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Oh DJ, Ko MH, Min DW, Jung YH. Complete mitochondrial genome of the diving beetle, Cybister brevis Aubé, 1838 (Coleoptera, Dytiscidae) from Jeju Island. Mitochondrial DNA B Resour 2024; 9:295-299. [PMID: 38406669 PMCID: PMC10885740 DOI: 10.1080/23802359.2024.2317327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
The mitochondrial genome of Cybister brevis Aubé, 1838, is 16,198 bp long and includes 37 genes that are highly conserved in the family Dytiscidae. Phylogenetic analysis revealed that all genera in Dytiscidae, except Hydroporus and Oreodytes, are monophyletic. The Hydroporini tribe was found to be polyphyletic and closely associated with the Hygrotini, Bidessini, and Hyphydrini tribes. Dytiscinae was found to be a highly divergent polyphyletic group comprising three distinct clades. This study also revealed that C. brevis is closely related to Cybister japonicus and that the tribe Cybistrini diverged relatively early compared to other tribes in Hydroporinae. These findings are consistent with those of previous studies and provide new insights into the phylogeny of the Dytiscidae family, which has previously shown discrepancies between morphological characteristics and molecular data. The genome-level analyses conducted in this study serve as a valuable foundation for future investigations into the Dysticidae evolutionary history.
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Affiliation(s)
- Dae-Ju Oh
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Jeju, Republic of Korea
| | - Min-Hee Ko
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Jeju, Republic of Korea
| | | | - Yong-Hwan Jung
- Biodiversity Research Institute, Jeju Technopark, Seogwipo, Jeju, Republic of Korea
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Hájek J, Reiter A, Vondráček D. Molecular analysis and morphological variability confirm Hydaticus dhofarensis Pederzani, 2003 as the westernmost population of the Indomalayan H. bipunctatus Wehncke, 1876 (Coleoptera: Dytiscidae). ZOOLOGY IN THE MIDDLE EAST 2021. [DOI: 10.1080/09397140.2021.1918191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jiří Hájek
- Department of Entomology, National Museum, Prague, Czech Republic
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Temreshev II. Review of the predaceous diving beetles of the genus Hydaticus Leach, 1817 (Coleoptera: Dytiscidae) of Kazakhstan. ACTA BIOLOGICA SIBIRICA 2018. [DOI: 10.14258/abs.v4i3.4369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Rota J, Malm T, Chazot N, Peña C, Wahlberg N. A simple method for data partitioning based on relative evolutionary rates. PeerJ 2018; 6:e5498. [PMID: 30186687 PMCID: PMC6118207 DOI: 10.7717/peerj.5498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 08/01/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns. METHODS We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder. RESULTS Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset. DISCUSSION We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.
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Affiliation(s)
- Jadranka Rota
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Carlos Peña
- HipLead, San Francisco, CA, United States of America
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Li X, Li W, Ding S, Cameron SL, Mao M, Shi L, Yang D. Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha). Int J Mol Sci 2017; 18:E773. [PMID: 28420076 PMCID: PMC5412357 DOI: 10.3390/ijms18040773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/23/2017] [Accepted: 04/01/2017] [Indexed: 11/17/2022] Open
Abstract
The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Wenliang Li
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, China.
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
| | - Meng Mao
- Department of Plant and Environmental Protection Science, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Li Shi
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
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Gustafson GT, Miller KB. Systematics and evolution of the whirligig beetle tribe Dineutini (Coleoptera: Gyrinidae: Gyrininae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Baca SM, Toussaint EF, Miller KB, Short AE. Molecular phylogeny of the aquatic beetle family Noteridae (Coleoptera: Adephaga) with an emphasis on data partitioning strategies. Mol Phylogenet Evol 2017; 107:282-292. [DOI: 10.1016/j.ympev.2016.10.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 10/11/2016] [Accepted: 10/22/2016] [Indexed: 01/06/2023]
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8
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Jiang F, Pan X, Li X, Yu Y, Zhang J, Jiang H, Dou L, Zhu S. The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe. Sci Rep 2016; 6:36426. [PMID: 27812024 PMCID: PMC5095552 DOI: 10.1038/srep36426] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/14/2016] [Indexed: 11/09/2022] Open
Abstract
The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species - D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene. There is a possibility that the TA stop codon in COI is the synapomorphy in Bactrocera group in the genus Bactrocera comparing with other Tephritidae species. Phylogenetic analyses based on the mitogenome data from Tephritidae were inferred by Bayesian and Maximum-likelihood methods, strongly supported the sister relationship between Zeugodacus and Dacus.
