1
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Ani CJ, Haller-Bull V, Gilmour JP, Robson BJ. Connectivity modelling identifies sources and sinks of coral recruitment within reef clusters. Sci Rep 2024; 14:13564. [PMID: 38866879 PMCID: PMC11169499 DOI: 10.1038/s41598-024-64388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024] Open
Abstract
Connectivity aids the recovery of populations following disturbances, such as coral bleaching and tropical cyclones. Coral larval connectivity is a function of physical connectivity and larval behaviour. In this study, we used OceanParcels, a particle tracking simulator, with 2D and 3D velocity outputs from a high resolution hydrodynamic-biogeochemical marine model (RECOM) to simulate the dispersal and settlement of larvae from broadcast spawning Acropora corals in the Moore Reef cluster, northern Great Barrier Reef, following the annual spawning events in 2015, 2016 and 2017. 3D velocity simulations showed 19.40-68.80% more links and sinks than those of 2D simulations. Although the patterns of connectivity among sites vary over days and years, coral larvae consistently dispersed from east to west in the cluster domain, with some sites consistently acting as sources or sinks for local larval recruitment. Results can inform coral reef intervention plans for climate change, such as the design of marine protected areas and the deployment of proposed interventions within reef clusters. For example, the wider benefits of interventions (e.g., deployment of heat adapted corals) may be optimised when deployed at locations that are a source of larvae to others within comparable habitats across the reef cluster.
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Affiliation(s)
- Chinenye J Ani
- Australian Institute of Marine Science, PMB3 Townsville, Townsville, QLD 4810, Australia.
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.
| | - Vanessa Haller-Bull
- Australian Institute of Marine Science, PMB3 Townsville, Townsville, QLD 4810, Australia
| | - James P Gilmour
- Australian Institute of Marine Science, Indian Ocean Marine Research Centre, The University of Western Australia, Crawley, Western Australia, Australia
- Oceans Institute, The University of Western Australia, Crawley, Western Australia, Australia
| | - Barbara J Robson
- Australian Institute of Marine Science, PMB3 Townsville, Townsville, QLD 4810, Australia
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
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2
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Sterling JJ, Sakihara TS, Brannock PM, Pearson ZG, Maclaine KD, Santos SR, Havird JC. Primary microbial succession in the anchialine ecosystem. Integr Comp Biol 2022; 62:275-287. [PMID: 35687002 DOI: 10.1093/icb/icac087] [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: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 11/13/2022] Open
Abstract
When new land is created, initial microbial colonization lays the foundation for further ecological succession of plant and animal communities. Primary microbial succession of new aquatic habitats formed during volcanic activity has received little attention. The anchialine ecosystem, which includes coastal ponds in young lava flows, offers an opportunity to examine this process. Here, we characterized microbial communities of anchialine habitats in Hawaii that were created during volcanic eruptions in 2018. Benthic samples from three habitats were collected ∼2 years after their formation and at later time points spanning ∼1 year. Sequence profiling (16S and 18S) of prokaryotic and eukaryotic communities was used to test whether communities were similar to those from older, established anchialine habitats, and if community structure changed over time. Results show that microbial communities from the new habitats were unlike any from established anchialine microbial communities, having higher proportions of Planctomycetota and Chloroflexi but lower proportions of green algae. Each new habitat also harbored its own unique community relative to other habitats. While community composition in each habitat underwent statistically significant changes over time, they remained distinctive from established anchialine habitats. New habitats also had highly elevated temperatures compared to other habitats. These results suggest idiosyncratic microbial consortia form during early succession of Hawaiian anchialine habitats. Future monitoring will reveal whether the early communities described here remain stable after temperatures decline and macro-organisms become more abundant, or if microbial communities will continue to change and eventually resemble those of established habitats. This work is a key first step in examining primary volcanic succession in aquatic habitats and suggests young anchialine habitats may warrant special conservation status.
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Affiliation(s)
- James J Sterling
- Dept. of Integrative Biology, The University of Texas at Austin, Austin, TX
| | - Troy S Sakihara
- Division of Aquatic Resources, Department of Land and Natural Resources, State of Hawaii Hilo, HI, USA
| | | | - Zoe G Pearson
- Dept. of Biology, Rollins College, Winter Park, FL, USA
| | - Kendra D Maclaine
- Dept. of Integrative Biology, The University of Texas at Austin, Austin, TX
| | - Scott R Santos
- Dept. of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Justin C Havird
- Dept. of Integrative Biology, The University of Texas at Austin, Austin, TX
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3
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Phylogeography and genetic diversity of the commercially-collected Caribbean blue-legged hermit crab (Clibanarius tricolor). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Yorisue T, Iguchi A, Yasuda N, Mizuyama M, Yoshioka Y, Miyagi A, Fujita Y. Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191731. [PMID: 33204436 PMCID: PMC7657918 DOI: 10.1098/rsos.191731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Marine cave habitats in the Ryukyu Islands, Indo-West Pacific, are located at the northern edge of the distribution of many cave-dwelling species. At distribution margins, gene flow is often more restricted than that among core populations due to the smaller effective population size. Here, we used high-throughput sequencing technology to investigate the gene flow pattern among three sampling sites of a marine cave-dwelling species at the margin of its distribution range. We collected individuals of the barbouriid shrimp Parhippolyte misticia from three marine caves in the Ryukyu Islands and performed population genetic analyses by means of multiplexed inter-simple sequence repeat genotyping by sequencing. Based on 62 single-nucleotide polymorphism markers, no clear population structure or directional gene flow pattern was found among the three sites. These results were unexpected because previous studies of other stygobitic shrimps in this region did find significant population genetic structures and northward directional gene flow patterns. Together, these inconsistent findings imply that marine cave-dwelling species in the region have different mechanisms of larval dispersal. Future studies on larval ecology and the biotic and abiotic factors influencing gene flow patterns are needed to clarify the mechanisms underlying the population dynamics of marine cave-dwelling species.
