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Laifi-Necibi N, Amor N, Merella P, Mohammed OB, Medini L. DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia. Mitochondrial DNA A DNA Mapp Seq Anal 2024:1-11. [PMID: 38899428 DOI: 10.1080/24701394.2024.2363350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/14/2024] [Indexed: 06/21/2024]
Abstract
Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.
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Affiliation(s)
- Nermine Laifi-Necibi
- Faculté des Sciences de Tunis, Laboratoire Diversité, Gestion et Conservation des Systèmes Biologiques, Université de Tunis El Manar, Tunis, Tunisia
| | - Nabil Amor
- Higher Institute of Applied Biological Sciences of Tunis, University Tunis EL Manar, Tunis, Tunisia
| | - Paolo Merella
- Parassitologia e Malattie Parassitarie, Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | | | - Lamia Medini
- Faculté des Sciences de Tunis, Laboratoire Diversité, Gestion et Conservation des Systèmes Biologiques, Université de Tunis El Manar, Tunis, Tunisia
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Dimitriou AC, Soares Campos-Filho I, Georgiou A, Taiti S, Sfenthourakis S. Intra-island patterns of cryptic diversity within an oceanic island: Insights from the differentiation of Schizidium Verhoeff, 1901 (Oniscidea, Armadillidiidae) within Cyprus, with descriptions of two new species. Mol Phylogenet Evol 2023; 187:107884. [PMID: 37467903 DOI: 10.1016/j.ympev.2023.107884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/11/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cyprus is a Mediterranean island of volcanic origin isolated for at least 5.3 Myr from surrounding continental areas. The present study focuses on the diversification of the isopod genus Schizidium within the island, including also specimens from surrounding continental areas. The genus Schizidium sensu lato is probably non monophyletic, comprising 26 species distributed from Greece to Iran. Up to date the only representative of the genus reported from Cyprus was Schizidium fissum. Aiming to investigate the patterns of genetic diversity within the focal island, to evaluate the morphology-based taxonomy of the species in the genus, and at the same time to explore phylogenetic relationships with mainland populations, we applied genome-wide ddRADseq as well as Sanger sequencing targeting three mitochondrial (16S, COI and 12S) and the nuclear NaK loci. Results of phylogenetic analyses support the existence of two distinct epigean Schizidium clades with well-defined geographic boundaries that conform to the known paleogeography of Cyprus, plus one endogean clade with restricted distribution within the island. Genetic data and morphology corroborate the assignment of this latter endogean clade to a new species, Schizidium myrrae n. sp. The two epigean clades are also considered as distinct species, one corresponding to the known S. fissum at the eastern part of the island (Pentadaktylos massif) and the other to the newly described S. christosi n. sp. distributed along the western part of the island (Troodos massif). Even though detailed examination of many specimens could not retrieve any morphological differences among representatives of these two clades, clado-chronological analysis indicates a long isolation between them, estimated at ∼ 9 Mya, as well as the sharing of a common ancestor with S. tiberianum from Israel at ∼ 15 Mya. Hence, we can consider these epigean Schizidium species as one more case of cryptic diversity on Cyprus, exhibiting similar patterns with the recently described case in the genus Armadillo.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus.
