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Santamaria CA, Griffiths CL. Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa. PeerJ 2023; 11:e16529. [PMID: 38077409 PMCID: PMC10702337 DOI: 10.7717/peerj.16529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.
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Affiliation(s)
- Carlos A. Santamaria
- Department of Biology, The University of Tampa, Tampa, FL, United States of America
| | - Charles L. Griffiths
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Rondebosch, South Africa
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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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Dimitriou AC, Antoniou A, Alexiou I, Poulakakis N, Parmakelis A, Sfenthourakis S. Diversification within an oceanic Mediterranean island: Insights from a terrestrial isopod. Mol Phylogenet Evol 2022; 175:107585. [PMID: 35810970 DOI: 10.1016/j.ympev.2022.107585] [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: 03/16/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
Understanding intra-island patterns of evolutionary divergence, including cases of cryptic diversity, is a crucial step towards deciphering speciation processes. Cyprus is an oceanic island isolated for at least 5.3 Mya from surrounding continental regions, while it remains unclear whether it was ever connected to the mainland, even during the Messinian Salinity Crisis. The terrestrial isopod species Armadillo officinalis, that is widespread across the Mediterranean, offers the opportunity to explore intra-island divergence patterns that might exhibit geographical structure related also to the region's known paleogeography. Genome-wide ddRADseq, as well as Sanger sequencing for four mitochondrial and three nuclear loci data were generated for this purpose. In total, 71 populations from Cyprus, neighbouring continental sites, i.e., Israel, Lebanon and Turkey, and other Mediterranean regions, i.e. Greece, Italy, and Tunisia, were included in the analysis. Phylogenetic reconstructions and population structure analyses support the existence of at least six genetically discrete groups across the study area. Five of these distinct genetic clades occur on Cyprus, four of which are endemic to the island and one is widely distributed along the circum-Mediterranean countries. The sixth clade is distributed in Israel. The closest evolutionary relationship of endemic Cypriot populations is with those from Israel, while the evolutionary clade that is present in countries all around the Mediterranean is very shallow. Cladochronological analyses date the origin of the species on the island at ∼6 Mya. Estimated f4 and D statistics as well as FST values indicate the genetic isolation between the populations sampled from Cyprus and surrounding continental areas, while there is evident gene flow among populations within the island. Species delimitation and population genetic metrics support the existence of three distinct taxonomic units across the study area, two of which occur on the island and correspond to the endemic clade and the widespread circum-Mediterranean one, respectively, while the third corresponds to Israel's clade. The islands' paleogeographic history and recent human activities seem to have shaped current patterns of genetic diversity in this group of species.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, University Campus, 2109 Aglantzia, Nicosia, Cyprus.
| | - Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes Pediados, Irakleio, P.O. Box 2214, 71003 Crete, Greece
| | - Ioannis Alexiou
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knosos Avenue, Irakleio 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Irakleio 70013, Greece
| | - Aristeidis Parmakelis
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyros Sfenthourakis
- Department of Biological Sciences, University of Cyprus, University Campus, 2109 Aglantzia, Nicosia, Cyprus
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Bellvert A, Gillespie RG, Arnedo MA. A happy family: systematic revision of the endemic Theridion spiders (Araneae, Theridiidae) of the Hawaiian Islands. INVERTEBR SYST 2021. [DOI: 10.1071/is20001] [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
Since the description in 1900 of the iconic Happy Face spider, Theridion grallator, Simon, along with nine relatives, the Theridion fauna of the Hawaiian Islands has remained unstudied. Here, we present a systematic revision of the Hawaiian Theridion, which includes the examination of abundant material collected during the last 50 years, with scanning of the genitalia of several species using SEM techniques, and a cladistic analysis based on 22 morphological characters, to provide a first hypothesis of the phylogenetic structure of the group. We describe eight new species, namely T. ariel, sp. nov., T. caliban, sp. nov., T. ceres, sp. nov., T. ferdinand, sp. nov., T. juno, sp. nov., T. miranda, sp. nov., T. prospero, sp. nov. and T. sycorax, sp. nov. Additionally, we provide new diagnoses for former species and illustrate and describe for the first time the male of T. kauaiense Simon, 1900 and the female of T. praetextum Simon, 1900. We further propose that T. campestratum Simon, 1900 is a junior synonym of T. melinum Simon, 1900 and T. praetextum concolor Simon, 1900 is a junior synonym of T. praetextum. Finally, we provide updated information on the distribution of the species. Most species are easily diagnosed based on the male and female genitalia, but we also reveal the existence of somatic characters that differ among species, such as the body size and the shape and size of the chelicerae, which may have played a role in the diversification and coexistence of some of the species. The preferred cladogram from the cladistic analysis, although compatible with a progression rule, also suggests a complex pattern of multiple back and forward colonisations, albeit most of the clades are poorly supported.
