More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae)
Mun Hua Tan A B C F , Han Ming Gan A B C , Gavin Dally D , Suzanne Horner D , Paula A. Rodríguez Moreno E , Sadequr Rahman B C and Christopher M. Austin A B C
+ Author Affiliations
- Author Affiliations
A Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University (Waurn Ponds campus), Geelong, Victoria 3220, Australia.
B School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia.
C Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500 Petaling Jaya, Selangor, Malaysia.
D Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, Northern Territory 0801, Australia.
E Direction des Collections – Invertébrés, Muséum National d’Histoire Naturelle (MNHN), 61, rue Buffon, CP 53, 75231 Paris Cedex 05, France.
F Corresponding author. Email: mun.tan@deakin.edu.au
Invertebrate Systematics 32(2) 448-456 https://doi.org/10.1071/IS17050
Submitted: 29 May 2017 Accepted: 4 August 2017 Published: 4 April 2018
Abstract
Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.
Additional keywords: mitochondrial genome, phylogenetics, museum specimens, NGS.
References
Abascal, F., Zardoya, R., and Telford, M. J. (2010). TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research 38(Suppl. 2), W7–13.Aberer, A. J., Kobert, K., and Stamatakis, A. (2014). ExaBayes: massively parallel Bayesian tree inference for the whole-genome Era. Molecular Biology and Evolution 31, 2553–2556.
| ExaBayes: massively parallel Bayesian tree inference for the whole-genome Era.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28Xht1CitLvJ&md5=92f82ab38c95c4da0133276bc063db42CAS |
Ahyong, S. T., and O’Meally, D. (2004). Phylogeny of the Decapoda Reptantia: resolution using three molecular loci and morphology. The Raffles Bulletin of Zoology 52, 673–693.
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.
| Basic local alignment search tool.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK3MXitVGmsA%3D%3D&md5=809ce3a35c5aca3c14ff6897d714e786CAS |
Amemiya, C. T., Alfoldi, J., Lee, A. P., Fan, S., Philippe, H., MacCallum, I., Braasch, I., Manousaki, T., Schneider, I., Rohner, N., Organ, C., Chalopin, D., Smith, J. J., Robinson, M., Dorrington, R. A., Gerdol, M., Aken, B., Biscotti, M. A., Barucca, M., Baurain, D., Berlin, A. M., Blatch, G. L., Buonocore, F., Burmester, T., Campbell, M. S., Canapa, A., Cannon, J. P., Christoffels, A., De Moro, G., Edkins, A. L., Fan, L., Fausto, A. M., Feiner, N., Forconi, M., Gamieldien, J., Gnerre, S., Gnirke, A., Goldstone, J. V., Haerty, W., Hahn, M. E., Hesse, U., Hoffmann, S., Johnson, J., Karchner, S. I., Kuraku, S., Lara, M., Levin, J. Z., Litman, G. W., Mauceli, E., Miyake, T., Mueller, M. G., Nelson, D. R., Nitsche, A., Olmo, E., Ota, T., Pallavicini, A., Panji, S., Picone, B., Ponting, C. P., Prohaska, S. J., Przybylski, D., Saha, N. R., Ravi, V., Ribeiro, F. J., Sauka-Spengler, T., Scapigliati, G., Searle, S. M. J., Sharpe, T., Simakov, O., Stadler, P. F., Stegeman, J. J., Sumiyama, K., Tabbaa, D., Tafer, H., Turner-Maier, J., van Heusden, P., White, S., Williams, L., Yandell, M., Brinkmann, H., Volff, J.-N., Tabin, C. J., Shubin, N., Schartl, M., Jaffe, D. B., Postlethwait, J. H., Venkatesh, B., Di Palma, F., Lander, E. S., Meyer, A., and Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature 496, 311–316.
| The African coelacanth genome provides insights into tetrapod evolution.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXmtV2lsrg%3D&md5=245f146740c8c6b900de05617cafdfe9CAS |
Aznar-Cormano, L., Brisset, J., Chan, T.-Y., Corbari, L., Puillandre, N., Utge, J., Zbinden, M., Zuccon, D., and Samadi, S. (2015). An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods. Genetica 143, 195–205.
| An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC2MrltlKksg%3D%3D&md5=fdab2da0f4f32f3ceb2918b5a7095851CAS |
Bergsten, J. (2005). A review of long-branch attraction. Cladistics 21, 163–193.