| | | | - Anastasia Georgiou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
| | - Stefano Taiti
- Istituto di Ricerca sugli Ecosistemi Terrestri, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy; Museo di Storia Naturale dell'Università di Firenze, Sezione di Zoologia "La Specola", Via Romana 17, 50125 Florence, Italy
| | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus
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Stebbins TD, Wetzer R. Review and guide to the isopods (Crustacea, Isopoda) of littoral and sublittoral marine habitats in the Southern California Bight. Zookeys 2023; 1162:1-167. [PMID: 37235199 PMCID: PMC10206732 DOI: 10.3897/zookeys.1162.100390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 05/28/2023] Open
Abstract
The isopod crustaceans reported from or expected to occur in littoral and sublittoral marine habitats of the Southern California Bight (SCB) in the northeastern Pacific Ocean are reviewed. A total of 190 species, representing 105 genera in 42 families and six suborders are covered. Approximately 84% of these isopods represent described species with the remaining 16% comprising well-documented "provisional" but undescribed species. Cymothoida and Asellota are the most diverse of the six suborders, accounting for ca. 36% and 29% of the species, respectively. Valvifera and Sphaeromatidea are the next most speciose suborders with between 13-15% of the species each, while the suborder Limnorioidea represents fewer than 2% of the SCB isopod fauna. Finally, the mostly terrestrial suborder Oniscidea accounts for ca. 5% of the species treated herein, each which occurs at or above the high tide mark in intertidal habitats. A key to the suborders and superfamilies is presented followed by nine keys to the SCB species within each of the resultant groups. Figures are provided for most species. Bathymetric range, geographic distribution, type locality, habitat, body size, and a comprehensive list of references are included for most species.
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Affiliation(s)
- Timothy D. Stebbins
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
- City of San Diego Marine Biology Laboratory (retired), Public Utilities Department, San Diego, California 92101, USACity of San Diego Marine Biology LaboratorySan DiegoUnited States of America
| | - Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
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Wang J, Yang J, Zeng X, Li W. Integrative taxonomy on the rare sky-island Ligidium species from southwest China (Isopoda, Oniscidea, Ligiidae). BMC ZOOL 2022; 7:26. [PMID: 37170338 PMCID: PMC10127345 DOI: 10.1186/s40850-022-00120-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The sky-island Ligidium species fauna in southwest China is poorly known. Before this study, six of the seven sky-island species of the genus were known to be endemic to southwest China. In morphology, Ligidium species are often difficult to identify, and an appraisal of integrative taxonomy is needed.
Results
We integrated morphology and molecular analyses to delimit Ligidium species. Molecular species delimitation based on distance- and evolutionary models recovered seven-candidate lineages from five gene markers (COI, 12S rRNA, 18S rRNA, 28S rRNA and NAK). We also estimated that the species divergences of sky-island Ligidium in southwest China started in late Eocene (40.97 Mya) to middle Miocene (15.19 Mya).
Four new species (L. duospinatum Li, sp. nov., L. acuminatum Li, sp. nov., L. rotundum Li, sp. nov. and L. tridentatum Li, sp. nov.) are described. Morphological confusion among L. denticulatum Shen, 1949, L. inerme Nunomura & Xie, 2000 and L. sichuanense Nunomura, 2002 is clarified by integrative taxonomy.
Conclusion
This work confirms that an integrative approach to Ligidium taxonomy is fundamental for objective classification, and deduced the uplift of Qinghai-Tibetan Plateau in the late Eocene and middle Miocene as one of the principal reasons for the species divergences of sky-island Ligidium in southwest China. We also inferred that sky-island mountains have a huge reserve of higher Ligidium species diversity.
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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6
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Zuykova EI, Bochkarev NA, Kotov AA. Specific and Genetic Structure of the Daphnia longispina s. l. Complex (Cladocera, Daphniidae) in Water Bodies of Southern Siberia. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021070323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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A comprehensive evaluation of the potential of semiterrestrial isopods, Ligia exotica, as a new animal food. Sci Rep 2021; 11:7213. [PMID: 33785800 PMCID: PMC8009950 DOI: 10.1038/s41598-021-86561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 03/17/2021] [Indexed: 11/22/2022] Open
Abstract
The semiterrestrial isopod, Ligia exotica represents one of the oldest documented species introductions of marine organisms and is known as an intermediate form between marine and strictly terrestrial isopods. In order to explore the potential value of Ligia as an animal food source, this study focused on the growth rate under laboratory rearing conditions and conducted a detailed analysis of the overall nutrient content of the species in comparison to two other marine food media (krill and fish meal). Evaluation of the growth rate of juveniles suggests it is a relatively fast-growing species of the Ligiidae family. The essential amino acids content Ligia meal is the lowest amongst the three studied media but the proportion of flavor amino acids, and in particular taurine, was higher. The most restricted amino acids of isopod meal are methionine and cysteine. The significantly unbalanced amino acid composition of Ligia meal may affect the absorption and utilization by consumers. In terms of fatty acids, the total polyunsaturated fatty acids in the isopod is very low. A total of 12 vitamins were examined. The VK1, VE, VB2, VB3, VB5 content of isopod meal were significantly higher than those of krill meal and fish meal. Similarly, most of the 11 mineral elements are highest in the isopod meal. Ligia therefore offers potential as an alternative natural food source in animal given the growth rate under culture and the overall nutrient content. But Ligia collected in most of the field would be deemed unfit for human consumption because of the relatively low nutritional value and heavy metal content exceeding the provided standard. Further study is warranted to elucidate the biological characteristics of isopods and how its diet is reflected in its nutritional value to consumers.
