1
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Schultz JA, Hebert PDN. Do pseudogenes pose a problem for metabarcoding marine animal communities? Mol Ecol Resour 2022; 22:2897-2914. [PMID: 35700118 DOI: 10.1111/1755-0998.13667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 06/01/2022] [Indexed: 11/30/2022]
Abstract
Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.
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Affiliation(s)
- Jessica A Schultz
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
| | - Paul D N Hebert
- Department of Integrative Biology, University of Guelph, Guelph, ON, CANADA.,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, CANADA
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2
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Raupach MJ, Rulik B, Spelda J. Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). Zookeys 2022; 1082:103-125. [PMID: 35115867 PMCID: PMC8794987 DOI: 10.3897/zookeys.1082.69851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.
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3
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Ashrafi H, Hultgren KM. Integrative methods resolve taxonomy and relationships of snapping shrimps in the genus Synalpheus (Decapoda: Alpheidae) collected during the MNHN ‘Madibenthos’ expedition. INVERTEBR SYST 2022. [DOI: 10.1071/is21057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Zhu L, Zhu Z, Zhu L, Wang D, Wang J, Lin Q. The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics. PLoS One 2021; 16:e0255547. [PMID: 34735446 PMCID: PMC8568142 DOI: 10.1371/journal.pone.0255547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/21/2021] [Indexed: 11/25/2022] Open
Abstract
In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. The mitochondrial gene arrangement of eight species of the Hippolytidae were compared with the order of genes of Decapoda ancestors, finding that the gene arrangement order of the Lebbeus groenlandicus had not changed, but the gene arrangement order of other species changed to varying degrees. The positions of the two tRNAs genes (trnA and trnR) of the L. vittata had translocations, which also showed that the Hippolytidae species were relatively unconserved in evolution. Phylogenetic analysis of 50 shrimp showed that L. vittata formed a monophyletic clade with Lysmata/Exhippolysmata species. This study should be helpful to better understand the evolutionary status, and population genetic diversity of L. vittata and related species.
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Affiliation(s)
- Longqiang Zhu
- Fisheries Research Institute of Fujian, Xiamen, China
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Xiamen, China
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Zhihuang Zhu
- Fisheries Research Institute of Fujian, Xiamen, China
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Xiamen, China
| | - Leiyu Zhu
- Fisheries Research Institute of Fujian, Xiamen, China
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Xiamen, China
| | - Dingquan Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Jianxin Wang
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
| | - Qi Lin
- Fisheries Research Institute of Fujian, Xiamen, China
- Key Laboratory of Cultivation and High-value Utilization of Marine Organisms in Fujian Province, Xiamen, China
- Marine Microorganism Ecological & Application Lab, Zhejiang Ocean University, Zhejiang, China
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5
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Liu F, Shi W, Ye H, Zeng C, Zhu Z. Insulin-like androgenic gland hormone 1 (IAG1) regulates sexual differentiation in a hermaphrodite shrimp through feedback to neuroendocrine factors. Gen Comp Endocrinol 2021; 303:113706. [PMID: 33359802 DOI: 10.1016/j.ygcen.2020.113706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
Insulin-like androgenic gland hormone (IAG) is regarded as a key sexual differentiation regulator in gonochoristic crustaceans. However, until now the knowledge concerning its functions in hermaphroditic crustaceans is scanty. Herein, we investigated the function of IAG (Lvit-IAG1) in peppermint shrimp Lysmata vittata, a species that possesses protandric simultaneous hermaphroditism (PSH) reproductive system, which is rare among crustaceans. Lvit-IAG1 was exclusively expressed in the androgenic gland. The qRT-PCR demonstrated that its mRNA expression level was relatively high at the functional male phase but decreased sharply in the subsequent euhermaphrodite phase. Both the short-term and long-term silencing experiments showed that Lvit-IAG1 negatively regulated both the gonad-inhibiting hormone (Lvit-GIH) and crustacean female sex hormone (Lvit-CFSH) expressions in the eyestalk ganglion. Besides, Lvit-IAG1 gene knockdown induced a retarded development of the appendices masculinae (AM) and male gonopores while suppressing the germ cells at the primary spermatocyte stage. Also, Lvit-IAG1 gene silencing hindered ovarian development. This in turn led to small vitellogenic oocytes and decreased expression of vitellogenin and vitellogenin receptor genes in hepatopancreas and ovarian region, respectively. Generally, this study's findings imply that Lvit-IAG1 modulated the male sexual differentiation in PSH species L. vittata, and exhibited negative feedback on Lvit-GIH and Lvit-CFSH genes expression in the species' eyestalk ganglion.