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Affiliation(s)
- Takefumi Yorisue
- Integrative Aquatic Biology, Onagawa Field Center, Graduate School of Agricultural Science, Tohoku University, 3-1 Mukai, Konori-hama, Onagawa, Oshika, Miyagi 986-2242, Japan
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
- Institute of Natural and Environmental Sciences, University of Hyogo, 6 Yayoigaoka, Sanda, Hyogo 669-1546, Japan
- Division of Nature and Environmental Management, Museum of Nature and Human Activities, Hyogo, 6 Yayoigaoka, Sanda, Hyogo 669-1546, Japan
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Nina Yasuda
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Gakuenkibana-dai Nishi 1-1, Miyazaki 889-2192, Japan
| | - Masaru Mizuyama
- Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa 905-2192, Japan
| | - Aika Miyagi
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa 905-2192, Japan
| | - Yoshihisa Fujita
- General Educational Center, Okinawa Prefectural University of Arts, 1-4, Shuri Tounokura-cho, Naha-shi, Okinawa 903-8602, Japan
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5
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Weaver RJ, Gonzalez BK, Santos SR, Havird JC. Red Coloration in an Anchialine Shrimp: Carotenoids, Genetic Variation, and Candidate Genes. THE BIOLOGICAL BULLETIN 2020; 238:119-130. [PMID: 32412843 DOI: 10.1086/708625] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Red coloration is a widely distributed phenotype among animals, yet the pigmentary and genetic bases for this phenotype have been described in relatively few taxa. Here we show that the Hawaiian endemic anchialine shrimp Halocaridina rubra is red because of the accumulation of astaxanthin. Laboratory colonies of phylogenetically distinct lineages of H. rubra have colony-specific amounts of astaxanthin that are developmentally, and likely genetically, fixed. Carotenoid supplementation and restriction experiments failed to change astaxanthin content from the within-colony baseline levels, suggesting that dietary limitation is not a major factor driving coloration differences. A possible candidate gene product predicted to be responsible for the production of astaxanthin in H. rubra and other crustaceans is closely related to the bifunctional cytochrome P450 family 3 enzyme CrtS found in fungi. However, homologs to the enzyme thought to catalyze ketolation reactions in birds and turtles, CYP2J19, were not found. This work is one of the first steps in linking phenotypic variation in red coloration of H. rubra to genotypic variation. Future work should focus on (1) pinpointing the genes that function in the bioconversion of dietary carotenoids to astaxanthin, (2) examining what genomic variants might drive variation in coloration among discrete lineages, and (3) testing more explicitly for condition-dependent carotenoid coloration in crustaceans.
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6
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Bribiesca-Contreras G, Pineda-Enríquez T, Márquez-Borrás F, Solís-Marín FA, Verbruggen H, Hugall AF, O'Hara TD. Dark offshoot: Phylogenomic data sheds light on the evolutionary history of a new species of cave brittle star. Mol Phylogenet Evol 2019; 136:151-163. [PMID: 30981811 DOI: 10.1016/j.ympev.2019.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 11/28/2022]
Abstract
Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.
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Affiliation(s)
- Guadalupe Bribiesca-Contreras
- Museum Victoria, GPO Box 666, Melbourne 3001, Australia; School of Biosciences, University of Melbourne, Victoria 3010, Australia.
