@article {832, title = {Gene content evolution in the arthropods}, journal = {Genome Biology}, volume = {21}, year = {2020}, month = {23/01/2020}, pages = {1-14}, abstract = {

Background: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.
Results: Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception.
Conclusions: These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

}, keywords = {Arthropods, DNA methylation, Evolution, Gene content, Genome assembly, Genomics, Protein domains}, issn = {1474-760X}, doi = {10.1186/s13059-019-1925-7}, url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1925-7}, author = {Thomas, Gregg W. C. and Dohmen, Elias and Hughes, Daniel S. T. and Murali, Shwetha C. and Poelchau, Monica and Glastad, Karl and Anstead, Clare A. and Ayoub, Nadia A. and Batterham, Phillip and Bellair, Michelle and Binford, Greta J. and Chao, Hsu and Chen, Yolanda H. and Childers, Christopher and Dinh, Huyen and Doddapaneni, Harsha Vardhan and Duan, Jian J. and Dugan, Shannon and Esposito, Lauren A. and Friedrich, Markus and Garb, Jessica and Gasser, Robin B. and Goodisman, Michael A. D. and Gundersen-Rindal, Dawn E. and Han, Yi and Handler, Alfred M. and Hatakeyama, Masatsugu and Hering, Lars and Hunter, Wayne B. and Ioannidis, Panagiotis and Jayaseelan, Joy C. and Kalra, Divya and Khila, Abderrahman and Korhonen, Pasi K. and Lee, Carol Eunmi and Lee, Sandra L. and Li, Yiyuan and Lindsey, Amelia R. I. and Mayer, Georg and McGregor, Alistair P. and McKenna, Duane D. and Misof, Bernhard and Munidasa, Mala and Munoz-Torres, Monica and Muzny, Donna M. and Niehuis, Oliver and Osuji-Lacy, Nkechinyere and Palli, Subba R. and Panfilio, Kristen A. and Pechmann, Matthias and Perry, Trent and Peters, Ralph S. and Poynton, Helen C. and Prpic, Nikola-Michael and Qu, Jiaxin and Rotenberg, Dorith and Schal, Coby and Schoville, Sean D. and Scully, Erin D. and Skinner, Evette and Sloan, Daniel B. and Stouthamer, Richard and Strand, Michael R. and Szucsich, Nikolaus U. and Wijeratne, Asela and Young, Neil D. and Zattara, Eduardo E. and Benoit, Joshua B. and Zdobnov, Evgeny M. and Pfrender, Michael E. and Hackett, Kevin J. and Werren, John H. and Worley, Kim C. and Gibbs, Richard A. and Chipman, Ariel D. and Waterhouse, Robert M. and Bornberg-Bauer, Erich and Hahn, Matthew W. and Richards, Stephen} } @article {419, title = {Four myriapod relatives {\textendash} but who are sisters? No end to debates on relationships among the four major myriapod subgroups}, journal = {BMC Evolutionary Biology}, volume = {20}, year = {2020}, month = {04/11/2020}, pages = {1-15}, abstract = {

Background: Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data.

Results: We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda.

Conclusions: Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.

}, keywords = {Arthropod phylogeny, conflict, Confounding signal, Internal rooting, Phylogenetics, phylogenomics, Quartet topology, RNA-Seq, Transcriptomes}, issn = {1471-2148}, doi = {10.1186/s12862-020-01699-0}, url = {https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-020-01699-0}, author = {Szucsich, Nikolaus U. and Bartel, Daniela and Blanke, Alexander and B{\"o}hm, Alexander and Donath, Alexander and Fukui, Makiko and Grove, Simon and Liu, Shanlin and Macek, Oliver and Machida, Ryuichiro and Misof, Bernhard and Nakagaki, Yasutaka and Podsiadlowski, Lars and Sekiya, Kaoru and Tomizuka, Shigekazu and Von Reumont, Bj{\"o}rn M. and Waterhouse, Robert M. and Walzl, Manfred and Meng, Guanliang and Zhou, Xin and Pass, G{\"u}nther and Meusemann, Karen} }