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Affiliation(s)
- Fang Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Wenyuan Shi
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China
| | - Haihui Ye
- College of Fisheries, Jimei University, Xiamen 361021, People's Republic of China.
| | - Chaoshu Zeng
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Zhihuang Zhu
- Fisheries Research Institute of Fujian, Xiamen 361013, People's Republic of China
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6
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Šobánová A, Duriš Z. Unexpected diversity in the sponge-associated shrimps Onycocaridella Bruce, 1981 (Crustacea : Decapoda : Palaemonidae) revealed by bulk collecting techniques and molecular tools. INVERTEBR SYST 2021. [DOI: 10.1071/is20052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Multigene molecular revision of a series of specimens of the rare spongobiotic palaemonid shrimp genus, Onycocaridella Bruce, 1981, collected predominantly from Papua New Guinea, has doubled the known species diversity to six. Of the previously known species, O. monodoa (Fujino & Miyake, 1969) and O. stenolepis (Holthuis, 1952) were analysed in the present study, whereas sequenceable specimens of the type species, O. prima Bruce, 1981, were not available. The present molecular analysis (combined COI, 16S, H3 markers) recovered six separate genetic lineages, indicating the presence of four undescribed species. Three of the latter are described in the present study. Remarkably higher known species diversity of Onycocaridella is thus recorded from a single geographic region – Papua New Guinea. The increased diversity reported here was discovered by application of complementary collecting techniques (hand picking, stone brushing, dead-coral sorting, suction sampling). One of the present new species is also reported from Australia, and O. monodoa is newly recorded from New Caledonia. A revised diagnosis of the genus and a key to identification of all known species of Onycocaridella are provided.
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7
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Ricardo PC, Françoso E, Arias MC. Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification. Mitochondrion 2020; 53:243-254. [PMID: 32569843 DOI: 10.1016/j.mito.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/28/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.
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Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Elaine Françoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
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8
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Dickson MD, Behringer DC, Baeza JA. Life history traits and reproductive performance of the caridean shrimp Lysmata boggessi, a heavily traded invertebrate in the marine aquarium industry. PeerJ 2020; 8:e8231. [PMID: 32002320 PMCID: PMC6983297 DOI: 10.7717/peerj.8231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/18/2019] [Indexed: 11/20/2022] Open
Abstract
The most intense commercial harvest of marine aquarium species in North America occurs in the coastal waters surrounding Florida, yet very often little information exists on the life histories, population dynamics, or reproductive characteristics of these organisms. The peppermint shrimp Lysmata boggessi is one such species and is heavily targeted along the west coast of Florida. It is known primarily among aquarists for its ability to control pest anemones and in the scientific community for its unique sexual system, protandric simultaneous hermaphroditism. However, no study has addressed fishery interactions or long-term population dynamics for L. boggessi. We used monthly fisheries-dependent sampling, with a trained observer present, for a full year to assess seasonality in sex phase ratio (males to males + hermaphrodites), size at sex change, fecundity, embryo volume and reproductive output of an exploited L. boggessi population. L. boggessi exhibited distinct seasonality in size distribution, sex phase ratio, size at sex phase change and reproductive activity. The peak reproductive season was in spring, when the population was dominated by small but fecund hermaphrodites. Reproduction decreased during fall and winter and sex phase ratios favored male phase shrimp that exhibited delayed sex change. This population and individual level information is the first of its kind for L. boggessi and fills a much needed data gap for the informed management of this fishery.