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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9
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Santamaria CA. Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species. PeerJ 2019; 7:e7531. [PMID: 31435494 PMCID: PMC6698373 DOI: 10.7717/peerj.7531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/22/2019] [Indexed: 02/06/2023] Open
Abstract
Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai'i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.
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Affiliation(s)
- Carlos A. Santamaria
- Biology Faculty, College of Science and Mathematics, University of South Florida, Sarasota, FL, United States of America
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States of America
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10
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Zuykova EI, Simonov EP, Bochkarev NA, Taylor DJ, Kotov AA. Resolution of the Daphnia umbra problem (Crustacea: Cladocera) using an integrated taxonomic approach. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Elena I Zuykova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgeniy P Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Siberian Federal University, Svobodny pr., Krasnoyarsk, Russia
| | - Nikolay A Bochkarev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution, Leninsky Prospect, Moscow, Russia
- Kazan Federal University, Kazan, Russia
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11
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Greenan TM, Griffiths CL, Santamaria CA. Molecular approaches uncover cryptic diversity in intertidal Ligia isopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline. PeerJ 2018; 6:e4658. [PMID: 29686947 PMCID: PMC5911383 DOI: 10.7717/peerj.4658] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/31/2018] [Indexed: 12/11/2022] Open
Abstract
Recent phylogeographic studies along the coastline of southern Africa have uncovered cryptic diversity in several coastal invertebrates, including direct developing crustaceans in the superorder Peracarida. These findings indicating the possible existence of additional cryptic diversity in other yet to be studied peracarids, particularly those known to harbor said cryptic diversity in other regions of the world. Isopods in the genus Ligia are one such taxon. They inhabit patchy rocky beaches, are direct developers, avoid the open water, and exhibit other biological traits that severely constrain their dispersal potential (e.g., poor desiccation resistance). These traits are thought to have led to long-term isolation of populations, and allopatric diversification in Ligia species around the world; however, Ligia species in southern Africa, where three endemic Ligia species of uncertain validity are known to exist, remain unstudied to date. In this study, we used mitochondrial and nuclear markers to characterize Ligia collected in 18 localities from Namibia to the KwaZulu-Natal region of South Africa. We report the presence of cryptic lineages within Ligia species in the region that suggest the need for taxonomic reevaluation of these isopod species.