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MESH Headings
- Animals
- Base Sequence
- Bayes Theorem
- Codon, Terminator
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/metabolism
- Electron Transport Complex IV/chemistry
- Electron Transport Complex IV/genetics
- Genome, Mitochondrial
- High-Throughput Nucleotide Sequencing
- Mitochondria/genetics
- Phylogeny
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Tephritidae/classification
- Tephritidae/genetics
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Affiliation(s)
- Fan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xubin Pan
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xuankun Li
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Yanxue Yu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Junhua Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Hongshan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Liduo Dou
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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Molecular phylogeny and biogeography of the weevil subfamily Platypodinae reveals evolutionarily conserved range patterns. Mol Phylogenet Evol 2015; 92:294-307. [PMID: 26190520 DOI: 10.1016/j.ympev.2015.05.028] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 05/04/2015] [Accepted: 05/11/2015] [Indexed: 01/02/2023]
Abstract
Platypodinae is a peculiar weevil subfamily of species that cultivate fungi in tunnels excavated in dead wood. Their geographical distribution is generally restricted, with genera confined to a single continent or large island, which provides a useful system for biogeographical research. This study establishes the first detailed molecular phylogeny of the group, with the aim of testing hypotheses on classification, diversification, and biogeography. A phylogeny was reconstructed based on 3648 nucleotides from COI, EF-1α, CAD, ArgK, and 28S. Tree topology was well resolved and indicated a strong correlation with geography, more so than predicted by previous morphology-based classifications. Tesserocerini was paraphyletic, with Notoplatypus as the sister group to a clade consisting of three main lineages of Tesserocerini and the recently evolved Platypodini. Austroplatypus formed the sister group to all remaining Platypodini and hence confirmed its separate status from Platypus. The Indo-Australian genera of Platypodini were strikingly paraphyletic, suggesting that the taxonomy of this tribe needs careful revision. Ancestral-area reconstructions in Lagrange and S-DIVA were ambiguous for nodes roughly older than 80 Ma. More recent events were firmly assessed and involved post-Gondwanan long-distance dispersal. The Neotropics was colonized three times, all from the Afrotropical region, with the latest event less than 25 Ma that included the ancestor of all Neotropical Platypodini.
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Bukontaite R, Ranarilalatiana T, Randriamihaja JH, Bergsten J. In or out-of-Madagascar?--Colonization patterns for large-bodied diving beetles (Coleoptera: Dytiscidae). PLoS One 2015; 10:e0120777. [PMID: 25794184 PMCID: PMC4368551 DOI: 10.1371/journal.pone.0120777] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 02/01/2015] [Indexed: 12/21/2022] Open
Abstract
High species diversity and endemism within Madagascar is mainly the result of species radiations following colonization from nearby continents or islands. Most of the endemic taxa are thought to be descendants of a single or small number of colonizers that arrived from Africa sometime during the Cenozoic and gave rise to highly diverse groups. This pattern is largely based on vertebrates and a small number of invertebrate groups. Knowledge of the evolutionary history of aquatic beetles on Madagascar is lacking, even though this species-rich group is often a dominant part of invertebrate freshwater communities in both standing and running water. Here we focus on large bodied diving beetles of the tribes Hydaticini and Cybistrini. Our aims with this study were to answer the following questions 1) How many colonization events does the present Malagasy fauna originate from? 2) Did any colonization event lead to a species radiation? 3) Where did the colonizers come from--Africa or Asia--and has there been any out-of-Madagascar event? 4) When did these events occur and were they concentrated to any particular time interval? Our results suggest that neither in Hydaticini nor in Cybistrini was there a single case of two or more endemic species forming a monophyletic group. The biogeographical analysis indicated different colonization histories for the two tribes. Cybistrini required at least eight separate colonization events, including the non-endemic species, all comparatively recent except the only lotic (running water) living Cybister operosus with an inferred colonization at 29 Ma. In Hydaticini the Madagascan endemics were spread out across the tree, often occupying basal positions in different species groups. The biogeographical analyses therefore postulated the very bold hypothesis of a Madagascan origin at a very deep basal node within Hydaticus and multiple out-of-Madagascar dispersal events. This hypothesis needs to be tested with equally intense taxon sampling of mainland Africa as for Madagascar.