| A review of long-branch attraction.Crossref | GoogleScholarGoogle Scholar |
Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M., and Stadler, P. F. (2013). MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69, 313–319.
| MITOS: improved de novo metazoan mitochondrial genome annotation.Crossref | GoogleScholarGoogle Scholar |
Besnard, G., Bertrand, J. A. M., Delahaie, B., Bourgeois, Y. X. C., Lhuillier, E., and Thébaud, C. (2016). Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biological Journal of the Linnean Society. Linnean Society of London 117, 71–82.
| Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura).Crossref | GoogleScholarGoogle Scholar |
Boisselier-Dubayle, M.-C., Bonillo, C., Cruaud, C., Couloux, A., Richer de Forges, B., and Vidal, N. (2010). The phylogenetic position of the ‘living fossils’ Neoglyphea and Laurentaeglyphea (Decapoda: Glypheidea). Comptes Rendus Biologies 333, 755–759.
| The phylogenetic position of the ‘living fossils’ Neoglyphea and Laurentaeglyphea (Decapoda: Glypheidea).Crossref | GoogleScholarGoogle Scholar |
Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.
| Trimmomatic: a flexible trimmer for Illumina sequence data.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXht1Sqt7nP&md5=09f8ca2be9531d5818e4c5502962f737CAS |
Boore, J. L., Lavrov, D. V., and Brown, W. M. (1998). Gene translocation links insects and crustaceans. Nature 392, 667–668.
| Gene translocation links insects and crustaceans.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1cXjtVWmuro%3D&md5=c3b80a9eff0a5f374c4b4b78788a2781CAS |
Bracken, H. D., Toon, A., Felder, D. L., Martin, J. W., Finley, M., Rasmussen, J., Palero, F., and Crandall, K. (2009). The decapod tree of life: compiling the data and moving toward a consensus of decapod evolution. Arthropod Systematics & Phylogeny 67, 99–116.
Bracken, H. D., De Grave, S., Toon, A., Felder, D. L., and Crandall, K. A. (2010). Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda). Zoologica Scripta 39, 198–212.
| Phylogenetic position, systematic status, and divergence time of the Procarididea (Crustacea: Decapoda).Crossref | GoogleScholarGoogle Scholar |
Bracken-Grissom, H. D., Ahyong, S. T., Wilkinson, R. D., Feldmann, R. M., Schweitzer, C. E., Breinholt, J. W., Bendall, M., Palero, F., Chan, T.-Y., Felder, D. L., Robles, R., Chu, K.-H., Tsang, L.-M., Kim, D., Martin, J. W., and Crandall, K. A. (2014). The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida). Systematic Biology 63, 457–479.
| The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida).Crossref | GoogleScholarGoogle Scholar |
Capella-Gutiérrez, S., Silla-Martínez, J. M., and Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973.
| trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.Crossref | GoogleScholarGoogle Scholar |
Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540–552.
| Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXisVSgt7g%3D&md5=1b4ae107a4d41c6cf044947b82a73459CAS |
Charbonnier, S., Audo, D., Barriel, V., Garassino, A., Schweigert, G., and Simpson, M. (2015). Phylogeny of fossil and extant glypheid and litogastrid lobsters (Crustacea, Decapoda) as revealed by morphological characters. Cladistics 31, 231–249.
| Phylogeny of fossil and extant glypheid and litogastrid lobsters (Crustacea, Decapoda) as revealed by morphological characters.Crossref | GoogleScholarGoogle Scholar |
Crampton-Platt, A., Yu, D. W., Zhou, X., and Vogler, A. P. (2016). Mitochondrial metagenomics: letting the genes out of the bottle. GigaScience 5, 5–15.
| Mitochondrial metagenomics: letting the genes out of the bottle.Crossref | GoogleScholarGoogle Scholar |
Crandal, K. A., Harris, D. J., and Fetzner, J. W. (2000). The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proceedings of the Royal Society of London. Series B, Biological Sciences 267, 1679–1686.
| The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences.Crossref | GoogleScholarGoogle Scholar |
De Grave, S., and Fransen, C. (2011). Carideorum catalogus: the recent species of the dendrobranchiate, stenopodidean, procarididean and caridean shrimps (Crustacea: Decapoda). Zoölogische Mededeelingen 85, 195–589.