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Dimitriou AC, Taiti S, Sfenthourakis S. Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods. Sci Rep 2019; 9:18508. [PMID: 31811226 PMCID: PMC6898597 DOI: 10.1038/s41598-019-55071-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/21/2019] [Indexed: 11/10/2022] Open
Abstract
Among the few crustacean taxa that managed to inhabit terrestrial environments, Oniscidea includes the most successful colonizers in terms of species richness and abundance. However, neither morphological traits nor molecular markers have definitively resolved phylogenetic relationships among major Oniscidea clades or established the monophyly of the taxon. Herein, we employed the highly conserved, nuclear protein-coding genes Sodium-Potassium Pump (NAK) and Phosphoenolpyruvate Carboxykinase (PEPCK), along with the traditionally used 18 s and 28 s ribosomal RNA genes, in an attempt to clarify these questions. Our dataset included sequences representing all major Oniscidea clades and closely related aquatic taxa, as suggested by previous studies. We applied Bayesian Inference and Maximum Likelihood methods and produced a robust and fully resolved phylogenetic tree that offers strong evidence against the monophyly of Oniscidea. The amphibious genus Ligia appears to be more closely related to representatives of marine suborders, while the phylogenetic pattern of the remaining Oniscidea implies a complex history of the transition from the marine environment to land. With the exception of the basal clade, all other established major clades have been recovered as monophyletic, even though relationships within these clades call for a revised interpretation of morphological characters used in terrestrial isopod taxonomy.
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Affiliation(s)
- Andreas C Dimitriou
- Department of Biological Sciences, University of Cyprus, Panepistimiou Ave. 1, 2109, Aglantzia, Nicosia, Cyprus.
| | - Stefano Taiti
- Museo di Storia Naturale, 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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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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Sun J, Liu S, Yan Z, An S, You R, Li F, Zhang P. Influence of Body Weight and Gender on the Accumulation of Heavy Metals in Ligia cinerascens Based on Field Investigation and Cd Exposure Experiment. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 102:811-816. [PMID: 30989283 DOI: 10.1007/s00128-019-02607-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Isopods of the genus Ligia are deemed as excellent pollution monitoring organisms for coastal zones. A species of Ligia cinerascens was chosen to be tested, which was collected from three coastal zones in Dalian, China. The concentrations of metals followed the order of Cu>As ≈ Cd>Pb. Ligia collected from a municipal sewage outlet in Heishijiao showed the highest level of metals. Ligia from a natural bathing beach in Changshan Island showed the lowest level of metals as expected. Ligia grown in the same site could accumulate different levels of metals due to their different body weight. Both males and females conformably accumulated heavy metals in bodies. Taken together, this work suggests that L. cinerascens can serve as a biomonitor species. Within the range of 0.3-0.9 g body weights, body weight rather than gender should be taken into account as a factor in the process of environmental biomonitoring.
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Affiliation(s)
- Jingxian Sun
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Shuang Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- Key Laboratory of Hydrobiology in Liaoning Province, Dalian, 116023, China
| | - Ziwei Yan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- Key Laboratory of Hydrobiology in Liaoning Province, Dalian, 116023, China
| | - Shiqi An
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
- Key Laboratory of Hydrobiology in Liaoning Province, Dalian, 116023, China
| | - Ruhao You
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Fan Li
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
| | - Peng Zhang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China.
- Key Laboratory of Hydrobiology in Liaoning Province, Dalian, 116023, China.
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Sfenthourakis S, Hornung E. Isopod distribution and climate change. Zookeys 2018:25-61. [PMID: 30564031 PMCID: PMC6288265 DOI: 10.3897/zookeys.801.23533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/09/2018] [Indexed: 11/24/2022] Open
Abstract
The unique properties of terrestrial isopods regarding responses to limiting factors such as drought and temperature have led to interesting distributional patterns along climatic and other environmental gradients at both species and community level. This paper will focus on the exploration of isopod distributions in evaluating climate change effects on biodiversity at different scales, geographical regions, and environments, in view of isopods’ tolerances to environmental factors, mostly humidity and temperature. Isopod distribution is tightly connected to available habitats and habitat features at a fine spatial scale, even though different species may exhibit a variety of responses to environmental heterogeneity, reflecting the large interspecific variation within the group. Furthermore, isopod distributions show some notable deviations from common global patterns, mainly as a result of their ecological features and evolutionary origins. Responses to human disturbance are not always traceable, but a trend towards community homogenisation is often found under strong global urbanisation processes. In general, even though it is still not clear how predicted climate change will affect isopod distribution, there is evidence that mixed effects are to be expected, depending on the region under study. We still lack robust and extensive analyses of isopod distributions at different scales and at different biomes, as well as applications of distribution models that might help evaluate future trends.