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Affiliation(s)
- Rasa Bukontaite
- Department of Zoology, Swedish Museum of Natural History, Box 50007, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tolotra Ranarilalatiana
- Departement d’Entomologie, Faculté des Sciences, B.P. 906, Université d’Antananarivo, Antananarivo, Madagascar
- Programme National de Lutte contre le Paludisme de Madagascar, Androhibe, Antananarivo (101), Madagascar
| | - Jacquelin Herisahala Randriamihaja
- Departement d’Entomologie, Faculté des Sciences, B.P. 906, Université d’Antananarivo, Antananarivo, Madagascar
- Programme National de Lutte contre le Paludisme de Madagascar, Androhibe, Antananarivo (101), Madagascar
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Box 50007, Stockholm, Sweden
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Abstract
Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.
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Affiliation(s)
- David Kainer
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Robert Lanfear
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia National Evolutionary Synthesis Center, Durham, NC Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
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12
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Wang H, Wahlberg N, Holloway JD, Bergsten J, Fan X, Janzen DH, Hallwachs W, Wen L, Wang M, Nylin S. Molecular phylogeny of Lymantriinae (Lepidoptera, Noctuoidea, Erebidae) inferred from eight gene regions. Cladistics 2015; 31:579-592. [DOI: 10.1111/cla.12108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
- Houshuai Wang
- Department of Entomology; College of Natural Resources & Environment; South China Agricultural University; 510642 Guangzhou China
- Department of Zoology; University of Stockholm; SE-10691 Stockholm Sweden
| | - Niklas Wahlberg
- Department of Biology; Laboratory of Genetics; University of Turku; 2014 Turku Finland
| | - Jeremy D. Holloway
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Johannes Bergsten
- Department of Zoology; Swedish Museum of Natural History; SE-10405 Stockholm Sweden
| | - Xiaoling Fan
- Department of Entomology; College of Natural Resources & Environment; South China Agricultural University; 510642 Guangzhou China
| | - Daniel H. Janzen
- Department of Biology; University of Pennsylvania; Philadelphia PA 19104 USA
| | - Winnie Hallwachs
- Department of Biology; University of Pennsylvania; Philadelphia PA 19104 USA
| | - Lijun Wen
- Department of Entomology; College of Natural Resources & Environment; South China Agricultural University; 510642 Guangzhou China
| | - Min Wang
- Department of Entomology; College of Natural Resources & Environment; South China Agricultural University; 510642 Guangzhou China
| | - Sӧren Nylin
- Department of Zoology; University of Stockholm; SE-10691 Stockholm Sweden
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13
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Hidalgo-Galiana A, Sánchez-Fernández D, Bilton DT, Cieslak A, Ribera I. Thermal niche evolution and geographical range expansion in a species complex of western Mediterranean diving beetles. BMC Evol Biol 2014; 14:187. [PMID: 25205299 PMCID: PMC4180321 DOI: 10.1186/s12862-014-0187-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/11/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Species thermal requirements are one of the principal determinants of their ecology and biogeography, although our understanding of the interplay between these factors is limited by the paucity of integrative empirical studies. Here we use empirically collected thermal tolerance data in combination with molecular phylogenetics/phylogeography and ecological niche modelling to study the evolution of a clade of three western Mediterranean diving beetles, the Agabus brunneus complex. RESULTS The preferred mitochondrial DNA topology recovered A. ramblae (North Africa, east Iberia and Balearic islands) as paraphyletic, with A. brunneus (widespread in the southwestern Mediterranean) and A. rufulus (Corsica and Sardinia) nested within it, with an estimated origin between 0.60-0.25 Ma. All three species were, however, recovered as monophyletic using nuclear DNA markers. A Bayesian skyline plot suggested demographic expansion in the clade at the onset of the last glacial cycle. The species thermal tolerances differ significantly, with A. brunneus able to tolerate lower temperatures than the other taxa. The climatic niche of the three species also differs, with A. ramblae occupying more arid and seasonal areas, with a higher minimum temperature in the coldest month. The estimated potential distribution for both A. brunneus and A. ramblae was most restricted in the last interglacial, becoming increasingly wider through the last glacial and the Holocene. CONCLUSIONS The A. brunneus complex diversified in the late Pleistocene, most likely in south Iberia after colonization from Morocco. Insular forms did not differentiate substantially in morphology or ecology, but A. brunneus evolved a wider tolerance to cold, which appeared to have facilitated its geographic expansion. Both A. brunneus and A. ramblae expanded their ranges during the last glacial, although they have not occupied areas beyond their LGM potential distribution except for isolated populations of A. brunneus in France and England. On the islands and possibly Tunisia secondary contact between A. brunneus and A. ramblae or A. rufulus has resulted in introgression. Our work highlights the complex dynamics of speciation and range expansions within southern areas during the last glacial cycle, and points to the often neglected role of North Africa as a source of European biodiversity.