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Affiliation(s)
- Michael D Dickson
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, USA
| | - Donald C Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, USA.,Departamento de Biología Marina/Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
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9
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Baeza JA, Prakash S. An integrative taxonomic and phylogenetic approach reveals a complex of cryptic species in the ‘peppermint’ shrimp Lysmata wurdemanni sensu stricto. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zly084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo, Coquimbo, Chile
| | - Sanjeevi Prakash
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Centre for Climate Change Studies, Sathyabama Institute of Science and Technology, Rajiv Gandhi Salai, Chennai, Tamil Nadu, India
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10
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Alves DFR, López Greco LS, Barros-Alves SDP, Hirose GL. Sexual system, reproductive cycle and embryonic development of the red-striped shrimp Lysmata vittata, an invader in the western Atlantic Ocean. PLoS One 2019; 14:e0210723. [PMID: 30645636 PMCID: PMC6333369 DOI: 10.1371/journal.pone.0210723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/31/2018] [Indexed: 11/18/2022] Open
Abstract
Several decapod crustaceans are invaders, but little is known about the biological characteristics that potentiate the success of these decapods in invaded ecosystems. Here, we evaluate and describe some aspects of the reproductive biology and development of Lysmata vittata, an invasive shrimp species in the Atlantic Ocean. In addition, we intend to provide important insights into the biology of invasion by comparing the reproductive traits of this shrimp with some of the predictions about aquatic invasive species. We used experimental and laboratory observations to evaluate the functionality of protandric simultaneous hermaphroditism (PSH), the macro and microscopic development of the ovarian portion of the ovotestes, the reproductive cycle, and the embryonic development of L. vittata. We confirm the functionality of PSH in L. vittata. This shrimp has a rapid reproductive cycle; the ovarian portion of the ovotestes develops (mean ± SD) 6.28 ± 1.61 days after spawning. Embryonic development also occurs over a short time, with a mean (± SD) of 8.37 ± 0.85 days. The larvae hatch without macroscopically visible yolk reserves. Our study provides evidence that the invasive shrimp L. vittata has reproductive and embryonic developmental characteristics (i.e., short generation time and high reproductive capacity) that may be favorable to the establishment of populations during invasive processes.
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Affiliation(s)
- Douglas Fernandes Rodrigues Alves
- Departamento de Biologia, Universidade Federal de Sergipe–UFS, São Cristóvão, Sergipe, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe–UFS, São Cristóvão, Sergipe, Brazil
- * E-mail:
| | - Laura S. López Greco
- Universidad de Buenos Aires, CONICET, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Laboratorio de Biología de la Reproducción y el Crecimiento de Crustáceos Decápodos, Buenos Aires, Argentina
| | - Samara de Paiva Barros-Alves
- Laboratório de Ecologia de Ecossistemas Aquáticos, Universidade Federal de Uberlândia–UFU, Uberlândia, Minas Gerais, Brazil
| | - Gustavo Luis Hirose
- Departamento de Biologia, Universidade Federal de Sergipe–UFS, São Cristóvão, Sergipe, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe–UFS, São Cristóvão, Sergipe, Brazil
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11
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Giraldes BW, Macedo TP, Brandão MC, Baeza JA, Freire AS. Lysmata arvoredensis nov. sp. a new species of shrimp from the south coast of Brazil with a key to species of Lysmata (Caridea: Lysmatidae) recorded in the southwestern Atlantic. PeerJ 2018; 6:e5561. [PMID: 30202657 PMCID: PMC6129138 DOI: 10.7717/peerj.5561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 08/09/2018] [Indexed: 11/22/2022] Open
Abstract
Lysmata arvoredensis sp. nov. inhabits temperate waters in the south coast of Brazil and is named in tribute to the Marine Protected Area REBIO Arvoredo. This is the fourth species belonging to the genus Lysmata recorded for the region and the ninth for Brazil. L. arvoredensis sp. nov. can be distinguished from other species of Lysmata by the presence of a nearly completely fused accessory branch with a single free unguiform segment on the outer antennular flagellum; a rostrum with seven dorsal (2+5) and three ventral teeth; a stylocerite with a pointed tip bearing mesial setae; a second pereiopod with 22-24 carpal subsegments and 14-16 subsegments in the merus; a merus of the third pereiopod with five ventrolateral and 12 ventral spines on the propodus; and its color pattern, with red bands and patches in pleonites 2-3 that resemble a mask in dorsal view. Molecular characters demonstrate that L. arvoredensis sp. nov. is most closely related to other species of Lysmata belonging to the Neotropical and Cleaner clades. To support future ecological studies in the region, identification keys to the species of Lysmata recorded in the southwestern Atlantic Ocean are provided.