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Affiliation(s)
- Taylor M Greenan
- Biology Program, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, United States of America
| | - Charles L Griffiths
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, South Africa
| | - Carlos A Santamaria
- Biology Program, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, United States of America.,Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States of America
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12
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Hurtado LA, Mateos M, Wang C, Santamaria CA, Jung J, Khalaji-Pirbalouty V, Kim W. Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica. PeerJ 2018; 6:e4337. [PMID: 29576934 PMCID: PMC5853605 DOI: 10.7717/peerj.4337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/17/2018] [Indexed: 11/20/2022] Open
Abstract
The native ranges and invasion histories of many marine species remain elusive due to a dynamic dispersal process via marine vessels. Molecular markers can aid in identification of native ranges and elucidation of the introduction and establishment process. The supralittoral isopod Ligia exotica has a wide tropical and subtropical distribution, frequently found in harbors and ports around the globe. This isopod is hypothesized to have an Old World origin, from where it was unintentionally introduced to other regions via wooden ships and solid ballast. Its native range, however, remains uncertain. Recent molecular studies uncovered the presence of two highly divergent lineages of L. exotica in East Asia, and suggest this region is a source of nonindigenous populations. In this study, we conducted phylogenetic analyses (Maximum Likelihood and Bayesian) of a fragment of the mitochondrial 16S ribosomal (r)DNA gene using a dataset of this isopod that greatly expanded previous representation from Asia and putative nonindigenous populations around the world. For a subset of samples, sequences of 12S rDNA and NaK were also obtained and analyzed together with 16S rDNA. Our results show that L. exotica is comprised of several highly divergent genetic lineages, which probably represent different species. Most of the 16S rDNA genetic diversity (48 haplotypes) was detected in East and Southeast Asia. Only seven haplotypes were observed outside this region (in the Americas, Hawai'i, Africa and India), which were identical or closely related to haplotypes found in East and Southeast Asia. Phylogenetic patterns indicate the L. exotica clade originated and diversified in East and Southeast Asia, and only members of one of the divergent lineages have spread out of this region, recently, suggesting the potential to become invasive is phylogenetically constrained.
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Affiliation(s)
- Luis A. Hurtado
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Chang Wang
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
- Department of Biology, New York University, New York City, NY, United States of America
| | - Carlos A. Santamaria
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
- Biology Faculty, College of Science and Mathematics, University of South Florida, Sarasota, FL, United States of America
| | - Jongwoo Jung
- Department of Science Education, Ewha Women’s University, Seoul, South Korea
| | | | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul, South Korea
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13
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Santamaria CA, Bluemel JK, Bunbury N, Curran M. Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods. PeerJ 2017; 5:e3894. [PMID: 29018626 PMCID: PMC5633021 DOI: 10.7717/peerj.3894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/15/2017] [Indexed: 12/02/2022] Open
Abstract
Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
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Affiliation(s)
- Carlos A. Santamaria
- Biology Faculty, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, United States of America
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States of America
| | - Joanna K. Bluemel
- Marine Conservation Society Seychelles, Mahé, Seychelles
- Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, Suffolk, United Kingdom
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Outomuro D, Johansson F. A potential pitfall in studies of biological shape: Does size matter? J Anim Ecol 2017; 86:1447-1457. [PMID: 28699246 DOI: 10.1111/1365-2656.12732] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 01/26/2023]
Abstract
The number of published studies using geometric morphometrics (GM) for analysing biological shape has increased steadily since the beginning of the 1990s, covering multiple research areas such as ecology, evolution, development, taxonomy and palaeontology. Unfortunately, we have observed that many published studies using GM do not evaluate the potential allometric effects of size on shape, which normally require consideration or assessment. This might lead to misinterpretations and flawed conclusions in certain cases, especially when size effects explain a large part of the shape variation. We assessed, for the first time and in a systematic manner, how often published studies that have applied GM consider the potential effects of allometry on shape. We reviewed the 300 most recent published papers that used GM for studying biological shape. We also estimated how much of the shape variation was explained by allometric effects in the reviewed papers. More than one-third (38%) of the reviewed studies did not consider the allometric component of shape variation. In studies where the allometric component was taken into account, it was significant in 88% of the cases, explaining up to 87.3% of total shape variation. We believe that one reason that may cause the observed results is a misunderstanding of the process that superimposes landmark configurations, i.e. the Generalized Procrustes Analysis, which removes isometric effects of size on shape, but not allometric effects. Allometry can be a crucial component of shape variation. We urge authors to address, and report, size effects in studies of biological shape. However, we do not propose to always remove size effects, but rather to evaluate the research question with and without the allometric component of shape variation. This approach can certainly provide a thorough understanding of how much size contributes to the observed shaped variation.