| | - Tania Pineda-Enríquez
- Department of Biology, Division of Invertebrate Zoology, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA; Natural History Museum of Los Angeles County, 900 Exposition Blvd, Los Angeles, CA 90007, USA
| | - Francisco Márquez-Borrás
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico; Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Francisco A Solís-Marín
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Circuito Universitario s/n, Ciudad de México CP 04510, Mexico
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Victoria 3010, Australia
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7
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Meng X, Gao B, Li J, Liu P. The complete mitochondrial genome of the Shiba shrimp Metapenaeus joyneri (Miers, 1880) (Decapoda: Penaeidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1558118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xianliang Meng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Science, Qingdao, People’s Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People’s Republic of China
| | - Baoquan Gao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Science, Qingdao, People’s Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People’s Republic of China
| | - Jian Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Science, Qingdao, People’s Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People’s Republic of China
| | - Ping Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Science, Qingdao, People’s Republic of China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, People’s Republic of China
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8
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Meng X, Gao B, Li J, Liu P. Complete mitochondrial genome of smoothshell shrimp Parapenaeopsis tenella (Bate, 1888) (Crustacea: Decapoda: Penaeidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1567283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Xianliang Meng
- Key laboratory of Sustainable Development of Marine Fisheries Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute Chinese Academy of Fisheries Science, Qingdao, P. R. China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao P. R. China
| | - Baoquan Gao
- Key laboratory of Sustainable Development of Marine Fisheries Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute Chinese Academy of Fisheries Science, Qingdao, P. R. China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao P. R. China
| | - Jian Li
- Key laboratory of Sustainable Development of Marine Fisheries Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute Chinese Academy of Fisheries Science, Qingdao, P. R. China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao P. R. China
| | - Ping Liu
- Key laboratory of Sustainable Development of Marine Fisheries Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute Chinese Academy of Fisheries Science, Qingdao, P. R. China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao P. R. China
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9
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Wood LE, de Grave S, Daniels SR. A comparative evolutionary study reveals radically different scales of genetic structuring within two atyid shrimp species (Crustacea: Decapoda: Atyidae). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Louisa E Wood
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Sammy de Grave
- Oxford University Museum of Natural History, Parks Road, Oxford, UK
| | - Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
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10
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Jurado-Rivera JA, Pons J, Alvarez F, Botello A, Humphreys WF, Page TJ, Iliffe TM, Willassen E, Meland K, Juan C, Jaume D. Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps. Sci Rep 2017; 7:2852. [PMID: 28588246 PMCID: PMC5460120 DOI: 10.1038/s41598-017-03107-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/25/2017] [Indexed: 11/09/2022] Open
Abstract
Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (Atyidae) are restricted to specialised coastal subterranean habitats or nearby freshwaters and have a highly disconnected distribution (Eastern Pacific, Caribbean, Atlantic, Mediterranean, Madagascar, Australia). The combination of a wide distribution and a limited dispersal potential suggests a large-scale process has generated this geographic pattern. Tectonic plates that fragment ancestral ranges (vicariance) has often been assumed to cause this process, with the biota as passive passengers on continental blocks. The ancestors of these cave shrimps are believed to have inhabited the ancient Tethys Sea, with three particular geological events hypothesised to have led to their isolation and divergence; (1) the opening of the Atlantic Ocean, (2) the breakup of Gondwana, and (3) the closure of the Tethys Seaway. We test the relative contribution of vicariance and dispersal in the evolutionary history of this group using mitochondrial genomes to reconstruct phylogenetic and biogeographic scenarios with fossil-based calibrations. Given that the Australia/Madagascar shrimp divergence postdates the Gondwanan breakup, our results suggest both vicariance (the Atlantic opening) and dispersal. The Tethys closure appears not to have been influential, however we hypothesise that changing marine currents had an important early influence on their biogeography.
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Affiliation(s)
- José A Jurado-Rivera
- Dept. of Biology, Universitat de les Illes Balears. Ctra. Valldemossa km 7'5, Palma, 07122, Balearic Islands, Spain.
| | - Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies. C/ Miquel Marquès 21, Esporles, 07190, Balearic Islands, Spain
| | - Fernando Alvarez
- Colección Nacional de Crustáceos, Dpto. de Zoología, Instituto de Biología, UNAM. Tercer circuito s/n, Ciudad Universitaria, Copilco, Coyoacán, A.P. 70-153, México D.F. CP, 04510, Mexico
| | - Alejandro Botello
- Dept. de Ciencias Químico-Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez. Anillo del Pronaf y Estocolmo s/n, Ciudad Juarez, 32300, Chihuahua, Mexico
| | - William F Humphreys
- Western Australian Museum, Collections and Research, Locked Bag 49, Welshpool DC, WA, 6986, Australia
- School of Animal Biology, The University of Western Australia, Crawley, Perth, Western Australia, 6009, Australia
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland, 4111, Australia
- Water Planning Ecology, Queensland Dept. of Science, Information Technology and Innovation, Dutton Park, Queensland, 4102, Australia
| | - Thomas M Iliffe
- Dept. of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, OCSB #251, Galveston, TX, 77553, USA
| | - Endre Willassen
- Dept. of Natural History, University Museum of Bergen, Postboks 7800, N-5020, Bergen, Norway
| | - Kenneth Meland
- University of Bergen, Department of Biology, PO Box 7800, N-5020, Bergen, Norway
| | - Carlos Juan
- Dept. of Biology, Universitat de les Illes Balears. Ctra. Valldemossa km 7'5, Palma, 07122, Balearic Islands, Spain
