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Angst P, Dexter E, Stillman JH. Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae). G3 (Bethesda) 2024; 14:jkad281. [PMID: 38079165 PMCID: PMC10849366 DOI: 10.1093/g3journal/jkad281] [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] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 02/09/2024]
Abstract
Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Jonathon H Stillman
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Briffa M, Arnott G, Hardege JD. Hermit crabs as model species for investigating the behavioural responses to pollution. Sci Total Environ 2024; 906:167360. [PMID: 37774883 DOI: 10.1016/j.scitotenv.2023.167360] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/23/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/01/2023]
Abstract
Human impacts on the environment affect organisms at all levels of biological organisation and ultimately can change their phenotype. Over time, phenotypic change may arise due to selection but individual phenotypes are also subject to change via genotype × environment interactions. In animals, behaviour is the most flexible aspect of phenotype, and hence the most liable to change across environmental gradients including exposure to pollution. Here we review current knowledge on the impacts of pollution, broadly defined to include the release of substances, energy, and the effects of carbon emissions, on the behaviour of a highly studied group, the globally distributed hermit crabs. We first show how their obligate association with empty gastropod shells underpins their use as model organisms for the study of resource-assessment, contest, and risk-coping behaviours. Intense study of hermit crabs has advanced our understanding of how animals use information, and we discuss the ways in which pollutants can disrupt the cognitive processes involved. We then highlight current studies of hermit crabs, which paint a clear picture of behavioural changes due to multiple pollutants. Impacts on behaviour vary across pollutants and entire suites of behaviours can be influenced by a single pollutant, with the potential for interactive and cascade effects. Hermit crabs offer the opportunity for detailed behavioural analysis, including application of the repeated measures animal-personality framework, and they are highly amenable to experimental manipulations. As such, we show how they now provide a model system for studying the impacts of pollution on behaviour, yielding insights broadly applicable across animal diversity.
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Affiliation(s)
- Mark Briffa
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK.
| | - Gareth Arnott
- Queen's University Belfast, School of Biological Sciences, 19 Chlorine Gardens, Belfast BT9 5DL, Northern Ireland, UK
| | - Jörg D Hardege
- Scool of Natural Sciences, Biological Science, University of Hull, Cottingham Road, Hull HU6 7RX, UK
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Goldoni A, Pacheco MR, da Silva LB. Comet assay in Aegla platensis (Decapoda: Anomura) using a non-lethal hemolymph field sampling for in situ monitoring of freshwater genotoxicity. Ecotoxicology 2023; 32:160-165. [PMID: 36680665 DOI: 10.1007/s10646-023-02627-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
This study aimed to apply the comet assay on Aegla platensis crabs as a suitable non-destructive approach for in situ monitoring of freshwater genotoxicity. Animals were captured during four sampling periods in a stream under minor anthropogenic impacts in Southern Brazil. Crabs were captured with a hand net, then the hemolymph samples were collected, and the animals were released into the stream after a 20-min recovery time. Hemolymph samples were transported to the laboratory and used to perform the alkaline comet assay. Results showed an intermediate level in the DNA damage index (range 107.3-165.0 arbitrary unit). No significant differences were observed among the different sampling periods. Hemolymph was successfully used as a non-lethal source of biological samples, and the comet assay using A. platensis proved to be a feasible approach for genotoxicity studies.
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Affiliation(s)
- Angélica Goldoni
- Feevale University, ERS-239, 2755, Novo Hamburgo, Rio Grande do Sul, Brazil
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Pang X, Fu W, Feng J, Guo B, Lin X, Lu X. The Complete Mitochondrial Genome of the Hermit Crab Diogenes edwardsii (Anomura: Diogenidae) and Phylogenetic Relationships within Infraorder Anomura. Genes (Basel) 2023; 14:470. [PMID: 36833397 PMCID: PMC9956181 DOI: 10.3390/genes14020470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
A complete mitochondrial genome (mitogenome) can provide important information for gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few mitogenomes of hermit crabs (superfamily Paguridae) in the infraorder Anomura have been reported. This study reports the first complete mitogenome of the hermit crab Diogenes edwardsii assembled using high-throughput sequencing. The mitogenome of Diogenes edwardsii is 19,858 bp in length and comprises 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. There are 28 and six genes observed on the heavy and light strands, respectively. The genome composition was highly A + T biased (72.16%), and exhibited a negative AT-skew (-0.110) and positive GC-skew (0.233). Phylogenetic analyses based on the nucleotide dataset of 16 Anomura species indicated that D. edwardsii was closest related to Clibanarius infraspinatus in the same family, Diogenidae. Positive selection analysis showed that two residues located in cox1 and cox2 were identified as positively selected sites with high BEB value (>95%), indicating that these two genes are under positive selection pressure. This is the first complete mitogenome of the genus Diogenes, and this finding helps us to represent a new genomic resource for hermit crab species and provide data for further evolutionary status of Diogenidae in Anomura.