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Affiliation(s)
- Spyros Sfenthourakis
- Department of Biological Sciences, University Campus, University of Cyprus, Panepistimiou Ave. 1, 2109 Aglantzia, Nicosia, Cyprus University of Cyprus Nicosia Cyprus
| | - Elisabeth Hornung
- Department of Ecology, University of Veterinary Medicine, 1077 Budapest, Rottenbiller str. 50, Hungary University of Veterinary Medicine Budapest Hungary
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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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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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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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Molecular and morphometric data suggest the presence of a neglected species in the marine gastropod family Conidae. Mol Phylogenet Evol 2017; 109:421-429. [DOI: 10.1016/j.ympev.2017.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 02/12/2017] [Accepted: 02/15/2017] [Indexed: 11/15/2022]
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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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Javidkar M, Cooper SJ, King RA, Humphreys WF, Bertozzi T, Stevens MI, Austin AD. Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of central Western Australia. Mol Phylogenet Evol 2016; 104:83-98. [DOI: 10.1016/j.ympev.2016.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 10/21/2022]
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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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Catalano SA, Torres A. Phylogenetic inference based on landmark data in 41 empirical data sets. ZOOL SCR 2016. [DOI: 10.1111/zsc.12186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Santiago A. Catalano
- Consejo Nacional de Investigaciones Científicas y Técnicas; Unidad Ejecutora Lillo (UEL); FML-CONICET; Miguel Lillo 251, 4000 San Miguel de Tucumán Tucumán Argentina
| | - Ambrosio Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas; Unidad Ejecutora Lillo (UEL); FML-CONICET; Miguel Lillo 251, 4000 San Miguel de Tucumán Tucumán Argentina
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Bowen BW. The Three Domains of Conservation Genetics: Case Histories from Hawaiian Waters. J Hered 2016; 107:309-17. [PMID: 27001936 DOI: 10.1093/jhered/esw018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/17/2016] [Indexed: 11/14/2022] Open
Abstract
The scientific field of conservation biology is dominated by 3 specialties: phylogenetics, ecology, and evolution. Under this triad, phylogenetics is oriented towards the past history of biodiversity, conserving the divergent branches in the tree of life. The ecological component is rooted in the present, maintaining the contemporary life support systems for biodiversity. Evolutionary conservation (as defined here) is concerned with preserving the raw materials for generating future biodiversity. All 3 domains can be documented with genetic case histories in the waters of the Hawaiian Archipelago, an isolated chain of volcanic islands with 2 types of biodiversity: colonists, and new species that arose from colonists. This review demonstrates that 1) phylogenetic studies have identified previously unknown branches in the tree of life that are endemic to Hawaiian waters; 2) population genetic surveys define isolated marine ecosystems as management units, and 3) phylogeographic analyses illustrate the pathways of colonization that can enhance future biodiversity. Conventional molecular markers have advanced all 3 domains in conservation biology over the last 3 decades, and recent advances in genomics are especially valuable for understanding the foundations of future evolutionary diversity.
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Affiliation(s)
- Brian W Bowen
- From the Hawai'i Institute of Marine Biology, PO Box 1346, Kaneohe, HI 96744.
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Santamaria CA, Mateos M, DeWitt TJ, Hurtado LA. Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea). Ecol Evol 2016; 6:1537-54. [PMID: 26900449 PMCID: PMC4747314 DOI: 10.1002/ece3.1984] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 11/06/2022] Open
Abstract
Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show evidence of hybridization. Populations are highly isolated, some of which appear to be very small; thus, the effects of drift are expected to reduce the efficiency of selection. Large genetic divergences among lineages, marked environmental differences in their ranges, reproductive isolation, and/or high isolation of populations may have resulted in morphological differences in L. occidentalis, not detected yet by traditional taxonomy. We used landmark‐based geometric morphometric analyses to test for differences in body shape among highly divergent lineages of L. occidentalis, and among populations within these lineages. We analyzed a total of 492 individuals from 53 coastal localities from the southern California Bight to Central Mexico, including the Gulf of California. We conducted discriminant function analyses (DFAs) on body shape morphometrics to assess morphological variation among genetically differentiated lineages and their populations. We also tested for associations between phylogeny and morphological variation, and whether genetic divergence is correlated to multivariate morphological divergence. We detected significant differences in body shape among highly divergent lineages, and among populations within these lineages. Nonetheless, neither lineages nor populations can be discriminated on the basis of body shape, because correct classification rates of cross‐validated DFAs were low. Genetic distance and phylogeny had weak to no effect on body shape variation. The supralittoral environment appears to exert strong stabilizing selection and/or strong functional constraints on body shape in L. occidentalis, thereby leading to morphological stasis in this isopod.
