Alberto Valero Gracia

•  A. Valero-Gracia, N. G. Roberts, M. Yap-Chiongco, A. T. Capucho, K. M. Kocot, M. Matschiner, & T. H. Struck. (2024). First chromosome-level genome assembly of a ribbon worm from the Hoplonemertea clade, Emplectonema gracile, and its structural annotation. Genome Biology and Evolution, Volume 16, Issue 7 https://doi.org/10.1093/gbe/evae127

•  J. F. Fleming, A. Valero-Gracia, T. H. Struck (2023). Identifying and addressing Methodological Incongruence in Phylogenomics: A Review. Evolutionary Applications 16:1087–1104. https://doi.org/10.1111/eva.13565

•  A. Minelli, A. Valero-Gracia (2022). Spatially and Temporally Distributed Complexity—A Refreshed Framework for the Study of GRN Evolution. Cells 11, 1790. https://doi.org/10.3390/cells11111790

• A. Valero-Gracia (2019). Photoreception in Ambulacraria: A Comprehensive Approach. MPhil Thesis. The Open University.

• A. Valero-Gracia, L. Petrone, P. Oliveri, D-E. Nilsson, M. I. Arnone (2016). Non-directional photoreceptors in the pluteus of Strongylocentrotus purpuratus. Frontiers in Ecology and Evolution 4: 127

• A. Valero-Gracia*, R. Marino*, F. Crocetta, V. Nittoli, S. Tiozzo, P. Sordino (2016). Comparative localization of 5HT serotonin receptors in Thaliacea informs tunicate phylogeny. Frontiers in Zoology 13: 45 (*equal contribution)

• S. D’Aniello*, J. Delroisse*, A. Valero-Gracia, E. K. Lowe, M. Byrne, J. T. Cannon, K. M. Halanych, M. R. Elphick, J. Mallefet, S. Kaul-Strehlow, C. J. Lowe, P. Flammang, J. Smith, E. Ullrich-Lüter, A. Wanninger, M. I. Arnone (2015). Opsin evolution in the Ambulacraria. Marine genomics 24, 177-183 (*equal contribution)

• Gracia, Alberto Valero; Roberts, Nickellaus G; Yap-Chiongco, Meghan; Capucho, Ana Teresa; Kocot, Kevin M & Matschiner, Michael [Show all 7 contributors for this article] (2024). First Chromosome-Level Genome Assembly of a Ribbon Worm from the Hoplonemertea Clade, Emplectonema gracile, and Its Structural Annotation. Genome Biology and Evolution (GBE). 16(7). doi: 10.1093/gbe/evae127. Full text in Research Archive Show summary

  Genome-wide information has so far been unavailable for ribbon worms of the clade Hoplonemertea, the most species-rich class within the phylum Nemertea. While species within Pilidiophora, the sister clade of Hoplonemertea, possess a pilidium larval stage and lack stylets on their proboscis, Hoplonemertea species have a planuliform larva and are armed with stylets employed for the injection of toxins into their prey. To further compare these developmental, physiological, and behavioral differences from a genomic perspective, the availability of a reference genome for a Hoplonemertea species is crucial. Such data will be highly useful for future investigations toward a better understanding of molecular ecology, venom evolution, and regeneration not only in Nemertea but also in other marine invertebrate phyla. To this end, we herein present the annotated chromosome-level genome assembly for Emplectonema gracile (Nemertea; Hoplonemertea; Monostilifera; Emplectonematidae), an easily collected nemertean well suited for laboratory experimentation. The genome has an assembly size of 157.9 Mb. Hi-C scaffolding yielded chromosome-level scaffolds, with a scaffold N50 of 10.0 Mb and a score of 95.1% for complete BUSCO genes found as a single copy. Annotation predicted 20,684 protein-coding genes. The high-quality reference genome reaches an Earth BioGenome standard level of 7.C.Q50.

• Fleming, James Frederick; Gracia, Alberto Valero & Struck, Torsten H (2023). Identifying and addressing methodological incongruence in phylogenomics: A review. Evolutionary Applications. 16(6), p. 1087–1104. doi: 10.1111/eva.13565. Full text in Research Archive Show summary

  Abstract The availability of phylogenetic data has greatly expanded in recent years. As a result, a new era in phylogenetic analysis is dawning—one in which the methods we use to analyse and assess our data are the bottleneck to producing valuable phylogenetic hypotheses, rather than the need to acquire more data. This makes the ability to accurately appraise and evaluate new methods of phylogenetic analysis and phylogenetic artefact identification more important than ever. Incongruence in phylogenetic reconstructions based on different datasets may be due to two major sources: biological and methodological. Biological sources comprise processes like horizontal gene transfer, hybridization and incomplete lineage sorting, while methodological ones contain falsely assigned data or violations of the assumptions of the underlying model. While the former provides interesting insights into the evolutionary history of the investigated groups, the latter should be avoided or minimized as best as possible. However, errors introduced by methodology must first be excluded or minimized to be able to conclude that biological sources are the cause. Fortunately, a variety of useful tools exist to help detect such misassignments and model violations and to apply ameliorating measurements. Still, the number of methods and their theoretical underpinning can be overwhelming and opaque. Here, we present a practical and comprehensive review of recent developments in techniques to detect artefacts arising from model violations and poorly assigned data. The advantages and disadvantages of the different methods to detect such misleading signals in phylogenetic reconstructions are also discussed. As there is no one‐size‐fits‐all solution, this review can serve as a guide in choosing the most appropriate detection methods depending on both the actual dataset and the computational power available to the researcher. Ultimately, this informed selection will have a positive impact on the broader field, allowing us to better understand the evolutionary history of the group of interest.