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Affiliation(s)
- Amparo Hidalgo-Galiana
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - David Sánchez-Fernández
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - David T Bilton
- />Marine Biology and Ecology Research Centre, Plymouth University, Drake Circus, PL4 8AA Plymouth, UK
| | - Alexandra Cieslak
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Ignacio Ribera
- />Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37-49, 08003 Barcelona, Spain
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Andújar C, Soria-Carrasco V, Serrano J, Gómez-Zurita J. Congruence test of molecular clock calibration hypotheses based on Bayes factor comparisons. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12151] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carmelo Andújar
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; 30071 Murcia Spain
| | - Víctor Soria-Carrasco
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 08003 Barcelona Spain
| | - José Serrano
- Departamento de Zoología y Antropología Física; Facultad de Veterinaria; Universidad de Murcia; 30071 Murcia Spain
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution; Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra); Pg. Marítim de la Barceloneta 37 08003 Barcelona Spain
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15
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Bukontaite R, Miller KB, Bergsten J. The utility of CAD in recovering Gondwanan vicariance events and the evolutionary history of Aciliini (Coleoptera: Dytiscidae). BMC Evol Biol 2014; 14:5. [PMID: 24423391 PMCID: PMC3901756 DOI: 10.1186/1471-2148-14-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/30/2013] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Aciliini presently includes 69 species of medium-sized water beetles distributed on all continents except Antarctica. The pattern of distribution with several genera confined to different continents of the Southern Hemisphere raises the yet untested hypothesis of a Gondwana vicariance origin. The monophyly of Aciliini has been questioned with regard to Eretini, and there are competing hypotheses about the intergeneric relationship in the tribe. This study is the first comprehensive phylogenetic analysis focused on the tribe Aciliini and it is based on eight gene fragments. The aims of the present study are: 1) to test the monophyly of Aciliini and clarify the position of the tribe Eretini and to resolve the relationship among genera within Aciliini, 2) to calibrate the divergence times within Aciliini and test different biogeographical scenarios, and 3) to evaluate the utility of the gene CAD for phylogenetic analysis in Dytiscidae. RESULTS Our analyses confirm monophyly of Aciliini with Eretini as its sister group. Each of six genera which have multiple species are also supported as monophyletic. The origin of the tribe is firmly based in the Southern Hemisphere with the arrangement of Neotropical and Afrotropical taxa as the most basal clades suggesting a Gondwana vicariance origin. However, the uncertainty as to whether a fossil can be used as a stem-or crowngroup calibration point for Acilius influenced the result: as crowngroup calibration, the 95% HPD interval for the basal nodes included the geological age estimate for the Gondwana break-up, but as a stem group calibration the basal nodes were too young. Our study suggests CAD to be the most informative marker between 15 and 50 Ma. Notably, the 2000 bp CAD fragment analyzed alone fully resolved the tree with high support. CONCLUSIONS 1) Molecular data confirmed Aciliini as a monophyletic group. 2) Bayesian optimizations of the biogeographical history are consistent with an influence of Gondwana break-up history, but were dependent on the calibration method. 3) The evaluation using a method of phylogenetic signal per base pair indicated Wnt and CAD as the most informative of our sampled genes.
