meet oxygen demands at a large size. Our combined data phylogenetic tree also suggests that, during penaeid evolution, the adoption of mangrove forests as habitats for young shrimp occurred multiple times independently.
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Affiliation(s)
- Javier Robalino
- Department of Anatomical Sciences, HSC T-8 (040), Stony Brook University, Stony Brook, New York, United States of America
| | - Blake Wilkins
- Department of Biology, Florida International University, Biscayne Bay Campus, North Miami, Florida, United States of America
| | - Heather D. Bracken-Grissom
- Department of Biology, Florida International University, Biscayne Bay Campus, North Miami, Florida, United States of America
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, Republic of China
| | - Maureen A. O’Leary
- Department of Anatomical Sciences, HSC T-8 (040), Stony Brook University, Stony Brook, New York, United States of America
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22
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Chen CL, Goy JW, Bracken-Grissom HD, Felder DL, Tsang LM, Chan TY. Corrigendum to: Phylogeny of Stenopodidea (Crustacea : Decapoda) shrimps inferred from nuclear and mitochondrial genes reveals non-monophyly of the families Spongicolidae and Stenopididae and most of their composite genera. INVERTEBR SYST 2016. [DOI: 10.1071/is16024_co] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The infraorder Stenopodidea is a relatively small group of marine decapod crustaceans including the well known cleaner shrimps, but their higher taxonomy has been rather controversial. This study provides the most comprehensive molecular phylogenetic analyses of Stenopodidea using sequence data from two mitochondrial (16S and 12S rRNA) and two nuclear (histone H3 and sodium–potassium ATPase ?-subunit (NaK)) genes. We included all 12 nominal genera from the three stenopodidean families in order to test the proposed evolutionary hypothesis and taxonomic scheme of the group. The inferred phylogeny did not support the familial ranking of Macromaxillocarididae and rejected the reciprocal monophyly of Spongicolidae and Stenopididae. The genera Stenopus, Richardina, Spongiocaris, Odontozona, Spongicola and Spongicoloides are showed to be poly- or paraphyletic, with monophyly of only the latter three genera strongly rejected in the analysis. The present results only strongly support the monophyly of Microprosthema and suggest that Paraspongiola should be synonymised with Spongicola. The three remaining genera, Engystenopus, Juxtastenopus and Globospongicola, may need to be expanded to include species from other genera if their statuses are maintained. All findings suggest that the morphological characters currently adopted to define genera are mostly invalid and substantial taxonomic revisions are required. As the intergeneric relationships were largely unresolved in the present attempt, the hypothesis of evolution of deep-sea sponge-associated taxa from shallow-water free-living species could not be verified here. The present molecular phylogeny, nevertheless, provides some support that stenopoididean shrimps colonised the deep sea in multiple circumstances.
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23
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Chen CL, Goy JW, Bracken-Grissom HD, Felder DL, Tsang LM, Chan TY. Phylogeny of Stenopodidea (Crustacea : Decapoda) shrimps inferred from nuclear and mitochondrial genes reveals non-monophyly of the families Spongicolidae and Stenopididae and most of their composite genera. INVERTEBR SYST 2016. [DOI: 10.1071/is16024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The infraorder Stenopodidea is a relatively small group of marine decapod crustaceans including the well known cleaner shrimps, but their higher taxonomy has been rather controversial. This study provides the most comprehensive molecular phylogenetic analyses of Stenopodidea using sequence data from two mitochondrial (16S and 12S rRNA) and two nuclear (histone H3 and sodium–potassium ATPase α-subunit (NaK)) genes. We included all 12 nominal genera from the three stenopodidean families in order to test the proposed evolutionary hypothesis and taxonomic scheme of the group. The inferred phylogeny did not support the familial ranking of Macromaxillocarididae and rejected the reciprocal monophyly of Spongicolidae and Stenopididae. The genera Stenopus, Richardina, Spongiocaris, Odontozona, Spongicola and Spongicoloides are showed to be poly- or paraphyletic, with monophyly of only the latter three genera strongly rejected in the analysis. The present results only strongly support the monophyly of Microprosthema and suggest that Paraspongiola should be synonymised with Spongicola. The three remaining genera, Engystenopus, Juxtastenopus and Globospongicola, may need to be expanded to include species from other genera if their statuses are maintained. All findings suggest that the morphological characters currently adopted to define genera are mostly invalid and substantial taxonomic revisions are required. As the intergeneric relationships were largely unresolved in the present attempt, the hypothesis of evolution of deep-sea sponge-associated taxa from shallow-water free-living species could not be verified here. The present molecular phylogeny, nevertheless, provides some support that stenopoididean shrimps colonised the deep sea in multiple circumstances.
