Biology subjects

Ramsfjell, M. H.

Publications and source records attributed to Ramsfjell, M. H..

3 recordsLinked to original sources

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↗

bioRxiv2020

A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified bodywall layer in ascus-bearing cheilostomes) and asked if its presence has any bearing on the diversification rates of cheilostomes.

evolutionary biology↗

bioRxiv2020

Molecular phylogeny of historical micro-invertebrate specimens using de novo sequence assembly

Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we present a pipeline that utilizes both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among understudied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer sequencing of air-dried bryozoans, utilizing a recent library preparation method for low DNA input. We use the de novo mitogenome assembly from the target specimen itself as reference for iterative mapping, and the comparison thereof. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree. Finally, the methodological success is emphasized by circularizing a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships between species.

evolutionary biology↗