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies. C/ Miquel Marquès 21, Esporles, 07190, Balearic Islands, Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies. C/ Miquel Marquès 21, Esporles, 07190, Balearic Islands, Spain
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11
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Gonzalez BC, Martínez A, Borda E, Iliffe TM, Fontaneto D, Worsaae K. Genetic spatial structure of an anchialine cave annelid indicates connectivity within - but not between - islands of the Great Bahama Bank. Mol Phylogenet Evol 2017; 109:259-270. [DOI: 10.1016/j.ympev.2017.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 12/30/2016] [Accepted: 01/04/2017] [Indexed: 12/18/2022]
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12
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Dudley BD, MacKenzie RA, Sakihara TS, Riney MH, Ostertag R. Effects of invasion at two trophic levels on diet, body condition, and population size structure of Hawaiian red shrimp. Ecosphere 2017. [DOI: 10.1002/ecs2.1682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Bruce D. Dudley
- Department of Biology; University of Hawai‛i at Hilo; 200 West Kawili Street Hilo Hawai‛i 96720 USA
| | - Richard A. MacKenzie
- Institute of Pacific Islands Forestry; USDA Forest Service; 60 Nowelo Street Hilo Hawai‛i 96720 USA
| | - Troy S. Sakihara
- Division of Aquatic Resources; Department of Land and Natural Resources; State of Hawai‛i; 1160 Kamehameha Avenue Hilo Hawai‛i 96720 USA
| | - Michael H. Riney
- Institute of Pacific Islands Forestry; USDA Forest Service; 60 Nowelo Street Hilo Hawai‛i 96720 USA
| | - Rebecca Ostertag
- Department of Biology; University of Hawai‛i at Hilo; 200 West Kawili Street Hilo Hawai‛i 96720 USA
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13
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Alda F, Gagne RB, Walter RP, Hogan JD, Moody KN, Zink F, McIntyre PB, Gilliam JF, Blum MJ. Colonization and demographic expansion of freshwater fauna across the Hawaiian archipelago. J Evol Biol 2016; 29:2054-2069. [DOI: 10.1111/jeb.12929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/05/2016] [Accepted: 06/28/2016] [Indexed: 12/25/2022]
Affiliation(s)
- F. Alda
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
- Tulane-Xavier Center for Bioenvironmental Research; Tulane University; New Orleans LA USA
| | - R. B. Gagne
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
| | - R. P. Walter
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
- Department of Biological Science; California State University, Fullerton; Fullerton CA USA
| | - J. D. Hogan
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
- Department of Life Sciences; Texas A & M University - Corpus Christi; Corpus Christi TX USA
| | - K. N. Moody
- Tulane-Xavier Center for Bioenvironmental Research; Tulane University; New Orleans LA USA
- Department of Biological Sciences; Clemson University; Clemson SC USA
| | - F. Zink
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
| | - P. B. McIntyre
- Center for Limnology; University of Wisconsin-Madison; Madison WI USA
| | - J. F. Gilliam
- Department of Biological Sciences; North Carolina State University; Raleigh NC USA
| | - M. J. Blum
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA USA
- Tulane-Xavier Center for Bioenvironmental Research; Tulane University; New Orleans LA USA
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14
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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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15
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Cánovas F, Jurado-Rivera JA, Cerro-Gálvez E, Juan C, Jaume D, Pons J. DNA barcodes, cryptic diversity and phylogeography of a W Mediterranean assemblage of thermosbaenacean crustaceans. ZOOL SCR 2016. [DOI: 10.1111/zsc.12173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Fernando Cánovas
- Centro de Ciências do Mar (CCMAR); Universidade do Algarve; Campus de Gambelas 8005-139 Faro Portugal
| | - José A. Jurado-Rivera
- Departament de Biologia; Universitat de les Illes Balears; Edifici Guillem Colom; Campus Universitari Ctra. Valldemossa, km 7'5 07122 Palma de Mallorca Illes Balears Spain
| | - Elena Cerro-Gálvez
- IMEDEA (CSIC-UIB); Instituto Mediterráneo de Estudios Avanzados; C/Miquel Marquès 21 07190 Esporles Illes Balears Spain
| | - Carlos Juan
- Departament de Biologia; Universitat de les Illes Balears; Edifici Guillem Colom; Campus Universitari Ctra. Valldemossa, km 7'5 07122 Palma de Mallorca Illes Balears Spain
- IMEDEA (CSIC-UIB); Instituto Mediterráneo de Estudios Avanzados; C/Miquel Marquès 21 07190 Esporles Illes Balears Spain
| | - Damià Jaume
- IMEDEA (CSIC-UIB); Instituto Mediterráneo de Estudios Avanzados; C/Miquel Marquès 21 07190 Esporles Illes Balears Spain
| | - Joan Pons
- IMEDEA (CSIC-UIB); Instituto Mediterráneo de Estudios Avanzados; C/Miquel Marquès 21 07190 Esporles Illes Balears Spain
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16
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Havird JC, Vaught RC, Weese DA, Santos SR. Reproduction and development in Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae) clarifies larval ecology in the Hawaiian anchialine ecosystem. THE BIOLOGICAL BULLETIN 2015; 229:134-142. [PMID: 26504154 DOI: 10.1086/bblv229n2p134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Larvae in aquatic habitats often develop in environments different from those they inhabit as adults. Shrimp in the Atyidae exemplify this trend, as larvae of many species require salt or brackish water for development, while adults are freshwater-adapted. An exception within the Atyidae family is the "anchialine clade," which are euryhaline as adults and endemic to habitats with subterranean fresh and marine water influences. Although the Hawaiian anchialine atyid Halocaridina rubra is a strong osmoregulator, its larvae have never been observed in nature. Moreover, larval development in anchialine species is poorly studied. Here, reproductive trends in laboratory colonies over a 5-y period are presented from seven genetic lineages and one mixed population of H. rubra; larval survivorship under varying salinities is also discussed. The presence and number of larvae differed significantly among lineages, with the mixed population being the most prolific. Statistical differences in reproduction attributable to seasonality also were identified. Larval survivorship was lowest (12% settlement rate) at a salinity approaching fresh water and significantly higher in brackish and seawater (88% and 72%, respectively). Correlated with this finding, identifiable gills capable of ion transport did not develop until metamorphosis into juveniles. Thus, early life stages of H. rubra are apparently excluded from surface waters, which are characterized by lower and fluctuating salinities. Instead, these stages are restricted to the subterranean (where there is higher and more stable salinity) portion of Hawaii's anchialine habitats due to their inability to tolerate low salinities. Taken together, these data contribute to the understudied area of larval ecology in the anchialine ecosystem.