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Affiliation(s)
- Xiaoke Pang
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Wenjing Fu
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jianfeng Feng
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Biao Guo
- Department of Fishery Resources, Tianjin Fisheries Research Institute, Tianjin 300457, China
| | - Xiaolong Lin
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
| | - Xueqiang Lu
- Tianjin Key Laboratory of Environmental Technology for Complex Trans-Media Pollution and Tianjin International Joint Research Center for Environmental Biogeochemical Technology, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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Sliadovskii D, Ponomareva T, Molchanov M, Pozdnyakova-Filatova I, Timchenko M, Marchenkov V, Gusev O, Sogorin E. β-elimination of hyaluronate by red king crab hyaluronidase. Sci Rep 2021; 11:22600. [PMID: 34799594 PMCID: PMC8604925 DOI: 10.1038/s41598-021-01890-3] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022] Open
Abstract
Crustacean hyaluronidases are poorly understood both in terms of their enzymatic properties and in terms of their structural features. In this work, we show that the hepatopancreas homogenate of the red king crab has a hyaluronidase activity that is an order of magnitude higher than its commercial counterpart. Zymography revealed that the molecular weight of a protein with hyalorunidase activity is 40-50 kDa. Analysis of the hepatopancreas transcriptome and results of cloning and sequencing of cDNA revealed a hyaluronidase sequence with an expected molecular weight of 42.5 kDa. Further analysis showed that hyaluronat enzymatic cleavage follows the [Formula: see text]-elimination mechanism, which is well known for bacterial hyaluronidases. The results of ion-exchange chromatography showed that the final product of hyaluronate degradation is unsaturated tetrasaccharide. Thus, we identified a new hyaluronidase of higher eukaryotes, which is not integrated into the modern classification of hyaluronidases.
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Affiliation(s)
- Dmitrii Sliadovskii
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290
| | - Tatyana Ponomareva
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290
| | - Maxim Molchanov
- Institute of Theoretical and Experimental Biophysics of the RAS, Pushchino, Russia, 142290
| | - Irina Pozdnyakova-Filatova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russia, 142290
| | - Maria Timchenko
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290
| | | | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia, 420012
- Graduate School of Medicine, Juntendo University, Tokyo , 113-8421, Japan
| | - Evgeny Sogorin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the RAS", Pushchino, Russia, 142290.
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Yan RJ, Schnabel KE, Guo XZ, Gardner JPA. Development and characterization of 20 polymorphic microsatellite loci in the deep sea squat lobster, Munida isos Ahyong and Poore, 2004 and cross-amplification in two congeneric species. J Genet 2019; 98:11. [PMID: 30945689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Munida isos is a deep sea squat lobster species that is widely distributed across the New Zealand and east Australian region, and is often associated with deep sea vulnerable marine ecosystems. To investigate its population genetic structure and patterns of regional connectivity, microsatellite loci were developed for M. isos from two genomic libraries using the Illumina HiSeq 2500 sequencing platform. Twenty-six loci amplified consistently in M. isos from the Tasman Sea, among which 20 were polymorphic and selectively neutral. Evidence of null alleles was observed at eight loci. Most loci exhibited moderate to high levels of polymorphism, with an average polymorphic information content value of 0.482. The mean number of alleles per locus was 7.45, with a mean expected heterozygosity of 0.520. Thirteen loci exhibited significant deviation from Hardy-Weinberg equilibrium, while only one locus pair was in linkage disequilibrium after false discovery rate correction for multiple testing (P < 0.05). Cross-species amplification tests revealed that the transferability of 14 loci (70%) was positive for the two congeners M. endeavourae and M. gracilis. The accessibility to new polymorphic microsatellite loci will facilitate population genetic studies and aid in developing conservation and management strategies for vulnerable marine ecosystems.
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Affiliation(s)
- Ruo-Jin Yan
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
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Kostin NN, Bobik TV, Shurdova EM, Ziganshin RH, Surina EA, Shagin DA, Shagina IA, Knorre VD, Isaev VA, Rudenskaya GN, Gabibov AG, Smirnov IV. Cloning and characterization of serpin from red king crab Paralithodes camtschaticus. Fish Shellfish Immunol 2018; 81:99-107. [PMID: 30006043 DOI: 10.1016/j.fsi.2018.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/14/2018] [Revised: 06/28/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Serpins are a family of serine protease inhibitors that are involved in numerous physiological processes and are known to regulate innate immunity pathways. To advance our understanding of their role in P. camtschaticus, a commercially significant species, we cloned and characterized a serpin from this species, designated serpin PC, that has anticoagulant and anticomplement effects on human blood. We found that serpin PC is a secreted protein with a typical serpin-like primary structure that is similar to other known crustacean serpins. Recombinant serpin PC was found to have inhibitory activity against R/K-specific bovine cationic trypsin. The reaction proceeds through the formation of a stable covalent complex of peptidase with P1 residue R383 of serpin PC. This interaction is characterized by a relatively high overall inhibition constant kass=(2.3 ± 0.7) × 106 M-1s-1 and an SI of 4.7 ± 0.8. Protein localization by western blotting showed that serpin PC is present in the muscles and, to a lesser extent, the heart, whereas it is transcribed predominantly in hemocytes and the heart. Through peptidase activity profiling of hemocytes and plasma, we found that serpin PC inhibits at least two R/K-specific activities and showed that it inhibits phenoloxidase (PO) activity induction in hemocytes.