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Affiliation(s)
- Rasa Bukontaite
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Kelly B Miller
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Johannes Bergsten
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Bergsten J, Nilsson AN, Ronquist F. Bayesian tests of topology hypotheses with an example from diving beetles. Syst Biol 2013; 62:660-73. [PMID: 23628960 PMCID: PMC3739882 DOI: 10.1093/sysbio/syt029] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/16/2013] [Accepted: 04/23/2013] [Indexed: 01/18/2023] Open
Abstract
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
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Affiliation(s)
- Johannes Bergsten
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Anders N. Nilsson
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Entomology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden; Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden; and Department of Biodiversity Informatics, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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Leavitt JR, Hiatt KD, Whiting MF, Song H. Searching for the optimal data partitioning strategy in mitochondrial phylogenomics: A phylogeny of Acridoidea (Insecta: Orthoptera: Caelifera) as a case study. Mol Phylogenet Evol 2013; 67:494-508. [DOI: 10.1016/j.ympev.2013.02.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 02/10/2013] [Accepted: 02/15/2013] [Indexed: 11/24/2022]
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ANDÚJAR CARMELO, GÓMEZ-ZURITA JESÚS, RASPLUS JEANYVES, SERRANO JOSÉ. Molecular systematics and evolution of the subgenusMesocarabusThomson, 1875 (Coleoptera: Carabidae:Carabus), based on mitochondrial and nuclear DNA. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2012.00866.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Andújar C, Serrano J, Gómez-Zurita J. Winding up the molecular clock in the genus Carabus (Coleoptera: Carabidae): assessment of methodological decisions on rate and node age estimation. BMC Evol Biol 2012; 12:40. [PMID: 22455387 PMCID: PMC3368785 DOI: 10.1186/1471-2148-12-40] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rates of molecular evolution are known to vary across taxa and among genes, and this requires rate calibration for each specific dataset based on external information. Calibration is sensitive to evolutionary model parameters, partitioning schemes and clock model. However, the way in which these and other analytical aspects affect both the rates and the resulting clade ages from calibrated phylogenies are not yet well understood. To investigate these aspects we have conducted calibration analyses for the genus Carabus (Coleoptera, Carabidae) on five mitochondrial and four nuclear DNA fragments with 7888 nt total length, testing different clock models and partitioning schemes to select the most suitable using Bayes Factors comparisons. RESULTS We used these data to investigate the effect of ambiguous character and outgroup inclusion on both the rates of molecular evolution and the TMRCA of Carabus. We found considerable variation in rates of molecular evolution depending on the fragment studied (ranging from 5.02% in cob to 0.26% divergence/My in LSU-A), but also on analytical conditions. Alternative choices of clock model, partitioning scheme, treatment of ambiguous characters, and outgroup inclusion resulted in rate increments ranging from 28% (HUWE1) to 1000% (LSU-B and ITS2) and increments in the TMRCA of Carabus ranging from 8.4% (cox1-A) to 540% (ITS2). Results support an origin of the genus Carabus during the Oligocene in the Eurasian continent followed by a Miocene differentiation that originated all main extant lineages. CONCLUSIONS The combination of several genes is proposed as the best strategy to minimise both the idiosyncratic behaviors of individual markers and the effect of analytical aspects in rate and age estimations. Our results highlight the importance of estimating rates of molecular evolution for each specific dataset, selecting for optimal clock and partitioning models as well as other methodological issues potentially affecting rate estimation.
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Affiliation(s)
- Carmelo Andújar
- Departamento de Zoología y Antropología Física. Facultad de Veterinaria, Universidad de Murcia, 30071 Murcia, Spain
| | - José Serrano
- Departamento de Zoología y Antropología Física. Facultad de Veterinaria, Universidad de Murcia, 30071 Murcia, Spain
| | - Jesús Gómez-Zurita
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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Trizzino M, Audisio PA, Antonini G, Mancini E, Ribera I. Molecular phylogeny and diversification of the “Haenydra” lineage (Hydraenidae, genus Hydraena), a north-Mediterranean endemic-rich group of rheophilic Coleoptera. Mol Phylogenet Evol 2011; 61:772-83. [DOI: 10.1016/j.ympev.2011.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Revised: 07/27/2011] [Accepted: 07/31/2011] [Indexed: 11/24/2022]
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Hidalgo-Galiana A, Ribera I. Late Miocene diversification of the genus Hydrochus (Coleoptera, Hydrochidae) in the west Mediterranean area. Mol Phylogenet Evol 2011; 59:377-85. [DOI: 10.1016/j.ympev.2011.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 11/18/2010] [Accepted: 01/30/2011] [Indexed: 10/18/2022]
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Jordal BH, Sequeira AS, Cognato AI. The age and phylogeny of wood boring weevils and the origin of subsociality. Mol Phylogenet Evol 2011; 59:708-24. [PMID: 21435394 DOI: 10.1016/j.ympev.2011.03.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/20/2011] [Accepted: 03/12/2011] [Indexed: 01/18/2023]
Abstract
A large proportion of the hyperdiverse weevils are wood boring and many of these taxa have subsocial family structures. The origin and relationship between certain wood boring weevil taxa has been problematic to solve and hypotheses on their phylogenies change substantially between different studies. We aimed at testing the phylogenetic position and monophyly of the most prominent wood boring taxa Scolytinae, Platypodinae and Cossoninae, including a range of weevil outgroups with either the herbivorous or wood boring habit. Many putatively intergrading taxa were included in a broad phylogenetic analysis for the first time in this study, such as Schedlarius, Mecopelmus, Coptonotus, Dactylipalpus, Coptocorynus and allied Araucariini taxa, Dobionus, Psepholax, Amorphocerus-Porthetes, and some peculiar wood boring Conoderini with bark beetle behaviour. Data analyses were based on 128 morphological characters, rDNA nucleotides from the D2-D3 segment of 28S, and nucleotides and amino acids from the protein encoding gene fragments of CAD, ArgK, EF-1α and COI. Although the results varied for some of the groups between various data sets and analyses, one may conclude the following from this study: Scolytinae and Platypodinae are likely sister lineages most closely related to Coptonotus; Cossoninae is monophyletic (including Araucariini) and more distantly related to Scolytinae; Amorphocerini is not part of Cossoninae and Psepholax may belong to Cryptorhynchini. Likelihood estimation of ancestral state reconstruction of subsociality indicated five or six origins as a conservative estimate. Overall the phylogenetic results were quite dependent on morphological data and we conclude that more genetic loci must be sampled to improve phylogenetic resolution. However, some results such as the derived position of Scolytinae were consistent between morphological and molecular data. A revised time estimation of the origin of Curculionidae and various subfamily groups were made using the recently updated fossil age of Scolytinae (100 Ma), which had a significant influence on node age estimates.