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Affiliation(s)
- Justin C Havird
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, Alabama 36849
| | - Rebecca C Vaught
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, Alabama 36849
| | - David A Weese
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, Alabama 36849
| | - Scott R Santos
- Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies, Auburn University, 101 Rouse Life Sciences Bldg., Auburn, Alabama 36849
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Mirimin L, Kitchin N, Impson DN, Clark PF, Richard J, Daniels SR, Roodt-Wilding R. Genetic and Morphological Characterization of Freshwater Shrimps (Caridina africana Kingsley, 1882) Reveals the Presence of Alien Shrimps in the Cape Floristic Region, South Africa. J Hered 2015; 106:711-8. [PMID: 26297730 DOI: 10.1093/jhered/esv063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 07/24/2015] [Indexed: 11/14/2022] Open
Abstract
Morphological identification and molecular data (mtDNA COI) were used to resolve the taxonomic identity of a non-native freshwater shrimp in the Cape Floristic Region (CFR) of South Africa and to evaluate levels of genetic diversity and differentiation in the species' core natural distribution. The species was morphologically and genetically identified as Caridina africana Kingsley, 1882, whose main natural distribution is in the KwaZulu-Natal (KZN) Province, more than 1200 km from the point of new discovery. Subsequently, sequence data from natural populations occurring in seven rivers throughout KZN showed the presence of nuclear copies of the mtDNA COI gene (NUMTs) in 46 out of 140 individuals. Upon removal of sequences containing NUMTs, levels of genetic diversity were low in the alien population (possibly as a consequence of a bottleneck event), while varying levels of genetic diversity and differentiation were found in natural populations, indicating habitat heterogeneity, fragmentation and restricted gene flow between rivers. Following the present study, the alien shrimp has survived the Western Cape's winter and dispersed into a nearby tributary of the Eerste River System, hence posing an additional potential threat to endangered endemics. Understanding the biology of this alien species will aid detection and eradication procedures.
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Affiliation(s)
- Luca Mirimin
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels).
| | - Natasha Kitchin
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Dean N Impson
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Paul F Clark
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Jasmine Richard
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Savel R Daniels
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
| | - Rouvay Roodt-Wilding
- From the Molecular Breeding and Biodiversity Research Group, Department of Genetics, Stellenbosch University, JC Smuts Building, van der Bjl Street, Stellenbosch 7600, South Africa (Mirimin, Kitchin, and Roodt-Wilding); Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Galway, Ireland (Mirimin); Scientific Services, Cape Nature, Jonkershoek , Stellenbosch, South Africa (Impson); Invertebrates Division, Life Sciences Department, Natural History Museum, London, UK (Clark and Richard); and Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa (Daniels)
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Justice JL, Weese DA, Santos SR. Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2710-8. [PMID: 26061341 DOI: 10.3109/19401736.2015.1046161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Atyidae are caridean shrimp possessing hair-like setae on their claws and are important contributors to ecological services in tropical and temperate fresh and brackish water ecosystems. Complete mitochondrial genomes have only been reported from five of the 449 species in the family, thus limiting understanding of mitochondrial genome evolution and the phylogenetic utility of complete mitochondrial sequences in the Atyidae. Here, comparative analyses of complete mitochondrial genomes from eight genetic lineages of Halocaridina rubra, an atyid endemic to the anchialine ecosystem of the Hawaiian Archipelago, are presented. Although gene number, order, and orientation were syntenic among genomes, three regions were identified and further quantified where conservation was substantially lower: (1) high length and sequence variability in the tRNA-Lys and tRNA-Asp intergenic region; (2) a 317-bp insertion between the NAD6 and CytB genes confined to a single lineage and representing a partial duplication of CytB; and (3) the putative control region. Phylogenetic analyses utilizing complete mitochondrial sequences provided new insights into relationships among the H. rubra genetic lineages, with the topology of one clade correlating to the geologic sequence of the islands. However, deeper nodes in the phylogeny lacked bootstrap support. Overall, our results from H. rubra suggest intra-specific mitochondrial genomic diversity could be underestimated across the Metazoa since the vast majority of complete genomes are from just a single individual of a species.
