Project 2216: R. Fernández, G. D. Edgecombe, G. Giribet. 2016. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. Systematic Biology. 65 (5):871-889.
Abstract
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.Read the article »
Article DOI: 10.1093/sysbio/syw041
Project DOI: 10.7934/P2216, http://dx.doi.org/10.7934/P2216
This project contains | Matrices |
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Download Project SDD File | Total scored cells: 10027 Total media associated with cells: 0 Total labels associated with cell media: 0 |
Characters | |
Total characters: 232 Total characters with associated media: 0 Total characters with media with labels: 0 Total character states: 528 Total character states with associated media: 0 Total character states with media with labels:0 Total unordered/ordered characters:227/5 |
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MorphoBank Project 2216
MorphoBank Project 2216
- Creation Date:
19 July 2015 - Publication Date:
03 October 2017 - Project views: 21011
- Media downloads: 1
- Matrix downloads: 15
This research
supported by
Authors' Institutions
- Natural History Museum, London
- Harvard University
Members
member name | taxa | specimens | media | media notes | chars | character
| cell scorings (scored, NPA, "-") | cell
| rules | ||||||||||||||
Gonzalo Giribet Project Administrator | 61 | 0 | 0 | 0 | 232 | 0 | 0 | 0 | 0 | 10027 (7448, 0, 2579) | 0 | 5 | 0 | 0 | 0 | ||||||||
Greg Edgecombe Full membership | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 (0, 0, 0) | 0 | 0 | 0 | 0 | 0 |
Taxonomic Overview for Matrix 'M23457' (61 Taxa)
taxon | unscored cells |
scored cells |
no cell support |
NPA cells |
"-" cells | cell images | labels on cell images |
member access |
[1] Peripatopsis capensis Last Modified in 07/19/15 | 60 | 37 | 37 | 0 | 135 | 0 | 0 | 2 |
[2] Anoplodactylus insignis Last Modified in 10/03/17 | 95 | 41 | 41 | 0 | 96 | 0 | 0 | 2 |
[3] Limulus polyphemus Last Modified in 10/03/17 | 110 | 58 | 58 | 0 | 64 | 0 | 0 | 2 |
[4] Liphistius malayanus Last Modified in 07/19/15 | 115 | 55 | 55 | 0 | 62 | 0 | 0 | 2 |
[5] Damon variegatus Last Modified in 07/19/15 | 116 | 54 | 54 | 0 | 62 | 0 | 0 | 2 |
[6] Mastigoproctus giganteus Last Modified in 07/19/15 | 112 | 56 | 56 | 0 | 64 | 0 | 0 | 2 |
[7] Centruroides vittatus Last Modified in 07/19/15 | 116 | 54 | 54 | 0 | 62 | 0 | 0 | 2 |
[8] Proscorpius osborni Last Modified in 07/19/15 | 172 | 23 | 23 | 0 | 37 | 0 | 0 | 2 |
[9] Metasiro americanus Last Modified in 07/19/15 | 120 | 49 | 49 | 0 | 63 | 0 | 0 | 2 |
[10] Calanus finmarchicus Last Modified in 10/03/17 | 141 | 51 | 51 | 0 | 40 | 0 | 0 | 2 |