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24
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Wong JM, Pérez-Moreno JL, Chan TY, Frank TM, Bracken-Grissom HD. Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda). Mol Phylogenet Evol 2014; 83:278-92. [PMID: 25482362 DOI: 10.1016/j.ympev.2014.11.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/17/2014] [Accepted: 11/22/2014] [Indexed: 12/17/2022]
Abstract
Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores. Phylogenetic analyses can be useful for tracing the evolution of bioluminescence, however, the few studies that have attempted to reconcile the relationships within Oplophoridae have generated trees with low-resolution. We present the most comprehensive phylogeny of Oplophoridae to date, with 90% genera coverage using seven genes (mitochondrial and nuclear) across 30 oplophorid species. We use our resulting topology to trace the evolution of bioluminescence within Oplophoridae. Previous studies have suggested that oplophorid visual systems may be tuned to differentiate the separate modes of bioluminescence. While all oplophorid shrimp possess a visual pigment sensitive to blue-green light, only those bearing photophores have an additional pigment sensitive to near-ultraviolet light. We attempt to characterize opsins, visual pigment proteins essential to light detection, in two photophore-bearing species (Systellaspis debilis and Oplophorus gracilirostris) and make inferences regarding their function and evolutionary significance.
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Affiliation(s)
- Juliet M Wong
- Florida International University, Department of Biological Sciences, 3000 NE 151st St, North Miami, FL 33181, United States.
| | - Jorge L Pérez-Moreno
- Florida International University, Department of Biological Sciences, 3000 NE 151st St, North Miami, FL 33181, United States.
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan, ROC.
| | - Tamara M Frank
- Nova Southeastern University, Oceanographic Center, 8000 North Ocean Drive, Dania Beach, FL 33004, United States.
| | - Heather D Bracken-Grissom
- Florida International University, Department of Biological Sciences, 3000 NE 151st St, North Miami, FL 33181, United States.
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25
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Speiser DI, Pankey MS, Zaharoff AK, Battelle BA, Bracken-Grissom HD, Breinholt JW, Bybee SM, Cronin TW, Garm A, Lindgren AR, Patel NH, Porter ML, Protas ME, Rivera AS, Serb JM, Zigler KS, Crandall KA, Oakley TH. Using phylogenetically-informed annotation (PIA) to search for light-interacting genes in transcriptomes from non-model organisms. BMC Bioinformatics 2014; 15:350. [PMID: 25407802 PMCID: PMC4255452 DOI: 10.1186/s12859-014-0350-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. Results We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/). Conclusions Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/s12859-014-0350-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel I Speiser
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA. .,Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.
| | - M Sabrina Pankey
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Alexander K Zaharoff
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara A Battelle
- The Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University-Biscayne Bay Campus, North Miami, FL, USA.
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | - Thomas W Cronin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA.
| | - Anders Garm
- Department of Biology, Marine Biological Section, University of Copenhagen, Copenhagen, Denmark.
| | - Annie R Lindgren
- Department of Biology, Portland State University, Portland, OR, USA.
| | - Nipam H Patel
- Department of Molecular and Cell Biology & Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Megan L Porter
- Department of Biology, University of South Dakota, Vermillion, SD, USA.
| | - Meredith E Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA, USA.
| | - Ajna S Rivera
- Department of Biology, University of the Pacific, Stockton, CA, USA.
| | - Jeanne M Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
| | - Kirk S Zigler
- Department of Biology, Sewanee: The University of the South, Sewanee, TN, USA.
| | - Keith A Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA. .,Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Todd H Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, USA.
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Felder DL, Thoma BP, Schmidt WE, Sauvage T, Self-Krayesky SL, Chistoserdov A, Bracken-Grissom HD, Fredericq S. Seaweeds and Decapod Crustaceans on Gulf Deep Banks after the Macondo Oil Spill. Bioscience 2014. [DOI: 10.1093/biosci/biu119] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Bracken-Grissom HD, Ahyong ST, Wilkinson RD, Feldmann RM, Schweitzer CE, Breinholt JW, Bendall M, Palero F, Chan TY, Felder DL, Robles R, Chu KH, Tsang LM, Kim D, Martin JW, Crandall KA. The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida). Syst Biol 2014; 63:457-79. [PMID: 24562813 DOI: 10.1093/sysbio/syu008] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A rich fossil history coupled with dense taxon coverage allowed us to estimate and compare divergence times and origins of major lineages using two drastically different approaches. Age priors were constructed and/or included based on fossil age information or fossil discovery, age, and extant species count data. Results from the two approaches were largely congruent across deep to shallow taxonomic divergences across major lineages. The origin of the first lobster-like decapod (Polychelida) was estimated in the Devonian (∼409-372 Ma) with all infraorders present in the Carboniferous (∼353-318 Ma). Fossil calibration subsampling studies examined the influence of sampling density (number of fossils) and placement (deep, middle, and shallow) on divergence time estimates. Results from our study suggest including at least 1 fossil per 10 operational taxonomic units (OTUs) in divergence dating analyses. [Dating; decapods; divergence; lobsters; molecular; morphology; phylogenetics.].