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Affiliation(s)
- N N Kostin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - T V Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - E M Shurdova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - R H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - E A Surina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D A Shagin
- Central Research Institute of Epidemiology, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - I A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - V D Knorre
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - V A Isaev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - G N Rudenskaya
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - I V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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Landschoff J, Komai T, du Plessis A, Gouws G, Griffiths CL. MicroCT imaging applied to description of a new species of Pagurus Fabricius, 1775 (Crustacea: Decapoda: Anomura: Paguridae), with selection of three-dimensional type data. PLoS One 2018; 13:e0203107. [PMID: 30256803 PMCID: PMC6157836 DOI: 10.1371/journal.pone.0203107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/14/2018] [Indexed: 01/06/2023] Open
Abstract
A new species of hermit crab, Pagurus fraserorum n. sp. (family Paguridae) is described from rocky subtidal reefs off KwaZulu-Natal, South Africa, and illustrated using both conventional drawings and colour photographs, and via three-dimensional (3D) X-ray micro-computed tomography (μCT). Because of the limitation μCT has in detecting very fine and soft structures, a novel approach of manually drawing setation and spinulation onto the two-dimensional images of the 3D visualizations was used to illustrate the pereopods. In addition, an interactive figure and rotation movie clips in the supplement section complement the species description, and the 3D raw data of the 3D type data are downloadable from the Gigascience Database repository. The new species is the sixth species of Pagurus Fabricius, 1775 reported from South Africa and is closely allied to the Indo-Pacific P. boriaustraliensis Morgen, 1990 and P. pitagsaleei McLaughlin, 2002, from which it differs by its shorter ocular peduncles, by the armature of the carpus of the right cheliped, and also in colouration. This study presents the first description of a hermit crab in which a majority of taxonomic details are illustrated through 3D volume-rendered illustrations. In addition, colour photographs and COI molecular barcodes are provided, and the latter compared to COI sequences of specimens from Western Australia previously identified as P. boriaustraliensis and of specimens of P. pitagsaleei from Taiwan, as well as to three additional South African members of the genus. The South African taxon was confirmed to be genetically distinct from all species tested.
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Affiliation(s)
- Jannes Landschoff
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, Western Cape, South Africa
| | - Tomoyuki Komai
- Natural History Museum and Institute, Aoba-cho, Chuo-ku, Chiba, Japan
| | - Anton du Plessis
- CT Scanner, Central Analytical Facility, Stellenbosch University, Stellenbosch, Western Cape, South Africa
| | - Gavin Gouws
- National Research Foundation–South African Institute for Aquatic Biodiversity, Grahamstown, Eastern Cape, South Africa
| | - Charles L. Griffiths
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, Western Cape, South Africa
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Wang C, Agrawal S, Laudien J, Häussermann V, Held C. Discrete phenotypes are not underpinned by genome-wide genetic differentiation in the squat lobster Munida gregaria (Crustacea: Decapoda: Munididae): a multi-marker study covering the Patagonian shelf. BMC Evol Biol 2016; 16:258. [PMID: 27903261 PMCID: PMC5131467 DOI: 10.1186/s12862-016-0836-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 08/17/2016] [Accepted: 11/21/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers. The widespread squat lobster Munida gregaria comprises two discrete ecotypes, gregaria s. str. and subrugosa, which were long regarded as different species due to marked differences in morphological, ecological and behavioral traits. We studied the morphometry and genetics of M. gregaria s. l. and tested (1) whether the phenotypic differences remain stable after continental-scale sampling and inclusion of different life stages, (2) and whether each phenotype is underpinned by a specific genotype. RESULTS A total number of 219 gregaria s. str. and subrugosa individuals from 25 stations encompassing almost entire range in South America were included in morphological and genetic analyses using nine unlinked hypervariable microsatellites and new COI sequences. Results from the PCA and using discriminant functions demonstrated that the morphology of the two forms remains discrete. The mitochondrial data showed a shallow, star-like haplotype network and complete overlap of genetic distances within and among ecotypes. Coalescent-based species delimitation methods, PTP and GMYC, coherently suggested that haplotypes of both ecotypes forms a single species. Although all microsatellite markers possess sufficient genetic variation, AMOVA, PCoA and Bayesian clustering approaches revealed no genetic clusters corresponding to ecotypes or geographic units across the entire South-American distribution. No evidence of isolation-by-distance could be detected for this species in South America. CONCLUSIONS Despite their pronounced bimodal morphologies and different lifestyles, the gregaria s. str. and subrugosa ecotypes form a single, dimorphic species M. gregaria s. l.. Based on adequate geographic coverage and multiple independent polymorphic loci, there is no indication that each phenotype may have a unique genetic basis, leaving phenotypic plasticity or localized genomic islands of speciation as possible explanations.
