InvertOmics - Filogeni og evolusjon av virvelløse dyr (strengt tatt Lophotrochozoa) basert på genomiske data

• Bachmann, Lutz; Beermann, Jan; Brey, Thomas; de Boer, Hugo; Dannheim, Jennifer & Edvardsen, Bente [Vis alle 20 forfattere av denne artikkelen] (2023). The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. Zoologica Scripta. ISSN 0300-3256. 52(3), s. 187–214. doi: 10.1111/zsc.12593. Fulltekst i vitenarkiv
• Fleming, James Frederick & Struck, Torsten H (2023). nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. BMC Bioinformatics. ISSN 1471-2105. 24. doi: 10.1186/s12859-023-05270-8. Fulltekst i vitenarkiv
• Fleming, James Frederick; Eriksen, Pia Merete & Struck, Torsten H (2023). Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric. F1000 Research. ISSN 2046-1402. 12(945). doi: 10.12688/f1000research.139356.1. Fulltekst i vitenarkiv
• Struck, Torsten H; Golombek, Anja; Hoesel, Christoph; Dimitrov, Dimitar & Elgetany, Asmaa Haris (2023). Mitochondrial Genome Evolution in Annelida—A Systematic Study on Conservative and Variable Gene Orders and the Factors Influencing its Evolution . Systematic Biology. ISSN 1063-5157. 72(4), s. 925–945. doi: 10.1093/sysbio/syad023. Fulltekst i vitenarkiv
• Fleming, James Frederick; Pisani, Davide & Arakawa, Kazuharu (2023). The evolution of temperature and desiccation-related protein families in Tardigrada reveals the complex acquisition of extremotolerance. Genome Biology and Evolution (GBE). ISSN 1759-6653. 16(1). doi: 10.1093/gbe/evad217.
• Fleming, James Frederick; Valero Gracia, Alberto & Struck, Torsten H (2023). Identifying and addressing methodological incongruence in phylogenomics: A review. Evolutionary Applications. ISSN 1752-4571. 16(6), s. 1087–1104. doi: 10.1111/eva.13565. Fulltekst i vitenarkiv
• Howard, Richard J.; Giacomelli, Mattia; Lozano-Fernandez, Jesus; Edgecombe, Gregory D.; Fleming, James Frederick & Kristensen, Reinhardt M. [Vis alle 13 forfattere av denne artikkelen] (2022). The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data. Journal of the Geological Society. ISSN 0016-7649. 179(4). doi: 10.1144/jgs2021-107. Fulltekst i vitenarkiv
• Fleming, James Frederick & Struck, Torsten H (2022). nRCFV: A new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. Research Square. ISSN 2693-5015. doi: 10.21203/rs.3.rs-2354937/v1.
• Struck, Torsten H & Cerca, José (2022). Connecting micro- and macro-evolutionary research – extant cryptic species as systems to understand macro-evolutionary stasis. I Monro, Alexandre K. & Mayo, Simon J. (Red.), Cryptic species - Morphological Stasis, Circumscription, and Hidden Diversity. Cambridge University Press. ISSN 9781316513644. s. 143–168. doi: doi:10.1017/9781009070553.006. Vis sammendrag

  ‘Cryptic species’ are nowadays commonplace in systematics, and, with the application of barcoding approaches, increasing numbers of species are shown to be supposedly cryptic. However, the use of the term is inconsistent in the literature. Moreover, processes associated with the formation of cryptic species are generally not taken into account. These processes comprise (I) recent divergence, (II) parallel or (III) convergent phenotypic evolution, or (IV) phenotypic stasis. This causes confusion and imprecision in attempting to resolve the origins, evolutionary trajectories and ecological importance of cryptic species. Here, we will briefly present these four processes based on a recently proposed conceptual framework for the definition of cryptic species. The four categories differ from each other in their temporal scale, phylogenetic context, and underlying selection. In focusing on the phenomenon of stasis, that is the absence of change over long geological periods, we discuss the overlap between stasis seen in the paleontological record and as observed in cryptic species, and we further consider that the challenge of integrating stasis into current evolutionary thinking is due to several different factors. These include microevolutionary research findings in extant species that seem to indicate abundant variation in both genetic markers and quantitative traits and development. Hence, there are contradictions between micro- and macroevolutionary scales. Cryptic species can provide study systems of extant species, which make it possible to bridge the gap between micro- and macroevolutionary research. Here we discuss this potential and provide an outlook on future research directions exploiting cryptic species.

