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Thalen, F.

Publications and source records attributed to Thalen, F..

2 recordsLinked to original sources

Probing the evolutionary dynamics of whole-body regeneration within planarian flatworms

Why some animals can regenerate while many others cannot remains a fascinating question. Even amongst planarian flatworms, well-known for their ability to regenerate complete animals from small body fragments, species exist that have restricted regeneration abilities or are entirely regeneration incompetent. Towards the goal of probing the evolutionary dynamics of regeneration, we have assembled a diverse live collection of planarian species from around the world. The combined quantification of species-specific head regeneration abilities and comprehensive transcriptome-based phylogeny reconstructions reveals multiple independent transitions between robust whole-body regeneration and restricted regeneration in the freshwater species. Our demonstration that the RNAi-mediated inhibition of canonical Wnt signalling can nevertheless bypass all experimentally tractable head regeneration defects in the current collection indicates that the pathway may represent a hot spot in the evolution of planarian regeneration defects. Combined with our finding that Wnt signalling has multiple roles in the reproductive system of the model species S. mediterranea, this raises the possibility of a trade-off between egg-laying and asexual reproduction by fission/regeneration as a driver of regenerative trait evolution. Although initial quantitative comparisons of Wnt signalling levels, reproductive investment, and regenerative abilities across the collection confirm some of the models predictions, they also highlight the diversification of molecular mechanisms amongst the divergent planarian lineages. Overall, our study establishes a framework for the mechanistic evolution of regenerative abilities and planarians as model taxon for comparative regeneration research.

evolutionary biology↗

Patchwork: alignment-based retrieval and concatenation of phylogenetic markers from genomic data

MotivationIncreased output from the latest short-read sequencers makes low-coverage whole-genome sequencing (LC-WGS) an increasingly affordable approach to large-scale phylogenetics. Despite offering several advantages over prevailing sequencing strategies, few tools exist to work with this data type within a phylogenomic context. Due to the fragmented nature of LC-WGS genomes, their use have mostly been restricted to easy-to-assemble, high-copy-number regions such as organelle genomes and or ribosomal genes. ResultsWe here present a new method for mining phylogenetic markers directly from an assembled genome. Homologous regions are obtained via an alignment search, followed by a "hit-stitching" phase, in which adjacent or overlapping regions are concatenated together. Finally, a novel sliding window technique is used to trim non-coding regions from the alignments. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs (USCOs) in the annelid Dimorphilus gyrociliatus. AvailabilityPatchwork is available from Github under the GNU General Public license version 3. Contactfelix.thalen@uni-goettingen.de Supplementary informationSupplementary data are available at github.com/Animal-Evolution-and-Biodiversity/benchmarking-patchwork.

bioinformatics↗