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Affiliation(s)
- Chen Wang
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Shobhit Agrawal
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Jürgen Laudien
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Vreni Häussermann
- Universidad Católica de Valparaíso, Facultad de Recursos Naturales, Escuela de Ciencias del Mar, Avda. Brasil 2950, Valparaíso, Chile
- Huinay Scientific Field Station, Huinay, Los Lagos Chile
| | - Christoph Held
- Alfred Wegener Institute, Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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Thatje S, Marsh L, Roterman CN, Mavrogordato MN, Linse K. Adaptations to Hydrothermal Vent Life in Kiwa tyleri, a New Species of Yeti Crab from the East Scotia Ridge, Antarctica. PLoS One 2015; 10:e0127621. [PMID: 26107940 PMCID: PMC4480985 DOI: 10.1371/journal.pone.0127621] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/15/2015] [Indexed: 11/18/2022] Open
Abstract
Hydrothermal vents in the Southern Ocean are the physiologically most isolated chemosynthetic environments known. Here, we describe Kiwa tyleri sp. nov., the first species of yeti crab known from the Southern Ocean. Kiwa tyleri belongs to the family Kiwaidae and is the visually dominant macrofauna of two known vent sites situated on the northern and southern segments of the East Scotia Ridge (ESR). The species is known to depend on primary productivity by chemosynthetic bacteria and resides at the warm-eurythermal vent environment for most of its life; its short-range distribution away from vents (few metres) is physiologically constrained by the stable, cold waters of the surrounding Southern Ocean. Kiwa tylerihas been shown to present differential life history adaptations in response to this contrasting thermal environment. Morphological adaptations specific to life in warm-eurythermal waters, as found on – or in close proximity of – vent chimneys, are discussed in comparison with adaptations seen in the other two known members of the family (K. hirsuta, K. puravida), which show a preference for low temperature chemosynthetic environments.
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Affiliation(s)
- Sven Thatje
- Ocean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH, United Kingdom
- * E-mail:
| | - Leigh Marsh
- Ocean and Earth Science, University of Southampton, European Way, Southampton, SO14 3ZH, United Kingdom
| | | | - Mark N. Mavrogordato
- Engineering Sciences, μ-VIS CT Imaging Centre, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Katrin Linse
- British Antarctic Survey, High Cross Madingley Road, CB3 0ET, Cambridge, United Kingdom
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Thaler AD, Plouviez S, Saleu W, Alei F, Jacobson A, Boyle EA, Schultz TF, Carlsson J, Van Dover CL. Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis lauensis) from southwestern Pacific back-arc basins. PLoS One 2014; 9:e101345. [PMID: 24983244 PMCID: PMC4077841 DOI: 10.1371/journal.pone.0101345] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 06/05/2014] [Indexed: 12/03/2022] Open
Abstract
Studies of genetic connectivity and population structure in deep-sea chemosynthetic ecosystems often focus on endosymbiont-hosting species that are directly dependent on chemical energy extracted from vent effluent for survival. Relatively little attention has been paid to vent-associated species that are not exclusively dependent on chemosynthetic ecosystems. Here we assess connectivity and population structure of two vent-associated invertebrates—the shrimp Chorocaris sp. 2 and the squat lobster Munidopsis lauensis—that are common at deep-sea hydrothermal vents in the western Pacific. While Chorocaris sp. 2 has only been observed at hydrothermal vent sites, M. lauensis can be found throughout the deep sea but occurs in higher abundance around the periphery of active vents We sequenced mitochondrial COI genes and deployed nuclear microsatellite markers for both species at three sites in Manus Basin and either North Fiji Basin (Chorocaris sp. 2) or Lau Basin (Munidopsis lauensis). We assessed genetic differentiation across a range of spatial scales, from approximately 2.5 km to more than 3000 km. Population structure for Chorocaris sp. 2 was comparable to that of the vent-associated snail Ifremeria nautilei, with a single seemingly well-mixed population within Manus Basin that is genetically differentiated from conspecifics in North Fiji Basin. Population structure for Munidopsis lauensis was more complex, with two genetically differentiated populations in Manus Basin and a third well-differentiated population in Lau Basin. The unexpectedly high level of genetic differentiation between M. lauensis populations in Manus Basin deserves further study since it has implications for conservation and management of diversity in deep-sea hydrothermal vent ecosystems.