[11] Daphnia pulex Last Modified in 10/03/17 | 141 | 51 | 51 | 0 | 40 | 0 | 0 | 2 |
[12] Rehbachiella kinnekullensis Last Modified in 07/19/15 | 185 | 28 | 28 | 0 | 19 | 0 | 0 | 2 |
[13] Apis mellifera Last Modified in 10/03/17 | 135 | 63 | 63 | 0 | 34 | 0 | 0 | 2 |
[14] Drosophila melanogaster Last Modified in 10/03/17 | 126 | 61 | 61 | 0 | 45 | 0 | 0 | 2 |
[15] Hanseniella sp. Last Modified in 07/19/15 | 47 | 116 | 116 | 0 | 69 | 0 | 0 | 2 |
[16] Scutigerella sp. Last Modified in 07/19/15 | 42 | 121 | 121 | 0 | 69 | 0 | 0 | 2 |
[17] Eudigraphis taiwanensis Last Modified in 07/19/15 | 43 | 130 | 130 | 0 | 59 | 0 | 0 | 2 |
[18] Glomeris marginata Last Modified in 10/03/17 | 36 | 138 | 138 | 0 | 58 | 0 | 0 | 2 |
[19] Cyliosoma sp. Last Modified in 07/19/15 | 44 | 130 | 130 | 0 | 58 | 0 | 0 | 2 |
[20] Glomeridesmus sp. Last Modified in 07/19/15 | 55 | 117 | 117 | 0 | 60 | 0 | 0 | 2 |
[21] Cowiedesmus eroticopodus Last Modified in 07/19/15 | 193 | 28 | 28 | 0 | 11 | 0 | 0 | 2 |
[22] Archidesmus macnicoli Last Modified in 07/19/15 | 151 | 45 | 45 | 0 | 36 | 0 | 0 | 2 |
[23] Petaserpes sp. Last Modified in 07/19/15 | 68 | 115 | 115 | 0 | 49 | 0 | 0 | 2 |
[24] Brachycybe lecontii Last Modified in 07/19/15 | 59 | 119 | 119 | 0 | 54 | 0 | 0 | 2 |
[25] Pseudopolydesmus sp. Last Modified in 07/19/15 | 38 | 133 | 133 | 0 | 61 | 0 | 0 | 2 |
[26] Prostemmiulus sp. Last Modified in 07/19/15 | 61 | 120 | 120 | 0 | 51 | 0 | 0 | 2 |
[27] Abacion magnum Last Modified in 07/19/15 | 65 | 117 | 117 | 0 | 50 | 0 | 0 | 2 |
[28] Cleidogona sp. Last Modified in 07/19/15 | 63 | 119 | 119 | 0 | 50 | 0 | 0 | 2 |
[29] Gaspestria genselorum Last Modified in 07/19/15 | 178 | 31 | 31 | 0 | 23 | 0 | 0 | 2 |
[30] Narceus americanus Last Modified in 07/19/15 | 39 | 136 | 136 | 0 | 57 | 0 | 0 | 2 |
[31] Cambala annulata Last Modified in 07/19/15 | 69 | 116 | 116 | 0 | 47 | 0 | 0 | 2 |
[32] Cylindroiulus sp. Last Modified in 07/19/15 | 41 | 134 | 134 | 0 | 57 | 0 | 0 | 2 |
[33] Crussolum spp. Last Modified in 07/19/15 | 212 | 20 | 20 | 0 | 0 | 0 | 0 | 2 |
[34] Scutigerina weberi Last Modified in 07/19/15 | 27 | 177 | 177 | 0 | 28 | 0 | 0 | 2 |
[35] Sphendononema guildingii Last Modified in 10/03/17 | 27 | 177 | 177 | 0 | 28 | 0 | 0 | 2 |
[36] Scutigera coleoptrata Last Modified in 07/19/15 | 0 | 198 | 198 | 0 | 34 | 0 | 0 | 2 |
[37] Lithobius forficatus Last Modified in 07/19/15 | 0 | 202 | 202 | 0 | 30 | 0 | 0 | 2 |
[38] Eupolybothrus cavernicolus Last Modified in 07/19/15 | 18 | 184 | 184 | 0 | 30 | 0 | 0 | 2 |
[39] Anopsobius giribeti Last Modified in 07/19/15 | 18 | 184 | 184 | 0 | 30 | 0 | 0 | 2 |
[40] Paralamyctes validus Last Modified in 07/19/15 | 21 | 182 | 182 | 0 | 29 | 0 | 0 | 2 |