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Affiliation(s)
| | - Thais P. Macedo
- Laboratório de Crustáceos e Plâncton, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Manoela C. Brandão
- Laboratório de Crustáceos e Plâncton, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer, France
| | - J. Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
- Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, USA
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Andrea S. Freire
- Laboratório de Crustáceos e Plâncton, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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12
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Affiliation(s)
- Amy Willis
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Rayna Bell
- Smithsonian Institution, National Museum of Natural History, Washington, DC
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13
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Baeza JA, Behringer DC. Integrative taxonomy of the ornamental 'peppermint' shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide. PeerJ 2017; 5:e3786. [PMID: 28948100 PMCID: PMC5607919 DOI: 10.7717/peerj.3786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across 550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, FL, United States of America.,Departamento de Biologia Marina, Universidad Catolica del Norte, Coquimbo, IV Region, Chile
| | - Donald C Behringer
- Program in Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, United States of America.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States of America
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14
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Machida RJ, Lin YY. Occurrence of mitochondrial CO1 pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization indicated by recombined nuclear mitochondrial pseudogenes. PLoS One 2017; 12:e0172710. [PMID: 28231343 PMCID: PMC5322918 DOI: 10.1371/journal.pone.0172710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/08/2017] [Indexed: 11/18/2022] Open
Abstract
A portion of the mitochondrial cytochrome c oxidase I gene was sequenced using both genomic DNA and complement DNA from three planktonic copepod Neocalanus species (N. cristatus, N. plumchrus, and N. flemingeri). Small but critical sequence differences in CO1 were observed between gDNA and cDNA from N. plumchrus. Furthermore, careful observation revealed the presence of recombination between sequences in gDNA from N. plumchrus. Moreover, a chimera of the N. cristatus and N. plumchrus sequences was obtained from N. plumchrus gDNA. The observed phenomena can be best explained by the preferential amplification of the nuclear mitochondrial pseudogenes from gDNA of N. plumchrus. Two conclusions can be drawn from the observations. First, nuclear mitochondrial pseudogenes are pervasive in N. plumchrus. Second, a mating between a female N. cristatus and a male N. plumchrus produced viable offspring, which further backcrossed to a N. plumchrus individual. These observations not only demonstrate intriguing mating behavior in these species, but also emphasize the importance of careful interpretation of species marker sequences amplified from gDNA.
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Affiliation(s)
- Ryuji J. Machida
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail:
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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15
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Shaver BR, Marchant S, Martin SB, Agudelo P. 18S rRNA and COI haplotype diversity of Trichodorus obtusus from turfgrass in South Carolina. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The stubby-root nematode, Trichodorus obtusus, was recently identified on zoysiagrass in South Carolina, USA. In Florida, T. obtusus causes more damage than other stubby-root nematodes encountered in turfgrass. The objective of this study was to use morphological analysis, mitochondrial DNA (COI: cytochrome oxidase 1) and nuclear (18S rRNA) sequence data to study the genetic structure and haplotype diversity of populations recovered from turfgrasses in South Carolina. Numerous morphological differences were observed among populations. Three 18S haplotypes were shared among South Carolina and Florida populations, and six mitochondrial haplotypes were identified in South Carolina samples. Of the six COI haplotypes, four haplotypes were restricted to one population from St Augustinegrass. The lowest haplotype diversity was found in samples from zoysiagrass. Sequences of the COI mtDNA gene of T. obtusus were published in GenBank and represent the first mtDNA sequences for the genus Trichodorus.
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Affiliation(s)
- Bradly R. Shaver
- Plant Nematology Laboratory, 210 BRC, Clemson University, Clemson, SC 29364, USA
| | - Sergio Marchant
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - S. Bruce Martin
- Pee Dee Research and Education Center, Clemson University, 2200 Pocket Road, Florence, SC 29506, USA
| | - Paula Agudelo
- Plant Nematology Laboratory, 210 BRC, Clemson University, Clemson, SC 29364, USA
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16
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Raupach MJ, Radulovici AE. Looking back on a decade of barcoding crustaceans. Zookeys 2015; 539:53-81. [PMID: 26798245 PMCID: PMC4714055 DOI: 10.3897/zookeys.539.6530] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023] Open
Abstract
Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Adriana E. Radulovici
- Biodiversity Institute of Ontario (BIO), University of Guelph, 50 Stone Road E, Guelph (ON) N1G 2W1, Ontario, Canada
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17
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Mirimin L, Kitchin N, Impson DN, Clark PF, Richard J, Daniels SR, Roodt-Wilding R. Genetic and Morphological Characterization of Freshwater Shrimps (Caridina africana Kingsley, 1882) Reveals the Presence of Alien Shrimps in the Cape Floristic Region, South Africa. J Hered 2015; 106:711-8. [PMID: 26297730 DOI: 10.1093/jhered/esv063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 07/24/2015] [Indexed: 11/14/2022] Open
Abstract
Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identified as Caridina africana Kingsley, 1882, whose main natural distribution is in the KwaZulu-Natal (KZN) Province, more than 1200 km from the point of new discovery. Subsequently, sequence data from natural populations occurring in seven rivers throughout KZN showed the presence of nuclear copies of the mtDNA COI gene (NUMTs) in 46 out of 140 individuals. Upon removal of sequences containing NUMTs, levels of genetic diversity were low in the alien population (possibly as a consequence of a bottleneck event), while varying levels of genetic diversity and differentiation were found in natural populations, indicating habitat heterogeneity, fragmentation and restricted gene flow between rivers. Following the present study, the alien shrimp has survived the Western Cape's winter and dispersed into a nearby tributary of the Eerste River System, hence posing an additional potential threat to endangered endemics. Understanding the biology of this alien species will aid detection and eradication procedures.