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Affiliation(s)
- Andrew David Thaler
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
- * E-mail:
| | - Sophie Plouviez
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - William Saleu
- Nautilus Minerals, Port Moresby, NCD, Papua New Guinea
| | - Freddie Alei
- Environmental Science and Geography Division, School of Natural and Physical Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Alixandra Jacobson
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - Emily A. Boyle
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - Thomas F. Schultz
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
| | - Jens Carlsson
- School of Biology & Environmental Science, University College Dublin, Dublin, Ireland
| | - Cindy Lee Van Dover
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, North Carolina, United States of America
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12
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Barber BR, Xu J, Pérez-Losada M, Jara CG, Crandall KA. Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis. PLoS One 2012; 7:e37105. [PMID: 22685541 PMCID: PMC3369872 DOI: 10.1371/journal.pone.0037105] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 04/17/2012] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Multiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS A nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand years ago. An isolation-with-migration analysis and maximum-likelihood estimates of gene flow showed asymmetrical exchange of genetic material between these two river systems exclusively in their headwaters. We used information theory to determine the best-fit demographic history between these two river systems under an isolation-with-migration model. The best-fit model suggests that the Negro and the ancestral populations have the same effective population sizes; whereas the Chico-Chubut population is smaller and shows that gene flow from the Chico-Chubut into the Negro is four times higher than in the reverse direction. Much of the Chico-Chubut system appears to have only been recently colonized while the Negro populations appear to have been in place for most of the evolutionary history of this taxon. CONCLUSIONS/SIGNIFICANCE Due to mitochondrial introgression, three nuclear loci provided different phylogeographic resolution than the three mitochondrial genes for an ancient fragmentation event observed in the nuclear phylogeny. However, the mitochondrial locus provided greater resolution on more recent evolutionary events. Our study, therefore, demonstrates the need to include both nuclear and mitochondrial loci for a more complete understanding of evolutionary histories and associated phylogeographic events. Our results suggest that gene flow between these systems, before and after fragmentation was through periodic paleolakes that formed in the headwaters region. Fragmentation between the Negro and Chico-Chubut systems was driven by the disappearance of these paleolakes during the Patagonian Glaciation.
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Affiliation(s)
- Brian R Barber
- Department of Biology, Brigham Young University, Provo, Utah, United States of America.
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13
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Matzen da Silva J, dos Santos A, Cunha MR, Costa FO, Creer S, Carvalho GR. Multigene molecular systematics confirm species status of morphologically convergent Pagurus hermit crabs. PLoS One 2011; 6:e28233. [PMID: 22174780 PMCID: PMC3235110 DOI: 10.1371/journal.pone.0028233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 11/04/2011] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION In spite of contemporary morphological taxonomy appraisals, apparent high morphological similarity raises uncertainty about the species status of certain Pagurus hermit crabs. This is exemplified between two European species, Pagurus excavatus (Herbst, 1791) and Pagurus alatus (Fabricius 1775), whose species status is still difficult to resolve using morphological criteria alone. METHODOLOGY/PRINCIPAL FINDINGS To address such ambiguities, we used combinations of Maximum Likelihood (ML) and Bayesian Inference (BI) methods to delineate species boundaries of P. alatus and P. excavatus and formulate an intermediate Pagurus phylogenetic hypothesis, based upon single and concatenated mitochondrial (cytochrome oxidase I [COI]) and nuclear (16S and 28s ribosomal RNA) gene partitions. The molecular data supported the species status of P. excavatus and P. alatus and also clearly resolved two divergent clades within hermit crabs from the Northeast Atlantic Ocean and the Mediterranean Sea. CONCLUSIONS/SIGNIFICANCE Despite the abundance and prominent ecological role of hermit crabs, Pagurus, in North East Atlantic Ocean and Mediterranean Sea ecosystems, many important aspects of their taxonomy, biology, systematics and evolution remain poorly explored. The topologies presented here should be regarded as hypotheses that can be incorporated into the robust and integrated understanding of the systematic relationships within and between species of the genus Pagurus inhabiting the Northeast Atlantic Ocean and the Mediterranean Sea.
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Affiliation(s)
- Joana Matzen da Silva
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
- * E-mail: (JMdS); (GRC)
| | | | - Marina R. Cunha
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar, Universidade de Aveiro, Aveiro, Portugal
| | - Filipe O. Costa
- Departamento de Biologia, Centro de Biologia Molecular e Ambiental (CBMA), Universidade do Minho, Braga, Portugal
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre for Wales, Bangor University, Bangor, Wales, United Kingdom
- * E-mail: (JMdS); (GRC)
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14
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Pérez-Losada M, Bond-Buckup G, Jara CG, Crandall KA. Conservation assessment of southern South American freshwater ecoregions on the basis of the distribution and genetic diversity of crabs from the genus Aegla. Conserv Biol 2009; 23:692-702. [PMID: 19236451 DOI: 10.1111/j.1523-1739.2008.01161.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We assessed the conservation priority of 18 freshwater ecoregions in southern South America on the basis of Aegla (genus of freshwater crabs) genetic diversity and distribution. Geographical distributions for 66 Aegla species were taken from the literature and plotted against ecoregions and main river basins of southern South America. Species richness and number of threatened and endemic species were calculated for each area. To assess taxonomic and phylogenetic diversity, we generated a molecular phylogeny based on DNA sequences for one nuclear (28S) and 4 mitochondrial (12S, 16S, COI, and COII) genes. All species richness and phylogenetic methods agreed, to a large extent, in their rankings of the importance of conservation areas, as indicated by the Spearman's rank correlation coefficient (p < 0.01); nonetheless, some of the lowest correlations were observed between taxonomic and phylogenetic diversity indices. The 5 ecoregions of the Laguna dos Patos Basin (Eastern Brazil), Central Chile, South Brazilian Coast, Chilean Lakes, and Subtropical Potamic Axis (northern Argentina and southern Uruguay and Paraguay) had the highest biodiversity scores. Conservation of these regions will preserve the largest number of species and the greatest amount of genetic diversity within the South American freshwater Aegla fauna. Biodiversity across rivers and within areas was heterogeneously distributed in the ecoregions of Upper Paraná, Ribeira do Iguape, Upper Uruguay, and South Brazilian Coast (i.e., one river showed significantly more biodiversity than any other river from the same ecoregion), but homogeneously distributed in the other ecoregions. Hence, conservation plans in the former regions will potentially require less effort than plans in the latter regions.