De Grave, S. N., Ahyong, S. T., Chan, T.-Y., Crandall, K. A., Dworschak, P. C., Felder, D. L., Feldmann, R. M., Fransen, C. H., Goulding, L. Y., and Lemaitre, R. (2009). A classification of living and fossil genera of decapod crustaceans. The Raffles Bulletin of Zoology 21, 1–109.
De Grave, S., Chan, T.-Y., Chu, K. H., Yang, C.-H., and Landeira, J. M. (2015). Phylogenetics reveals the crustacean order Amphionidacea to be larval shrimps (Decapoda: Caridea). Scientific Reports 5, 17464–17471.
| Phylogenetics reveals the crustacean order Amphionidacea to be larval shrimps (Decapoda: Caridea).Crossref | GoogleScholarGoogle Scholar |
Dixon, C., Ahyong, S., and Schram, F. (2003). A new hypothesis of decapod phylogeny. Crustaceana 76, 935–975.
| A new hypothesis of decapod phylogeny.Crossref | GoogleScholarGoogle Scholar |
Feldmann, R., Schweitzer, C., and Karasawa, H. (2015). Part R, Revised, Vol. 1, Chapter 8I: Systematic descriptions: Infraorder Glypheidea. Treatise Online 68, 1–28.
Forest, J. (2006a). Laurentaeglyphea, un nouveau genre pour la seconde espèce actuelle de Glyphéide récemment découverte (Crustacea Décapoda Glypheidae). Comptes Rendus Biologies 329, 841–846.
| Laurentaeglyphea, un nouveau genre pour la seconde espèce actuelle de Glyphéide récemment découverte (Crustacea Décapoda Glypheidae).Crossref | GoogleScholarGoogle Scholar |
Forest, J. (2006b). The recent glypheids and their relationship with their fossil relatives (Decapoda, Reptantia). Crustaceana 79, 795–820.
| The recent glypheids and their relationship with their fossil relatives (Decapoda, Reptantia).Crossref | GoogleScholarGoogle Scholar |
Forest, J., De Saint Laurent, M., and Chace, F. A. (1976). Neoglyphea inopinata: a crustacean ‘living fossil’ from the Philippines. Science 192, 884–884.
| Neoglyphea inopinata: a crustacean ‘living fossil’ from the Philippines.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BC3cvktlajsA%3D%3D&md5=aacd8824366ffe039d22fda94b97b801CAS |
Gan, H. M., Schultz, M. B., and Austin, C. M. (2014). Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evolutionary Biology 14, 19–26.
| Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes.Crossref | GoogleScholarGoogle Scholar |
Grandjean, F., Tan, M. H., Gan, H. M., Lee, Y. P., Kawai, T., Distefano, R. J., Blaha, M., Roles, A. J., and Austin, C. M. (2017). Rapid recovery of nuclear and mitochondrial genes by genome skimming from northern hemisphere freshwater crayfish. Zoologica Scripta, 1–11.
Hahn, C., Bachmann, L., and Chevreux, B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – a baiting and iterative mapping approach. Nucleic Acids Research 41, e129–e129.
| Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – a baiting and iterative mapping approach.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhtFSrtbvK&md5=5025d5bb399158f62bca63a156a92850CAS |
Holthuis, L. (1991). Volume 13, marine lobsters of the world. FAO species catalogue. FAO Fisheries Synopsis 125, 253.
Karasawa, H., Schweitzer, C. E., and Feldmann, R. M. (2013). Phylogeny and systematics of extant and extinct lobsters. Journal of Crustacean Biology 33, 78–123.
| Phylogeny and systematics of extant and extinct lobsters.Crossref | GoogleScholarGoogle Scholar |
Katoh, K., and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30, 772–780.
| MAFFT multiple sequence alignment software version 7: improvements in performance and usability.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXksFWisLc%3D&md5=923eb8b83abb772e70745a603d99fa8fCAS |
Kocher, A., Kamilari, M., Lhuillier, E., Coissac, E., Péneau, J., Chave, J., and Murienne, J. (2014). Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae). Gene 552, 184–194.
| Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXhsFyhsbbK&md5=3637dbf77d24f17f750045d08e325cb8CAS |
Kocher, A., Guilbert, É., Lhuillier, É., and Murienne, J. (2015). Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach. Comptes Rendus Biologies 338, 149–160.
| Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach.Crossref | GoogleScholarGoogle Scholar |
Kück, P., and Meusemann, K. (2010). FASconCAT: convenient handling of data matrices. Molecular Phylogenetics and Evolution 56, 1115–1118.