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Affiliation(s)
- Carlos A Santamaria
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas; Biology Faculty College of Arts and Sciences University of South Florida Sarasota-Manatee Sarasota Florida
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Thomas J DeWitt
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Luis A Hurtado
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
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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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Taiti S, Wynne JJ. The terrestrial Isopoda (Crustacea, Oniscidea) of Rapa Nui (Easter Island), with descriptions of two new species. Zookeys 2015; 515:27-49. [PMID: 26261438 PMCID: PMC4525033 DOI: 10.3897/zookeys.515.9477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/18/2015] [Indexed: 12/04/2022] Open
Abstract
Nine species of terrestrial isopods are reported for the Polynesian island of Rapa Nui (Easter Island) based upon museum materials and recent collections from field sampling. Most of these animals are non-native species, but two are new to science: Styloniscusmanuvaka sp. n. and Hawaiiosciarapui sp. n. Of these, the former is believed to be a Polynesian endemic as it has been recorded from Rapa Iti, Austral Islands, while the latter is identified as a Rapa Nui island endemic. Both of these new species are considered 'disturbance relicts' and appear restricted to the cave environment on Rapa Nui. A short key to all the oniscidean species presently recorded from Rapa Nui is provided. We also offered conservation and management recommendations for the two new isopod species.
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Affiliation(s)
- Stefano Taiti
- Istituto per lo Studio degli Ecosistemi, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Florence), Italy
| | - J. Judson Wynne
- Department of Biological Sciences, Colorado Plateau Biodiversity Center, Northern Arizona University, Box 5640, Flagstaff, Arizona 86011-5614, USA
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Hurtado LA, Lee EJ, Mateos M, Taiti S. Global diversification at the harsh sea-land interface: mitochondrial phylogeny of the supralittoral isopod genus Tylos (Tylidae, Oniscidea). PLoS One 2014; 9:e94081. [PMID: 24736501 PMCID: PMC3988090 DOI: 10.1371/journal.pone.0094081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/11/2014] [Indexed: 11/18/2022] Open
Abstract
The supralittoral environment, at the transition between sea and land, is characterized by harsh conditions for life. Nonetheless, evolution of terrestrial isopods (Oniscidea), the only group of Crustacea fully adapted to live on land, appears to have involved a transitional step within the supralittoral. The two most basal oniscidean lineages (Ligiidae and Tylidae) have representatives that successfully colonized the supralittoral. One of them is the genus Tylos, which is found exclusively in supralittoral sandy beaches from tropical and subtropical coasts around the world. Comprehensive phylogenetic hypotheses for this genus are lacking, which are necessary for understanding the evolution and biogeography of a lineage that successfully diversified in the harsh sea-land interface. Herein, we studied the phylogenetic relationships among 17 of the 21 currently recognized species of the genus Tylos, based on sequences from four mitochondrial genes (Cytochrome Oxidase I, Cytochrome b, 16S rDNA, and 12S rDNA). Maximum Likelihood and Bayesian phylogenetic analyses identified several lineages with deep divergences and discrete geographic distributions. Phylogenetic and distributional patterns of Tylos provide important clues on the biogeography and evolution of this group. Large divergences among the most basal clades are consistent with ancient splits. Due to the biological characteristics of Tylos, which likely prevent dispersal of these isopods across vast oceanic scales, we argue that tectonic events rather than trans-oceanic dispersal explain the distribution of Tylos in different continents. Overwater dispersal, however, likely enabled range expansions within some basins, and explains the colonization of volcanic oceanic islands. Present-day distributions were also likely influenced by sea level and climate changes. High levels of allopatric cryptic genetic differentiation are observed in different regions of the world, implying that the dispersal abilities of Tylos isopods are more limited than previously thought. Our results indicate that a taxonomic revision of this group is necessary.
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Affiliation(s)
- Luis A. Hurtado
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - Eun J. Lee
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Stefano Taiti
- Istituto per lo Studio degli Ecosistemi, CNR, Florence, Italy
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