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Affiliation(s)
- David Outomuro
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Frank Johansson
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Titus BM, Palombit S, Daly M. Endemic diversification in an isolated archipelago with few endemics: an example from a cleaner shrimp species complex in the Tropical Western Atlantic. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Hurtado LA, Mateos M, Liu S. Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods. Ecol Evol 2017; 7:346-357. [PMID: 28070297 PMCID: PMC5214745 DOI: 10.1002/ece3.2599] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/12/2016] [Accepted: 10/19/2016] [Indexed: 11/25/2022] Open
Abstract
A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea-land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species. Excirolana mayana is an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns of E. mayana in the Gulf of California and the Caribbean, based on maximum-likelihood and Bayesian phylogenetic analyses of DNA sequences from four mitochondrial genes (16S rDNA, 12S rDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns of E. mayana with those of the coastal isopods Ligia and Excirolana braziliensis (Gulf of California and Caribbean) and Tylos (Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic-Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns of E. mayana in the Gulf of California differ from those observed in Ligia and Tylos in this region. Nonetheless, several clades of E. mayana have similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected in E. mayana also pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.
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Affiliation(s)
- Luis A. Hurtado
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
| | - Mariana Mateos
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
| | - Shuang Liu
- Department of Wildlife and Fisheries SciencesTexas A&M UniversityCollege StationTXUSA
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Hurtado LA, Mateos M, Mattos G, Liu S, Haye PA, Paiva PC. Multiple transisthmian divergences, extensive cryptic diversity, occasional long-distance dispersal, and biogeographic patterns in a marine coastal isopod with an amphi-American distribution. Ecol Evol 2016; 6:7794-7808. [PMID: 30128130 PMCID: PMC6093162 DOI: 10.1002/ece3.2397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Excirolana braziliensis is a coastal intertidal isopod with a broad distribution spanning the Atlantic and Pacific tropical and temperate coasts of the American continent. Two separate regional studies (one in Panama and one in Chile) revealed the presence of highly genetically divergent lineages, implying that this taxon constitutes a cryptic species complex. The relationships among the lineages found in these two different regions and in the rest of the distribution, however, remain unknown. To better understand the phylogeographic patterns of E. braziliensis, we conducted phylogenetic analyses of specimens from much of its entire range. We obtained DNA sequences for fragments of four mitochondrial genes (16S rDNA, 12S rDNA, COI, and Cytb) and also used publicly available sequences. We conducted maximum likelihood and Bayesian phylogenetic reconstruction methods. Phylogeographic patterns revealed the following: (1) new highly divergent lineages of E. braziliensis; (2) three instances of Atlantic–Pacific divergences, some of which appear to predate the closure of the Isthmus of Panama; (3) the distributional limit of highly divergent lineages found in Brazil coincides with the boundary between two major marine coastal provinces; (4) evidence of recent long‐distance dispersal in the Caribbean; and (5) populations in the Gulf of California have closer affinities with lineages further south in the Pacific, which contrasts with the closer affinity with the Caribbean reported for other intertidal organisms. The high levels of cryptic diversity detected also bring about challenges for the conservation of this isopod and its fragile environment, the sandy shores. Our findings underscore the importance of comprehensive geographic sampling for phylogeographic and taxonomical studies of broadly distributed putative species harboring extensive cryptic diversity.
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Affiliation(s)
- Luis A Hurtado
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Gustavo Mattos
- Programa de Pós-Graduação em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Shuang Liu
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Pilar A Haye
- Departamento de Biología Marina Universidad Católica del Norte Coquimbo Chile.,Centro de Estudios Avanzados en Zonas Áridas (CEAZA) Coquimbo Chile.,Interdisciplinary Center for Aquaculture Research (INCAR) Universidad de Concepción Casilla 160-C Concepción Chile
| | - Paulo C Paiva
- Programa de Pós-Graduação em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil.,Departamento de Zoologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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