• Minelli, Alessandro & Gracia, Alberto Valero (2022). Spatially and Temporally Distributed Complexity—A Refreshed Framework for the Study of GRN Evolution. Cells. 11(11), p. 1–16. doi: 10.3390/cells11111790. Full text in Research Archive Show summary

  Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.

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• Gracia, Alberto Valero (2024). Genome dynamics among Nemertea clades. Full text in Research Archive
• Gracia, Alberto Valero (2024). Homeotic genes and 3D genomics in Nemertea. Full text in Research Archive
• Gracia, Alberto Valero (2023). HiFi de novo sequencing and genome architecture dynamics in nemerteans. Full text in Research Archive
• Gracia, Alberto Valero (2023). Group of the month: Rotifera – Blogs of the CEG research group. Full text in Research Archive
• Gracia, Alberto Valero (2023). Project interview by the Embassy of Spain in Norway. [Internet]. https://www.youtube.com/watch?v=qQgXlmvYDBY. Full text in Research Archive
• Gracia, Alberto Valero (2022). Gnathostomulida, an obscure and often neglected phylum – Blogs of the CEG research group. Full text in Research Archive
• Gracia, Alberto Valero & Austin, Rita M (2021). Field Trip to Sylt – Blogs of the CEG research group. Full text in Research Archive
• Gracia, Alberto Valero & Austin, Rita M (2021). Field Trip to Roscoff – Blogs of the CEG research group. Full text in Research Archive
• Capucho, Ana Teresa; Berggren, Matz; Haugen, Marianne Nilsen; Stach, Thomas; Valero-Gracia, Alberto & Döhren, Jörn von [Show all 8 contributors for this article] (2021). Assessing biodiversity in the marine algae belt. Full text in Research Archive Show summary

  The marine algae belt, more loosely interpreted, comprises kelp forests, seagrass meadows and rocky reefs with coralline red seaweeds. It is one of the most active primary producing environments in the sea and harbors a great diversity of animals including ascidians, nemerteans, entoprocts, serpulid worms, spionid worms and caprellids. The species of these groups occupy important ecological functions as herbivores, predators or filter feeding organisms and can be sessile or agile as well as solitary or colonial. Globally these taxa comprise more than 7,000 species with around 250 species documented from Norwegian waters. Despite this, the knowledge about their taxonomy and distribution in Norway is poor and in dire need of improvement. Specimens in museum collections are often quite old material, which additionally is often wrongly determined due to unresolved taxonomic issues including the high degree of cryptic species in these groups. Besides cryptic species, many of these taxa include invasive species causing high economic damage. This recently started project, funded by ArtsDatabanken, is focusing on the occurrence and habitat preferences of the above-mentioned taxa in the marine algae belt along the Norwegian coastline. Using both morphological and molecular methods, it aims to contribute to basic biosystematics, species distribution and nature conservation in groups that are still poorly understood and challenging to study. Fieldwork was conducted last summer in two locations: Oslofjord and Trondheim area. The Oslofjord sampling effort was carried out with the help of two students from the UiO:Life science project. First results include new records of species for both sampled locations and several high-quality barcodes (CO1 sequences) that will be uploaded to NorBOL. Revision of museum collections, species lists and popular and scientific papers will be prepared in the next months. We also hope for more exciting results following the DNA sequencing that will be carried out this autumn.

• Valero-Gracia, Alberto (2021). "InvertOmics", phylogeny and evolution of Spiralia based on genomic data: a first report. Full text in Research Archive
• Struck, Torsten H; Gracia, Alberto Valero; Bachmann, Lutz; Liow, Lee Hsiang; Suh, Alexander & Halanych, Kenneth M. [Show all 8 contributors for this article] (2020). A new Norwegian and international initiative "InvertOmics - Phylogeny and evolution of lophotrochozoan invertebrates based on genomic data". Full text in Research Archive
• Haugen, Marianne Nilsen; Gracia, Alberto Valero; Cerca, José; Fleming, James Frederick; Austin, Rita M & Gusarov, Vladimir [Show all 8 contributors for this article] (2020). International Happy Seasons – Blogs of the CEG research group. Full text in Research Archive
• Haugen, Marianne Nilsen; Gracia, Alberto Valero; Austin, Rita M; Bachmann, Lutz & Struck, Torsten H (2020). Combining group fun with genomic research – Blogs of the CEG research group. Full text in Research Archive
• Gracia, Alberto Valero; Bachmann, Lutz & Struck, Torsten H (2020). A new PhD student in town – Blogs of the CEG research group. Full text in Research Archive

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