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Florida International University, 3000 NE 151st Street, North Miami, FL 33181, USA;
| | - Shane T Ahyong
- Australian Museum, 6 College Street, Sydney, NSW 2010, Australia;University of New South Wales, Kensington, NSW 2052, Australia
| | | | | | - Carrie E Schweitzer
- Kent State University at Stark, 6000 Frank Avenue NW, North Canton, OH 44720, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Ferran Palero
- Unitat Mixta Genòmica i Salut CSISP-UV, Institut Cavanilles Universitat de Valencia, C/Catedrático Jose Beltran 2,46980 Paterna, Spain
| | - Tin-Yam Chan
- Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan, R.O.C
| | - Darryl L Felder
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Rafael Robles
- Laboratory of Bioecology and Crustacean Systematics, Department of Biology, FFCLRP, University of São Paulo (USP), Ave. Bandeirantes 3900, CEP 14040 - 901, Ribeirão Preto, SP Brazil
| | - Ka-Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ling-Ming Tsang
- Institute of Marine Biology and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan, R.O.C.;School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Dohyup Kim
- Brigham Young University, 401 WIDB, Provo, UT 84606, USA
| | - Joel W Martin
- Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Keith A Crandall
- George Washington University, Computational Biology Institute, Ashburn, VA 20147, USA
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Bracken-Grissom HD, Cannon ME, Cabezas P, Feldmann RM, Schweitzer CE, Ahyong ST, Felder DL, Lemaitre R, Crandall KA. A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda). BMC Evol Biol 2013; 13:128. [PMID: 23786343 PMCID: PMC3708748 DOI: 10.1186/1471-2148-13-128] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 05/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history-phylogeny, divergence times, character evolution and diversification-of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses. RESULTS Our best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224-296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae. CONCLUSIONS Our findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights into the origins of major lineages and events and the timing of morphological (body form) and ecological (habitat) transitions. Living anomuran biodiversity is the product of 2 major changes in the tempo of diversification; our initial insights suggest that the acquisition of a crab-like form did not act as a key innovation.
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Florida International University-Biscayne Bay Campus, North Miami, FL 33181, USA.
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Bracken-Grissom HD, Felder DL, Vollmer NL, Martin JW, Crandall KA. Phylogenetics links monster larva to deep-sea shrimp. Ecol Evol 2012; 2:2367-73. [PMID: 23145324 PMCID: PMC3492765 DOI: 10.1002/ece3.347] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/10/2012] [Accepted: 07/14/2012] [Indexed: 11/07/2022] Open
Abstract
Mid-water plankton collections commonly include bizarre and mysterious developmental stages that differ conspicuously from their adult counterparts in morphology and habitat. Unaware of the existence of planktonic larval stages, early zoologists often misidentified these unique morphologies as independent adult lineages. Many such mistakes have since been corrected by collecting larvae, raising them in the lab, and identifying the adult forms. However, challenges arise when the larva is remarkably rare in nature and relatively inaccessible due to its changing habitats over the course of ontogeny. The mid-water marine species Cerataspis monstrosa (Gray 1828) is an armored crustacean larva whose adult identity has remained a mystery for over 180 years. Our phylogenetic analyses, based in part on recent collections from the Gulf of Mexico, provide definitive evidence that the rare, yet broadly distributed larva, C. monstrosa, is an early developmental stage of the globally distributed deepwater aristeid shrimp, Plesiopenaeus armatus. Divergence estimates and phylogenetic relationships across five genes confirm the larva and adult are the same species. Our work demonstrates the diagnostic power of molecular systematics in instances where larval rearing seldom succeeds and morphology and habitat are not indicative of identity. Larval-adult linkages not only aid in our understanding of biodiversity, they provide insights into the life history, distribution, and ecology of an organism.
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Affiliation(s)
- Heather D Bracken-Grissom
- Department of Biology, Brigham Young University Provo, Utah, 84602 ; Department of Biology, Florida International University-Biscayne Bay Campus North Miami, Florida, 33181
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Bybee SM, Bracken-Grissom HD, Hermansen RA, Clement MJ, Crandall KA, Felder DL. Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea). ZOOL ANZ 2011. [DOI: 10.1016/j.jcz.2011.05.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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