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Affiliation(s)
- Joshua L Justice
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .,b Department of Microbiology , University of Alabama at Birmingham , Birmingham , AL , USA , and
| | - David A Weese
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA .,c Department of Biological and Environmental Sciences , Georgia College and State University , Milledgeville , GA , USA
| | - Scott Ross Santos
- a Department of Biological Sciences and Molette Laboratory for Climate Change and Environmental Studies , Auburn University , Auburn , AL , USA
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Santamaria CA, Mateos M, Taiti S, DeWitt TJ, Hurtado LA. A complex evolutionary history in a remote archipelago: phylogeography and morphometrics of the Hawaiian endemic Ligia isopods. PLoS One 2013; 8:e85199. [PMID: 24386463 PMCID: PMC3875554 DOI: 10.1371/journal.pone.0085199] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 11/23/2013] [Indexed: 12/04/2022] Open
Abstract
Compared to the striking diversification and levels of endemism observed in many terrestrial groups within the Hawaiian Archipelago, marine invertebrates exhibit remarkably lower rates of endemism and diversification. Supralittoral invertebrates restricted to specific coastal patchy habitats, however, have the potential for high levels of allopatric diversification. This is the case of Ligia isopods endemic to the Hawaiian Archipelago, which most likely arose from a rocky supralittoral ancestor that colonized the archipelago via rafting, and diversified into rocky supralittoral and inland lineages. A previous study on populations of this isopod from O'ahu and Kaua'i revealed high levels of allopatric differentiation, and suggested inter-island historical dispersal events have been rare. To gain a better understanding on the diversity and evolution of this group, we expanded prior phylogeographic work by incorporating populations from unsampled main Hawaiian Islands (Maui, Moloka'i, Lana'i, and Hawai'i), increasing the number of gene markers (four mitochondrial and two nuclear genes), and conducting Maximum likelihood and Bayesian phylogenetic analyses. Our study revealed new lineages and expanded the distribution range of several lineages. The phylogeographic patterns of Ligia in the study area are complex, with Hawai'i, O'ahu, and the Maui-Nui islands sharing major lineages, implying multiple inter-island historical dispersal events. In contrast, the oldest and most geographically distant of the major islands (Kaua'i) shares no lineages with the other islands. Our results did not support the monophyly of all the supralittoral lineages (currently grouped into L. hawaiensis), or the monophyly of the terrestrial lineages (currently grouped into L. perkinsi), implying more than one evolutionary transition between coastal and inland forms. Geometric-morphometric analyses of three supralittoral clades revealed significant body shape differences among them. A taxonomic revision of Hawaiian Ligia is warranted. Our results are relevant for the protection of biodiversity found in an environment subject to high pressure from disturbances.
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Affiliation(s)
- Carlos A. Santamaria
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
- Department of Biological Sciences, Sam Houston State University, Huntsville, 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
| | - Thomas J. DeWitt
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Luis A. Hurtado
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
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20
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Becking LE, Erpenbeck D, Peijnenburg KTCA, de Voogd NJ. Phylogeography of the sponge Suberites diversicolor in Indonesia: insights into the evolution of marine lake populations. PLoS One 2013; 8:e75996. [PMID: 24098416 PMCID: PMC3788070 DOI: 10.1371/journal.pone.0075996] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022] Open
Abstract
The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.
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Affiliation(s)
- Leontine E. Becking
- Naturalis Biodiversity Center, Department Marine Zoology, Leiden, The Netherlands
- Institute for Marine Resources and Ecosystem Studies (IMARES), Maritime Department, Den Helder, The Netherlands
- * E-mail:
| | - Dirk Erpenbeck
- Department of Earth- and Environmental Sciences, Palaeontology & Geobiology & GeoBio-Center, Ludwig-Maximilians-University, Munich, Germany
| | - Katja T. C. A. Peijnenburg
- Naturalis Biodiversity Center, Department Marine Zoology, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole J. de Voogd
- Naturalis Biodiversity Center, Department Marine Zoology, Leiden, The Netherlands
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21
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Weese DA, Fujita Y, Santos SR. Multiple colonizations lead to cryptic biodiversity in an island ecosystem: comparative phylogeography of anchialine shrimp species in the Ryukyu Archipelago, Japan. THE BIOLOGICAL BULLETIN 2013; 225:24-41. [PMID: 24088794 DOI: 10.1086/bblv225n1p24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Archipelagos of the Indo-West Pacific are considered to be among the richest in the world in biodiversity, and phylogeographic studies generally support either the center of origin or the center of accumulation hypothesis to explain this pattern. To differentiate between these competing hypotheses for organisms from the Indo-West Pacific anchialine ecosystem, defined as coastal bodies of mixohaline water fluctuating with the tides but having no direct oceanic connections, we investigated the genetic variation, population structure, and evolutionary history of three caridean shrimp species (Antecaridina lauensis, Halocaridinides trigonophthalma, and Metabetaeus minutus) in the Ryukyu Archipelago, Japan. We used two mitochondrial genes--cytochrome c oxidase subunit I (COI) and large ribosomal subunit (16S-rDNA)--complemented with genetic examination of available specimens from the same or closely related species from the Indian and Pacific Oceans. In the Ryukyus, each species encompassed 2-3 divergent (9.52%-19.2% COI p-distance) lineages, each having significant population structure and varying geographic distributions. Phylogenetically, the A. lauensis and M. minutus lineages in the Ryukyus were more closely related to ones from outside the archipelago than to one another. These results, when interpreted in the context of Pacific oceanographic currents and geologic history of the Ryukyus, imply multiple colonizations of the archipelago by the three species, consistent with the center of accumulation hypothesis. While this study contributes toward understanding the biodiversity, ecology, and evolution of organisms in the Ryukyus and the Indo-West Pacific, it also has potential utility in establishing conservation strategies for anchialine fauna of the Pacific Basin in general.