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Affiliation(s)
- Bjarte H Jordal
- Natural History Collections, Bergen Museum, University of Bergen, NO-5020 Bergen, Norway
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Chatzimanolis S, Cohen IM, Schomann A, Solodovnikov A. Molecular phylogeny of the mega-diverse rove beetle tribe Staphylinini (Insecta, Coleoptera, Staphylinidae). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00438.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pons J, Ribera I, Bertranpetit J, Balke M. Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Mol Phylogenet Evol 2010; 56:796-807. [DOI: 10.1016/j.ympev.2010.02.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Revised: 02/01/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022]
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Pinzón-Navarro S, Barrios H, Múrria C, Lyal CHC, Vogler AP. DNA-based taxonomy of larval stages reveals huge unknown species diversity in neotropical seed weevils (genus Conotrachelus): relevance to evolutionary ecology. Mol Phylogenet Evol 2010; 56:281-93. [PMID: 20188844 DOI: 10.1016/j.ympev.2010.02.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 02/12/2010] [Accepted: 02/20/2010] [Indexed: 11/28/2022]
Abstract
High diversity in tropical phytophagous insects may be linked to narrow host specificity and host shifts, but tests are complicated by incomplete taxonomy and difficulties in food source identification. Specimens of the highly diverse New World genus Conotrachelus (Coleoptera: Curculionoidea) were reared from >17,500 fruits (seeds) at six Central American rain forests. Interception traps were used for comparison with assemblages flying in the forest. Mitochondrial cox1 and the nuclear 28S genes were sequenced for 483 larval and adult specimens. A Yule-Coalescent technique was used to group cox1 sequences into putative species (17 from traps, 48 from rearing). Cox1 sequences of 24 species from museum collections provided matches for three species from traps and no match for the reared species. Inga (Fabaceae) was the predominant host among 15 other genera and 67% of the weevils were monophagous. A three gene tree (cox1, rrnL, 28S) recovered four well-supported clades feeding on Inga confirmed by phylogenetic community analyzes that showed phylogenetic conservation of host plant utilization. This suggests that host shifts are not directly involved in speciation, while the broad taxonomic host range and the evolutionary repeated shifts still contribute to the high species richness in Conotrachelus. The DNA-based approach combining species delimitation and phylogenetic analysis elucidated the evolutionary diversification of this lineage, despite insufficient taxonomic knowledge. Conotrachelus is an example of the diverse tropical groups that require DNA-based taxonomy to study their evolutionary ecology.
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Papadopoulou A, Anastasiou I, Vogler AP. Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration. Mol Biol Evol 2010; 27:1659-72. [PMID: 20167609 DOI: 10.1093/molbev/msq051] [Citation(s) in RCA: 473] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.
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Affiliation(s)
- Anna Papadopoulou
- Department of Entomology, Natural History Museum, London, United Kingdom.
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Papadopoulou A, Jones AG, Hammond PM, Vogler AP. DNA taxonomy and phylogeography of beetles of the Falkland Islands (Islas Malvinas). Mol Phylogenet Evol 2009; 53:935-47. [DOI: 10.1016/j.ympev.2009.08.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 08/15/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
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