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Affiliation(s)
- M Pérez-Losada
- Department of Biology and Monte L. Bean Life Science Museum, Brigham Young University, Provo UT 84602-5255, USA.
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15
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Sperstad SV, Haug T, Paulsen V, Rode TM, Strandskog G, Solem ST, Styrvold OB, Stensvåg K. Characterization of crustins from the hemocytes of the spider crab, Hyas araneus, and the red king crab, Paralithodes camtschaticus. Dev Comp Immunol 2009; 33:583-591. [PMID: 19041340 DOI: 10.1016/j.dci.2008.10.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/20/2008] [Accepted: 10/23/2008] [Indexed: 05/27/2023]
Abstract
Crustins are distributed across the decapods and are believed to play a significant part in the humoral defense system of their host. In this study, two crustin isoforms from Hyas araneus hemocytes were purified and tested for antimicrobial activity against selected microorganisms. They show both antibacterial and antifungal activity, with highest activity against the Gram-positive bacteria Corynebacterium glutamicum. Sequencing of the transcripts showed them to have a mature peptide of 90 amino acids and differing in three positions in the mature peptide. They were named CruHa1 and CruHa2. Real-time RT-PCR revealed that they mainly are expressed in hemocytes. Screening a cDNA library detected a crustin sequence in Paralithodes camtschaticus hemocytes, coding for a mature peptide of 98 amino acids. It was named CruPc. Based on phylogenetic inference and primary structure, CruHa1 and CruHa2 were placed within the Type I group of crustins, while CruPc belongs to the Type II.
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Affiliation(s)
- Sigmund V Sperstad
- Department of Marine Biotechnology, The Norwegian College of Fishery Science, University of Tromsø, N-9037 Tromsø, Norway
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16
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Zelenina DA, Miuge NS, Volkov AA, Sokolov VI. [Red king crab (Paralithodes camtschaticus) in the Barents Sea: a comparative study of introduced and native populations]. Genetika 2008; 44:983-991. [PMID: 18767547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Red king crab (Paralithodes camtschaticus) was introduced into the Barents Sea in the 1960-1970s. Its present habitation area spans on the coastal zone from Hammerfest (Northern Norway) to the Barents Sea Funnel in the north-east of the Kola Peninsula. We studied the polymorphism of a mitochondrial gene encoding cytochrome oxidase (COI) and five nuclear microsatellite loci in four samples from the Barents Sea and two donor populations from the Western Kamchatka and Primorye. No decrease in the genetic diversity of the introduced populations was detected. Microsatellite assay demonstrated that the sample from Varrangerfjord was distinct from the rest five populations. However, no significant differences between the rest samples were found. Possible reasons underlying this phenomenon are discussed.
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Schwab IR, Nilsson DE. A stranger in his own home. Br J Ophthalmol 2007; 91:709. [PMID: 17563928 PMCID: PMC1955607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- I R Schwab
- University of California, Davis, Sacramento, California 95817, USA.
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18
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Abstract
Hepatopancreas of king crab Paralithodes camtschatica produces a metalloprotease, which belongs to the astacin family, as cDNA cloning and sequencing showed. The metalloprotease has been purified chromatographically to apparent homogeneity. The purification factor was 16 and activity recovery was 20%. pH and temperature optimum have been determined. In its properties (molecular weight, pI, metal content) the metalloprotease is close to crayfish astacin. However, analysis of the enzyme sequences revealed differences, which account for differences in substrate specificities and imply a different activation mechanism.