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Affiliation(s)
- David A Weese
- Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, Alabama 36849
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22
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Dalton CM, Mokiao-Lee A, Sakihara TS, Weber MG, Roco CA, Han Z, Dudley B, MacKenzie RA, Hairston NG. Density- and trait-mediated top-down effects modify bottom-up control of a highly endemic tropical aquatic food web. OIKOS 2012. [DOI: 10.1111/j.1600-0706.2012.20696.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Goodall-Copestake WP, Tarling GA, Murphy EJ. On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals. Heredity (Edinb) 2012; 109:50-6. [PMID: 22434013 PMCID: PMC3375404 DOI: 10.1038/hdy.2012.12] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 11/10/2022] Open
Abstract
Estimates of genetic diversity represent a valuable resource for biodiversity assessments and are increasingly used to guide conservation and management programs. The most commonly reported estimates of DNA sequence diversity in animal populations are haplotype diversity (h) and nucleotide diversity (π) for the mitochondrial gene cytochrome c oxidase subunit I (cox1). However, several issues relevant to the comparison of h and π within and between studies remain to be assessed. We used population-level cox1 data from peer-reviewed publications to quantify the extent to which data sets can be re-assembled, to provide a standardized summary of h and π estimates, to explore the relationship between these metrics and to assess their sensitivity to under-sampling. Only 19 out of 42 selected publications had archived data that could be unambiguously re-assembled; this comprised 127 population-level data sets (n ≥ 15) from 23 animal species. Estimates of h and π were calculated using a 456-base region of cox1 that was common to all the data sets (median h=0.70130, median π=0.00356). Non-linear regression methods and Bayesian information criterion analysis revealed that the most parsimonious model describing the relationship between the estimates of h and π was π=0.0081 h(2). Deviations from this model can be used to detect outliers due to biological processes or methodological issues. Subsampling analyses indicated that samples of n>5 were sufficient to discriminate extremes of high from low population-level cox1 diversity, but samples of n ≥ 25 are recommended for greater accuracy.
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Affiliation(s)
- W P Goodall-Copestake
- Biological Sciences Division, British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - G A Tarling
- Biological Sciences Division, British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - E J Murphy
- Biological Sciences Division, British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
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Bird CE. Morphological and behavioral evidence for adaptive diversification of sympatric Hawaiian limpets (Cellana spp.). Integr Comp Biol 2011; 51:466-73. [PMID: 21700576 DOI: 10.1093/icb/icr050] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The endemic Hawaiian limpets (Cellana exarata, Cellana sandwicensis, and Cellana talcosa), reside at different elevations on wave-exposed rocky shores and comprise a monophyletic lineage that diversified within Hawai'i. Here, I report phenotypic differences in shell, soft tissue, and behavioral characters among these limpets and discuss their potential utility in exploiting their respective niches. The high-shore limpet, C. exarata, is characterized by a tall round shell, short mantle tentacles, and long evasion distance when confronted by a predatory gastropod. The mid-shore limpet, C. sandwicensis, is characterized by a shorter oblong shell, long mantle tentacles, and a short evasion distance when confronted by a predatory snail. The low-shore, shallow-subtidal limpet, C. talcosa, is characterized by a flat shell that is thin in juveniles and disproportionately massive in large adults (relative to the other two species), and mantle tentacles of varying lengths (some individuals exhibit short tentacles, some long). These species-specific suites of characters are likely to confer specific fitness advantages on the high shore (C. exarata) where thermal and desiccation stress is severe, on the mid shore (C. sandwicensis) where hydrodynamic forces are severe, and on the low-shallow subtidal shore (C. talcosa) where pelagic predators have free access to the limpets. These data add to the growing body of evidence for adaptive diversification and speciation in the Hawaiian Cellana, and in marine species in general.