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Affiliation(s)
- Luca Mirimin
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels).
| | - Natasha Kitchin
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Dean N Impson
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Paul F Clark
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Jasmine Richard
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Savel R Daniels
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Rouvay Roodt-Wilding
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
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18
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Holguin CM, Baeza JA, Mueller JD, Agudelo P. High genetic diversity and geographic subdivision of three lance nematode species (Hoplolaimus spp.) in the United States. Ecol Evol 2015; 5:2929-44. [PMID: 26306177 PMCID: PMC4541996 DOI: 10.1002/ece3.1568] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 05/05/2015] [Accepted: 05/18/2015] [Indexed: 11/17/2022] Open
Abstract
Lance nematodes (Hoplolaimus spp.) feed on the roots of a wide range of plants, some of which are agronomic crops. Morphometric values of amphimictic lance nematode species overlap considerably, and useful morphological characters for their discrimination require high magnification and significant diagnostic time. Given their morphological similarity, these Hoplolaimus species provide an interesting model to investigate hidden diversity in crop agroecosystems. In this scenario, H. galeatus may have been over-reported and the related species that are morphologically similar could be more widespread in the United States that has been recognized thus far. The main objectives of this study were to delimit Hoplolaimus galeatus and morphologically similar species using morphology, phylogeny, and a barcoding approach, and to estimate the genetic diversity and population structure of the species found. Molecular analyses were performed using sequences of the cytochrome c oxidase subunit 1 (Cox1) and the internal transcribed spacer (ITS1) on 23 populations. Four morphospecies were identified: H. galeatus, H. magnistylus, H. concaudajuvencus, and H. stephanus, along with a currently undescribed species. Pronounced genetic structure correlated with geographic origin was found for all species, except for H. galeatus. Hoplolaimus galeatus also exhibited low genetic diversity and the shortest genetic distances among populations. In contrast, H. stephanus, the species with the fewest reports from agricultural soils, was the most common and diverse species found. Results of this project may lead to better delimitation of lance nematode species in the United States by contributing to the understanding the diversity within this group.
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Affiliation(s)
- Claudia M Holguin
- Department of Agricultural and Environmental Sciences, Clemson UniversityClemson, South Carolina, 29634
| | - Juan A Baeza
- Department of Biological Sciences, Clemson UniversityClemson, South Carolina, 29634
| | - John D Mueller
- Edisto Research and Education Center, Clemson UniversityBlackville, South Carolina, 29817
| | - Paula Agudelo
- Department of Agricultural and Environmental Sciences, Clemson UniversityClemson, South Carolina, 29634
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Baeza JA, Bauer RT, Okuno J, Thiel M. Molecular phylogeny of hinge-beak shrimps (Decapoda: Caridea:RhynchocinetesandCinetorhynchus) and allies: a formal test of familiar and generic monophyly using a multilocus phylogeny. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J. Antonio Baeza
- Department of Biological Sciences; Clemson University; 132 Long Hall Clemson South Carolina 29634 USA
- Smithsonian Marine Station at Fort Pierce; 701 Seaway Drive Fort Pierce Florida 34949 USA
- Departamento de Biología Marina; Facultad de Ciencias del Mar; Universidad Católica del Norte; Larrondo 1281 Coquimbo Chile
| | - Raymond T. Bauer
- Department of Biology; University of Louisiana at Lafayette; P.O. Box 42451 Lafayette Louisiana USA
| | - Junji Okuno
- Coastal Branch of Natural History Museum and Institute; Chiba, 123 Yoshio, Katsuura Chiba 299-5242 Japan
| | - Martin Thiel
- Departamento de Biología Marina; Facultad de Ciencias del Mar; Universidad Católica del Norte; Larrondo 1281 Coquimbo Chile
- Centro de Estudios Avanzados en Zonas Aridas CEAZA; Coquimbo Chile
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