| FASconCAT: convenient handling of data matrices.Crossref | GoogleScholarGoogle Scholar |
Lartillot, N., Brinkmann, H., and Philippe, H. (2007). Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evolutionary Biology 7, S4.
| Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model.Crossref | GoogleScholarGoogle Scholar |
Lartillot, N., Rodrigue, N., Stubbs, D., and Richer, J. (2013). PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Systematic Biology 62, 611–615.
| PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXpsFCisbY%3D&md5=036211ff5c0bdc90c49904c3ae329d2bCAS |
Lavrov, D. V., Brown, W. M., and Boore, J. L. (2004). Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings. Biological Sciences 271, 537–544.
| Phylogenetic position of the Pentastomida and (pan)crustacean relationships.Crossref | GoogleScholarGoogle Scholar |
Lin, F.-J., Liu, Y., Sha, Z., Tsang, L. M., Chu, K. H., Chan, T.-Y., Liu, R., and Cui, Z. (2012). Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes. BMC Genomics 13, 631–642.
| Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXht1yru7g%3D&md5=0caacd79dbd2be4db46a2d70b459133aCAS |
Machado, D. J., Lyra, M. L., and Grant, T. (2016). Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs. Molecular Ecology Resources 16, 686–693.
| Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XlslWjsro%3D&md5=9c6a3fa93033f4c00301d55f80c57215CAS |
Miller, A. D., Nguyen, T. T. T., Burridge, C. P., and Austin, C. M. (2004). Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed. Gene 331, 65–72.
| Complete mitochondrial DNA sequence of the Australian freshwater crayfish, Cherax destructor (Crustacea: Decapoda: Parastacidae): a novel gene order revealed.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXjtFGntrs%3D&md5=e353a92d8ed81a2d6b495c134b8fe74fCAS |
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., and Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32, 268–274.
| IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXivFGltrs%3D&md5=2adc17ae2f13dc5cae640cf5d92522f3CAS |
Peng, Y., Leung, H. C. M., Yiu, S. M., and Chin, F. Y. L. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428.
| IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38Xns1Slt74%3D&md5=bede173ca776c49d99f770a477e11407CAS |
Place, A. R., Feng, X., Steven, C. R., Fourcade, H. M., and Boore, J. L. (2005). Genetic markers in blue crabs (Callinectes sapidus): II. Complete mitochondrial genome sequence and characterization of genetic variation. Journal of Experimental Marine Biology and Ecology 319, 15–27.
| Genetic markers in blue crabs (Callinectes sapidus): II. Complete mitochondrial genome sequence and characterization of genetic variation.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXkt1alu7s%3D&md5=1cbf9617ed390b4827f3f922d1125b9cCAS |
Porter, M. L., Pérez-Losada, M., and Crandall, K. A. (2005). Model-based multi-locus estimation of decapod phylogeny and divergence times. Molecular Phylogenetics and Evolution 37, 355–369.
| Model-based multi-locus estimation of decapod phylogeny and divergence times.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXhtFWhtL%2FJ&md5=85ef06de8a5f16949303851c4b2c1fb3CAS |
Richter, S., Schwarz, F., Hering, L., Böggemann, M., and Bleidorn, C. (2015). The utility of genome skimming for phylogenomic analyses as demonstrated for Glycerid relationships (Annelida, Glyceridae). Genome Biology and Evolution 7, 3443–3462.
| The utility of genome skimming for phylogenomic analyses as demonstrated for Glycerid relationships (Annelida, Glyceridae).Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC28XitVGls7rF&md5=194d87b84aa35f4c172e0776d5d204e8CAS |
Scholtz, G., and Richter, S. (1995). Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca). Zoological Journal of the Linnean Society 113, 289–328.
| Phylogenetic systematics of the reptantian Decapoda (Crustacea, Malacostraca).Crossref | GoogleScholarGoogle Scholar |
Schram, F., and Ahyong, S. (2002). The higher affinities of Neoglyphea inopinata in particular and the Glypheoidea (Decapoda, Reptantia) in general. Crustaceana 75, 629–635.
| The higher affinities of Neoglyphea inopinata in particular and the Glypheoidea (Decapoda, Reptantia) in general.Crossref | GoogleScholarGoogle Scholar |
Schweitzer, C. E., and Feldmann, R. M. (2014). Lobster (Decapoda) diversity and evolutionary patterns through time. Journal of Crustacean Biology 34, 820–847.