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Affiliation(s)
- Christopher E Bird
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Sciences, University of Hawai'i at Mānoa, PO BOX 1346, Kāne'ohe, HI 96744, USA.
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BIRD CHRISTOPHERE, HOLLAND BRENDENS, BOWEN BRIANW, TOONEN ROBERTJ. Diversification of sympatric broadcast-spawning limpets (Cellana spp.) within the Hawaiian archipelago. Mol Ecol 2011; 20:2128-41. [DOI: 10.1111/j.1365-294x.2011.05081.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Juan C, Guzik MT, Jaume D, Cooper SJB. Evolution in caves: Darwin’s ‘wrecks of ancient life’ in the molecular era. Mol Ecol 2010; 19:3865-80. [PMID: 20637049 DOI: 10.1111/j.1365-294x.2010.04759.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Carlos Juan
- Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, (Balearic Islands) Spain.
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27
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Weese DA, Santos SR. Genetic identification of source populations for an aquarium-traded invertebrate. Anim Conserv 2009. [DOI: 10.1111/j.1469-1795.2008.00215.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Page TJ, Humphreys WF, Hughes JM. Shrimps down under: evolutionary relationships of subterranean crustaceans from Western Australia (Decapoda: Atyidae: Stygiocaris). PLoS One 2008; 3:e1618. [PMID: 18286175 PMCID: PMC2229661 DOI: 10.1371/journal.pone.0001618] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Accepted: 01/18/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND We investigated the large and small scale evolutionary relationships of the endemic Western Australian subterranean shrimp genus Stygiocaris (Atyidae) using nuclear and mitochondrial genes. Stygiocaris is part of the unique cave biota of the coastal, anchialine, limestones of the Cape Range and Barrow Island, most of whose nearest evolutionary relations are found in coastal caves of the distant North Atlantic. The dominance of atyids in tropical waters and their food resources suggest they are pivotal in understanding these groundwater ecosystems. METHODOLOGY/PRINCIPLE FINDINGS Our nuclear and mitochondrial analyses all recovered the Mexican cave genus Typhlatya as the sister taxon of Stygiocaris, rather than any of the numerous surface and cave atyids from Australia or the Indo-Pacific region. The two described Stygiocaris species were recovered as monophyletic, and a third, cryptic, species was discovered at a single site, which has very different physiochemical properties from the sites hosting the two described species. CONCLUSIONS/SIGNIFICANCE Our findings suggest that Stygiocaris and Typhlatya may descend from a common ancestor that lived in the coastal marine habitat of the ancient Tethys Sea, and were subsequently separated by plate tectonic movements. This vicariant process is commonly thought to explain the many disjunct anchialine faunas, but has rarely been demonstrated using phylogenetic techniques. The Cape Range's geological dynamism, which is probably responsible for the speciation of the various Stygiocaris species, has also led to geographic population structure within species. In particular, Stygiocaris lancifera is split into northern and southern groups, which correspond to population splits within other sympatric subterranean taxa.
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Affiliation(s)
- Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia.
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29
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COOK BENJAMIND, PRINGLE CATHERINEM, HUGHES JANEM. °Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island. Mol Ecol 2008; 17:1066-75. [DOI: 10.1111/j.1365-294x.2007.03637.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ivey JL, Santos SR. The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene 2007; 394:35-44. [PMID: 17317038 DOI: 10.1016/j.gene.2007.01.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 12/22/2006] [Accepted: 01/08/2007] [Indexed: 11/22/2022]
Abstract
Shrimp of the family Atyidae are important members of nearly all tropical (and most temperate) fresh and brackish water ecosystems in the world. To date, a complete mitochondrial genome from this important crustacean group has not been reported. Here, we present the complete mitochondrial DNA sequence of the Hawaiian atyid Halocaridina rubra [Holthuis, L.B., 1963. On red coloured shrimps (Decapoda, Caridea) from tropical land-locked saltwater pools. Zool. Meded.16, 261-279.] (Crustacea: Decapoda: Atyidae). The genome is a circular molecule of 16,065 bp and encodes the 37 mitochondrial genes (13 protein-coding, 22 tRNAs, and two rRNAs) typically found in the metazoa. Gene order and orientation in the H. rubra mitochondrial genome is syntenic with most malacostracans that have been examined to date. Of special note is the absence of the dihydrouridine (DHU) arm stem from tRNA(Tyr) and the use of CCG as an initiation codon for cytochrome oxidase subunit I (COI); these represent the first reported examples of such phenomena in the Malacostraca. Phylogenetic analyses utilizing complete mitochondrial sequences from other malacostracans place H. rubra as sister to Macrobrachium rosenbergii, which also belongs to the Infraorder Caridea. However, the placement of this infraorder, as well as the Infraorder Dendrobrachiata, in the phylogeny of the Decapoda varied depending on outgroup selection. Data from additional mitochondrial genomes, such as basal decapods like the Stenopodidea, should contribute to a better overall understanding of decapod phylogenetics.
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Affiliation(s)
- Jennifer L Ivey
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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