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Affiliation(s)
- Svetlana A Semenova
- Chemistry Department of Moscow State University, Leninskie Gory, GSP-3, Moscow, 119899, Russia
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19
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Hiller A, Kraus H, Almon M, Werding B. The Petrolisthes galathinus complex: species boundaries based on color pattern, morphology and molecules, and evolutionary interrelationships between this complex and other Porcellanidae (Crustacea: Decapoda: Anomura). Mol Phylogenet Evol 2006; 40:547-69. [PMID: 16684610 DOI: 10.1016/j.ympev.2006.03.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2005] [Revised: 03/17/2006] [Accepted: 03/17/2006] [Indexed: 11/30/2022]
Abstract
While the amphi-American porcellanid crab Petrolistes galathinus has been traditionally viewed as a highly variable species containing several different color forms, we consider it to be a complex of at least 6 morphologically similar species with similar ecological requirements, but diagnosable through coloration. Here we surveyed sequence variation of the mitochondrial 16S rRNA gene, compared the morphology of adults and of the first larval stage (Zoea I), and explored shape variation of the sternal plate using geometric morphometric methods, to investigate boundaries among the species in the complex, and to confirm the validity of color and color pattern for distinguishing them. Sequences and larval morphological characters of other porcellanids were included to investigate the correspondence between genetic divergence and morphology of adults and larvae. The molecular and morphometric results support the validity of the species in the complex, and of color pattern for their distinction. The close relationship between the complex and the putative ancenstral porcellanid Parapetrolisthes tortugensis was indicated by the molecular and larval-morphology results. The adult morphology of this species is interpreted as a result of convergent evolution driven by a relatively rapid ecological adaptation to conditions in deeper waters. The nesting position in the phylogenetic trees of Petrocheles australiensis outside the Porcellanidae clade questions the monophyly of this family.
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Affiliation(s)
- Alexandra Hiller
- Department of Animal Ecology and Systematic Zoology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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Machordom A, Macpherson E. Rapid radiation and cryptic speciation in squat lobsters of the genus Munida (Crustacea, Decapoda) and related genera in the South West Pacific: molecular and morphological evidence. Mol Phylogenet Evol 2005; 33:259-79. [PMID: 15336662 DOI: 10.1016/j.ympev.2004.06.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Revised: 06/04/2004] [Indexed: 11/21/2022]
Abstract
Squat lobsters (genus Munida and related genera) are among the most diverse taxa of western Pacific crustaceans, though several features of their biology and phylogenetic relationships are unknown. This paper reports an extensive phylogenetic analysis based on mitochondrial DNA sequences (cytochrome c oxidase subunit I and 16S rRNA) and the morphology of 72 species of 12 genera of western Pacific squat lobsters. Our phylogenetic reconstruction using molecular data supports the recent taxonomic splitting of the genus Munida into several genera. Excluding one species (M. callista), the monophyly of the genus Munida was supported by Bayesian analysis of the molecular data. Three moderately diverse genera (Onconida, Paramunida, and Raymunida) also appeared monophyletic, both according to morphological and molecular data, always with high support. However, other genera (Crosnierita and Agononida) seem to be para- or polyphyletic. Three new cryptic species were identified in the course of this study. It would appear that the evolution of this group was marked by rapid speciation and stasis, or certain constraints, in its morphological evolution.
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Affiliation(s)
- Annie Machordom
- Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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21
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Pérez-Losada M, Bond-Buckup G, Jara CG, Crandall KA. Molecular Systematics and Biogeography of the Southern South American Freshwater “Crabs” Aegla (Decapoda: Anomura: Aeglidae) Using Multiple Heuristic Tree Search Approaches. Syst Biol 2004; 53:767-80. [PMID: 15545254 DOI: 10.1080/10635150490522331] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Recently new heuristic genetic algorithms such as Treefinder and MetaGA have been developed to search for optimal trees in a maximum likelihood (ML) framework. In this study we combined these methods with other standard heuristic approaches such as ML and maximum parsimony hill-climbing searches and Bayesian inference coupled with Markov chain Monte Carlo techniques under homogeneous and mixed models of evolution to conduct an extensive phylogenetic analysis of the most abundant and widely distributed southern South American freshwater"crab,"the Aegla(Anomura: Aeglidae). A total of 167 samples representing 64 Aegla species and subspecies were sequenced for one nuclear (28S rDNA) and four mitochondrial (12S and 16S rDNA, COI, and COII) genes (5352 bp total). Additionally, six other anomuran species from the genera Munida,Pachycheles, and Uroptychus(Galatheoidea), Lithodes(Paguroidea), and Lomis(Lomisoidea) and the nuclear 18S rDNA gene (1964 bp) were included in preliminary analyses for rooting the Aegla tree. Nonsignificantly different phylogenetic hypotheses resulted from all the different heuristic methods used here, although the best scored topologies found under the ML hill-climbing, Bayesian, and MetaGA approaches showed considerably better likelihood scores (Delta> 54) than those found under the MP and Treefinder approaches. Our trees provided strong support for most of the recognized Aegla species except for A. cholchol,A. jarai,A. parana,A. marginata, A. platensis, and A. franciscana, which may actually represent multiple species. Geographically, the Aegla group was divided into a basal western clade (21 species and subspecies) composed of two subclades with overlapping distributions, and a more recent central-eastern clade (43 species) composed of three subclades with fairly well-recognized distributions. This result supports the Pacific-Origin Hypothesis postulated for the group; alternative hypotheses of Atlantic or multiple origins were significantly rejected by our analyses. Finally, we combined our phylogenetic results with previous hypotheses of South American paleodrainages since the Jurassic to propose a biogeographical framework of the Aegla radiation.