| Lobster (Decapoda) diversity and evolutionary patterns through time.Crossref | GoogleScholarGoogle Scholar |
Segawa, R. D., and Aotsuka, T. (2005). The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication. Gene 355, 28–39.
| The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXntlSgsrw%3D&md5=0daedffb6196b4fd61a179e302a37648CAS |
Shen, H., Braband, A., and Scholtz, G. (2013). Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Molecular Phylogenetics and Evolution 66, 776–789.
| Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships.Crossref | GoogleScholarGoogle Scholar |
Shen, H., Braband, A., and Scholtz, G. (2015). The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida. Journal of Zoological Systematics and Evolutionary Research 53, 273–281.
| The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida.Crossref | GoogleScholarGoogle Scholar |
Shimodaira, H. (2002). An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51, 492–508.
| An approximately unbiased test of phylogenetic tree selection.Crossref | GoogleScholarGoogle Scholar |
Shimodaira, H., and Hasegawa, M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16, 1114–1116.
| Multiple comparisons of log-likelihoods with applications to phylogenetic inference.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1MXltVyksrg%3D&md5=b3c39e7d5a16aee97831ac3f550230daCAS |
Sokolov, E. P. (2000). An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues. The Journal of Molluscan Studies 66, 573–575.
| An improved method for DNA isolation from mucopolysaccharide-rich molluscan tissues.Crossref | GoogleScholarGoogle Scholar |
Straub, S. C. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R. C., and Liston, A. (2012). Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. American Journal of Botany 99, 349–364.
| Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC38XksValtbo%3D&md5=25261617f127273279580d2ff5010dd7CAS |
Sullivan, M. J., Petty, N. K., and Beatson, S. A. (2011). Easyfig: a genome comparison visualizer. Bioinformatics 27, 1009–1010.
| Easyfig: a genome comparison visualizer.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3MXkt1yqs7s%3D&md5=32b702895afb1986e267f21d9340554fCAS |
Sun, H., Zhou, K., and Song, D. (2005). Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene 349, 207–217.
| Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2MXjtFOls74%3D&md5=af2121db0dcae69313f212d824440917CAS |
Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30, 2725–2729.
| MEGA6: molecular evolutionary genetics analysis version 6.0.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhvVKhurzP&md5=213a455e206e1c198319858e32755a17CAS |
Tan, M. H., Gan, H. M., Schultz, M. B., and Austin, C. M. (2015). MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes. Molecular Phylogenetics and Evolution 85, 180–188.
| MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2MXjs1Oktrc%3D&md5=2762cdb8bf6a15c720e7b410eb24c591CAS |
Timm, L., and Bracken-Grissom, H. D. (2015). The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda. Journal of Crustacean Biology 35, 577–592.
| The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda.Crossref | GoogleScholarGoogle Scholar |
Tsang, L. M., Ma, K. Y., Ahyong, S. T., Chan, T. Y., and Chu, K. H. (2008). Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia. Molecular Phylogenetics and Evolution 48, 359–368.
| Phylogeny of Decapoda using two nuclear protein-coding genes: origin and evolution of the Reptantia.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXntlCkurc%3D&md5=dfa37ffdb3592fbce337870c4c0e251fCAS |
Tsang, L. M., Schubart, C. D., Ahyong, S. T., Lai, J. C. Y., Au, E. Y. C., Chan, T.-Y., Ng, P. K. L., and Chu, K. H. (2014). Evolutionary history of true crabs (Crustacea: Decapoda: Brachyura) and the origin of freshwater crabs. Molecular Biology and Evolution 31, 1173–1187.
| Evolutionary history of true crabs (Crustacea: Decapoda: Brachyura) and the origin of freshwater crabs.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC2cXmvFCis7o%3D&md5=587a67d04a4acce20aeeaff1264d62adCAS |
Wilson, K., Cahill, V., Ballment, E., and Benzie, J. (2000). The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Molecular Biology and Evolution 17, 863–874.
| The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods?Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXjvFygs74%3D&md5=0a9fd7852c0da70bceb4e078489f1622CAS |
Yang, J.-S., Lu, B., Chen, D.-F., Yu, Y.-Q., Yang, F., Nagasawa, H., Tsuchida, S., Fujiwara, Y., and Yang, W.-J. (2013). When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans. Molecular Biology and Evolution 30, 305–309.
| When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BC3sXhtFGlsLg%3D&md5=d1013b6633178169ab38ce2f02b93c45CAS |