[41] Devonobius delta Last Modified in 07/19/15 | 142 | 73 | 73 | 0 | 17 | 0 | 0 | 2 |
[42] Craterostigmus tasmanianus Last Modified in 07/19/15 | 12 | 188 | 188 | 0 | 32 | 0 | 0 | 2 |
[43] Craterostigmus crabilli Last Modified in 07/19/15 | 43 | 161 | 161 | 0 | 28 | 0 | 0 | 2 |
[44] Mazoscolopendra richardsoni Last Modified in 07/19/15 | 171 | 53 | 53 | 0 | 8 | 0 | 0 | 2 |
[45] Scolopendropsis bahiensis Last Modified in 07/19/15 | 26 | 178 | 177 | 0 | 29 | 0 | 0 | 2 |
[46] Akymnopellis chilensis Last Modified in 07/19/15 | 23 | 179 | 179 | 0 | 30 | 0 | 0 | 2 |
[47] Rhysida longipes Last Modified in 07/19/15 | 13 | 187 | 187 | 0 | 32 | 0 | 0 | 2 |
[48] Alipes grandidieri Last Modified in 07/19/15 | 20 | 180 | 180 | 0 | 32 | 0 | 0 | 2 |
[49] Cryptops hortensis Last Modified in 10/03/17 | 8 | 192 | 191 | 0 | 32 | 0 | 0 | 2 |
[50] Theatops spinicaudus Last Modified in 10/03/17 | 17 | 183 | 183 | 0 | 32 | 0 | 0 | 2 |
[51] Scolopocryptops sexspinosus Last Modified in 07/19/15 | 17 | 182 | 181 | 0 | 33 | 0 | 0 | 2 |
[52] Newportia adisi Last Modified in 07/19/15 | 17 | 183 | 183 | 0 | 32 | 0 | 0 | 2 |
[53] Mecistocephalus guildingii Last Modified in 07/19/15 | 12 | 184 | 184 | 0 | 36 | 0 | 0 | 2 |
[54] Tygarrup javanicus Last Modified in 07/19/15 | 27 | 169 | 169 | 0 | 36 | 0 | 0 | 2 |
[55] Notiphilides grandis Last Modified in 07/19/15 | 24 | 174 | 174 | 0 | 34 | 0 | 0 | 2 |
[56] Himantarium gabrielis Last Modified in 07/19/15 | 15 | 186 | 186 | 0 | 31 | 0 | 0 | 2 |
[57] Stenotaenia linearis Last Modified in 07/19/15 | 16 | 180 | 180 | 0 | 36 | 0 | 0 | 2 |
[58] Henia brevis Last Modified in 07/19/15 | 32 | 169 | 168 | 0 | 32 | 0 | 0 | 2 |
[59] Strigamia maritima Last Modified in 07/19/15 | 3 | 193 | 192 | 0 | 36 | 0 | 0 | 2 |
[60] Hydroschendyla submarina Last Modified in 07/19/15 | 23 | 176 | 176 | 0 | 33 | 0 | 0 | 2 |
[61] Kachinophilus pereirai Last Modified in 07/19/15 | 107 | 108 | 108 | 0 | 17 | 0 | 0 | 2 |
Project views
type | number of views | Individual items viewed (where applicable) |
Total project views | 21011 | |
Project overview | 2572 | |
Matrix views | 1418 | Matrix landing page (1116 views); Myriapod tree of Life (302 views); |
Taxon list | 9542 | |
Media views | 3696 | Media search (2955 views); M462274 (741 views); |
Specimen list | 1839 | |
Views for media list | 1124 | |
Bibliography | 818 | |
Documents list | 2 |
Project downloads
type | number of downloads | Individual items downloaded (where applicable) |
Total downloads from project | 281 | |
Matrix downloads | 15 | Myriapod tree of Life (15 downloads); |
Project downloads | 265 | |
Media downloads | 1 | M462274 (1 download); |