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Affiliation(s)
- Marcos Pérez-Losada
- Department of Integrative Biology, Brigham Young University, Provo, Utah 84602-5181, USA.
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Kislitsyn IA, Rebrikov DV, Dunaevskiĭ IE, Rudenskaia GN. [Isolation and primary structure of trypsin from the red king crab Paralithodes camtschaticus]. Bioorg Khim 2003; 29:269-76. [PMID: 12845802 DOI: 10.1023/a:1023932415680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Trypsin from hepatopancreas of the Paralithodes camtschaticus crab was isolated in homogeneous state by successive ion-exchange chromatography on DEAE-Sephadex, affinity chromatography on Agarose modified with peptide ligands from trypsin hydrolysate of salmin, and ion-exchange chromatography on a Mono Q column. The total yield of the protein was 64%. Its N-terminal amino acid sequence was determined (IVGGTEVTPG-). A sample of amplified total cDNA of hepatopancreas of king crab was obtained. The cDNA fragment containing the complete coding part of the gene was isolated on the basis of the known N-terminal amino acid sequence of the mature form of the trypsin. The polypeptide chain of the proenzyme consists of 266 aa. The mature trypsin involves 237 aa, which corresponds to its molecular mass of 24.8 kDa. A comparison of the amino acid sequence of the king crab trypsin with those of trypsins from other species of crustaceans demonstrated their high structural homology. The trypsin from the Penaeus vannamei shrimp appeared to be the most close in its primary structure to that of the king crab (70% identity).
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Affiliation(s)
- Iu A Kislitsyn
- Chemical Faculty, Moscow State University, Vorob'evy gory, Moscow, 119899 Russia
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Shagin DA, Rebrikov DV, Kozhemyako VB, Altshuler IM, Shcheglov AS, Zhulidov PA, Bogdanova EA, Staroverov DB, Rasskazov VA, Lukyanov S. A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. Genome Res 2002; 12:1935-42. [PMID: 12466298 PMCID: PMC187582 DOI: 10.1101/gr.547002] [Citation(s) in RCA: 191] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have characterized a novel nuclease from the Kamchatka crab, designated duplex-specific nuclease (DSN). DSN displays a strong preference for cleaving double-stranded DNA and DNA in DNA-RNA hybrid duplexes, compared to single-stranded DNA. Moreover, the cleavage rate of short, perfectly matched DNA duplexes by this enzyme is essentially higher than that for nonperfectly matched duplexes of the same length. Thus, DSN differentiates between one-nucleotide variations in DNA. We developed a novel assay for single nucleotide polymorphism (SNP) detection based on this unique property, termed "duplex-specific nuclease preference" (DSNP). In this innovative assay, the DNA region containing the SNP site is amplified and the PCR product mixed with signal probes (FRET-labeled short sequence-specific oligonucleotides) and DSN. During incubation, only perfectly matched duplexes between the DNA template and signal probe are cleaved by DSN to generate sequence-specific fluorescence. The use of FRET-labeled signal probes coupled with the specificity of DSN presents a simple and efficient method for detecting SNPs. We have employed the DSNP assay for the typing of SNPs in methyltetrahydrofolate reductase, prothrombin and p53 genes on homozygous and heterozygous genomic DNA.
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Affiliation(s)
- Dmitry A Shagin
- Shemiakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117871 Moscow, Russia
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Abstract
The entire mitochondrial gene order of the crustacean Pagurus longicarpus was determined by sequencing all but approximately 300 bp of the mitochondrial genome. We report the first major gene rearrangements found in the clade including Crustacea and Insecta. At least eight mitochondrial gene rearrangements have dramatically altered the gene order of the hermit crab P. longicarpus relative to the putatively ancestral crustacean gene order. These include two rearrangements of protein-coding genes, the first reported for any nonchelicerate arthropod. Codon usage and amino acid sequences do not deviate substantially from those reported for other crustaceans. Investigating the phylogenetic distribution of these eight rearrangements will add additional characters to help resolve decapod phylogeny.
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Affiliation(s)
- M J Hickerson
- Department of Zoology, Duke University, Durham, North Carolina, USA
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Abstract
King crabs (Family Lithodidae) are among the world's largest arthropods, having a crab-like morphology and a strongly calcified exoskeleton. The hermit crabs, by contrast, have depended on gastropod shells for protection for over 150 million years. Shell-living has constrained the morphological evolution of hermit crabs by requiring a decalcified asymmetrical abdomen capable of coiling into gastropod shells and by preventing crabs from growing past the size of the largest available shells. Whereas reduction in shell-living and acquisition of a crab-like morphology (carcinization) has taken place independently in several hermit crab lineages, and most dramatically in king crabs, the rate at which this process has occurred was entirely unknown. We present molecular evidence that king crabs are not only descended from hermit crabs, but are nested within the hermit crab genus Pagurus. We estimate that loss of the shell-living habit and the complete carcinization of king crabs has taken between 13 and 25 million years.
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Affiliation(s)
- C W Cunningham
- Department of Biology, Yale University, New Haven, Connecticut 06511
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