Biology subjects

Kuklinski, P.

Publications and source records attributed to Kuklinski, P..

4 recordsLinked to original sources

bioRxiv2025

Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758)

The phylum Bryozoa is an understudied, yet commonly-occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately little genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in 8 autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat (LTR) retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

genomics↗

bioRxiv2024

A long-term ecological research data set from the marine genetic monitoring programme ARMS-MBON 2018-2020

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic, and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to [~]5,500 amplicon sequence variants and [~]1,800 operational taxonomic units, and up to [~]250 and [~]50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least three to six months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programmes and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.

ecology↗

bioRxiv2022

DeepBryo: a web app for AI-assisted morphometric characterization of cheilostome bryozoans

O_LIBryozoans are becoming an increasingly popular study system in macroevolutionary, ecological, and paleobiological research. Members of this colonial invertebrate phylum are notable for displaying an exceptional degree of division of labor in the form of specialized modules (polymorphs), which allow for the inference of individual allocation of resources to reproduction, defense, and growth using simple morphometric tools. However, morphometric characterizations of bryozoans are notoriously labored, due to the high number of structures often captured per image, as well as the need for specialized knowledge necessary for classifying individual skeletal structures within those images. C_LIO_LIWe here introduce DeepBryo, a web application for deep learning-based morphometric characterization of cheilostome bryozoans. DeepBryo requires a single image as input and performs measurements automatically using instance segmentation algorithms. DeepBryo is capable of detecting objects belonging to six classes and outputting fourteen morphological shape measurements for each object based on the inferred segmentation maps. The users can visualize the predictions, check for errors, and directly filter model outputs on the web browser. Measurements can then be downloaded as a comma-separated values file. C_LIO_LIDeepBryo has been trained and validated on a total of 72,412 structures, belonging to six different object classes in 935 SEM images of cheilostome bryozoans belonging to 109 different families. The model shows high (>0.8) recall and precision for zooid-level structures. Its misclassification rate is low (~4%) and largely concentrated in a single object class (opesia). The models estimated structure-level area, height, and width measurements are statistically indistinguishable from those obtained via manual annotation (r2 varying from 0.89 to 0.98) and show no detectable bias. DeepBryo reduces the person-hours required for characterizing the zooids in individual colonies to less than 1% of the time required for manual annotation at no significant loss of measurement accuracy. C_LIO_LIOur results indicate that DeepBryo enables cost-, labor,- and time-efficient morphometric characterization of cheilostome bryozoans. DeepBryo can greatly increase the scale of macroevolutionary, ecological, taxonomic, and paleobiological analyses, as well as the accessibility of deep learning tools for this emerging model system. Finally, DeepBryo provides the building blocks necessary for adapting the current application to other study groups. C_LI

bioinformatics↗

bioRxiv2022

Temperature as a likely driver shaping global patterns in mineralogical composition in bryozoans: Implications for marine calcifiers under Global Change

The Southern Ocean is showing one of the most rapid responses to human-induced global change, thus acting as a sentinel of the effects on marine species and ecosystems. Ocean warming and acidification are already impacting benthic species with carbonate skeletons, but the magnitude of these changes to species and ecosystems remains largely unknown. Here we provide the largest carbonate mineralogical dataset to date for Southern Ocean bryozoans, which are diverse, abundant and important as carbonate producers, thus making them excellent for monitoring the effects of ocean warming and acidification. To improve our understanding of how bryozoans might respond to ocean warming and acidification, we assess latitudinal and seafloor temperature patterns of skeletal mineralogy using bryozoan species occurrences together with temperature data for the first time. Our findings, combining new mineralogical data with published data from warmer regions, show that the proportions of high-Mg calcite and bimineralic species increase significantly towards lower latitudes and with increasing seawater temperature. These patterns are consistent with the hypothesis that seawater temperature is likely a significant driver of variations in bryozoan mineralogy at a global scale.

ecology↗