• Jimenez, Miguel Angel Meca; Zhadan, Anna & Struck, Torsten H (2021). The early branching group of orbiniida sensu struck et al., 2015: Parergodrilidae and orbiniidae. Diversity. ISSN 1424-2818. 13:29(1), s. 1–31. doi: 10.3390/d13010029. Fulltekst i vitenarkiv
• Gower, David J.; Fleming, James Frederick; Pisani, Davide; Vonk, Freek J.; KERKKAMP, HARALD M I & PEICHL, LEO [Vis alle 12 forfattere av denne artikkelen] (2021). Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake. Genome Biology and Evolution (GBE). ISSN 1759-6653. doi: 10.1093/gbe/evab253.

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• Valero Gracia, Alberto (2023). Group of the month: Rotifera.
• Struck, Torsten H (2023). Systematics and ecosystem function – can they go together? .
• Struck, Torsten H (2023). The mitochondrial gene order of Annelida – extremely old, but still working .
• Struck, Torsten H (2023). ERGA pilot project – what can we learn for future genome projects.
• Struck, Torsten H (2023). Doing genomic research with a masonry trowel.
• Struck, Torsten H (2023). ERGA pilot project – the selected species .
• Fleming, James Frederick (2023). Whole Genome Data and Non-Model Organisms: Challenges and Pathways to the Future. Vis sammendrag

  The genomics revolution completely altered our understanding of phylogeny - the study of the relationships between animals. The identification of new cryptic species through phylogenetic methods that combine molecular and morphological data has led to an appreciation of phylogenetic relatedness as a biodiversity concept. Currently, however, phylogenetics has adopted a conservative stance towards this deluge of “big data”, selecting genes that fit well within our models of evolution - this has the benefit of evading artifactual topologies that violate these models, but may well be presenting us with hypotheses of evolution that are preselected according to our own biases, or incorrectly causing us to adopt great confidence in hypotheses that are not as well supported by the data as it first appears. This can have a powerful impact on our understanding of the relationships between taxa, which in turn could erroneously inform future sampling or conservation efforts. From this perspective, new phylogenetic methods that are optimized to make the most of “big data” may be of critical importance to advancing the field. As part of the University of Oslo’s Invertomics project, a small part of the broader European effort to sequence every Eukaryotic genome on the continent, we have developed new methods to assess phylogenetic data and new software to reconstruct phylogenetics optimized for whole genome data. We are additionally in the process of applying that to real genomic challenges across the second largest invertebrate superphylum, Lophotrochozoa. This talk will cover three new software packages, one of which has already been released, that hope to advance our understanding of organismal relationships in this new era of data. It will also explore the challenges of applying big data approaches to organismal phylogenetics.

• Struck, Torsten H (2023). Door 1: Sequencing genomes suggested by the community.
• Struck, Torsten H (2022). Door 17: The carbon footprint of our computational analyses.
• Struck, Torsten H (2022). Group of the month: hairybellies (Gastrotricha).
• Struck, Torsten H (2022). Launch of Biodiversity Genomics Europe – sequencing the genomes of European species.
• Fleming, James Frederick (2022). Group of the month: Tardigrades.
• Valero Gracia, Alberto (2022). Gnathostomulida, an obscure and often neglected phylum.
• Fleming, James Frederick (2022). Crustacean Silk from under the Sea. [Internett]. FEZ group blog.
• Struck, Torsten H (2021). Lophotrochozoan phylogeny.
• Struck, Torsten H (2021). Phylogenetic position of Annelida and the problem to resolve the phylogeny of Lophotrochozoa.
• Struck, Torsten H (2021). Vår fantastisk verden av små, nesten usynlige dyr.
• Haugen, Marianne Nilsen; Struck, Torsten H & Bachmann, Lutz (2021). Kryptiske arter utfordrer taksonomer og evolusjonsbiologer. Naturen. ISSN 0028-0887. 2021(1), s. 19–26. doi: 10.18261/issn.1504-3118-2021-01-03.
• Struck, Torsten H (2021). Finishing the tale of stone.
• Haugen, Marianne Nilsen; Valero-Gracia, Alberto; Austin, Rita M; Struck, Torsten H & Bachmann, Lutz (2020). Blog post "Combining group fun with genomic research".
• Struck, Torsten H & Bachmann, Lutz (2020). Blog post "The first door of the calendar ".
• Valero-Gracia, Alberto; Struck, Torsten H & Bachmann, Lutz (2020). Blog post "A new PhD student in town".
• Struck, Torsten H & Bachmann, Lutz (2020). Blog post "A tale of stone and ice".
• Fleming, James F; Struck, Torsten H & Bachmann, Lutz (2020). Blog post "Coming from Japan all the way to Norway".
• Cerca, Jose; Johnsen, Arild; Struck, Torsten H & Bachmann, Lutz (2020). Naturhistoriske samlinger i den molekylære æraen: En kostbar hobby eller en bærebjelke for moderne forskning? Naturen. ISSN 0028-0887. s. 110–116. doi: 10.18261/issn.1504-3118-2020-03-07.

Se alle arbeider i Cristin