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Article Reference Combined High-Throughput Imaging and Sequencing: Addressing the collections on demand requirement in SYNTHESYS+ project
Imagine you are a scientist, working on collections. You have your pet taxon and you need information which is distributed in a number of books and publications but also in the specimens deposited in$~$Museums or Herbaria. Instead of paying visits to these establishments, around the world, you wish there was a means to transform all the information you need into a digitized form of the physical objects, you can reach from the screen of your laptop, tablet or cell phone. You dream you were able to watch, inspect and even dissect the type material you need online but also to compare it with others they way sequences are blasted against large databases, these days. You plan to make global research on this taxon and try to derive patterns from both the molecular and organismal level of the biological organization and to link the patterns resulting to the drivers of change for this taxon.$~$This is the vision of the Virtual Museum of Natural History and one of the ways to achieve this vision is to address the “collections on demand” requirement. One of the possible means to address this requirement is the digitization through the use of the micro-ct technology. The micro-CT virtual laboratory (vLab), developed by LifeWatchGreece research infrastructure (RI), makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. This presentation shows the development of such a “collections on demand” function, implemented by the SYNTHESYS+ project (DiSSCo RI), which combines such high-throughput technologies, that is micro-ct and genomics, to address the scientific communityʼs requirements. We show that this approach to combine patterns deriving from the application of novel techniques, which represent different kinds of observations is possible and we propose certain case studies as examples. The innovation aspects of this function include: Expansion and development of cost models for Collections on Demand; Development of standards and guidelines for exchange of collection-derived imaging data; Construction of new data pipelines and standard workflows, enabling access to complex digital content such as 3D scans; Development of novel molecular lab protocols, workflows and informatics pipelines, to enable large scale; DNA sequencing of NH collections.
Located in Library / RBINS Staff Publications 2019
Techreport Reference Combining data and deterministic modelling to monitor and predict seabed evolution in areas of marine aggregate extraction. Abstract. 47th Internationl Liège Colloquium, Marine Environmental Monitoring, Modelling and Prediction.
Located in Library / RBINS Staff Publications
Proceedings Reference Combining offshore wind and wave energy extraction: an environmental perspective
Wind farm areas may provide an opportunity for the deployment of wave energy converters (WEC) in an environment with reduced risk of collision or accidental disturbance. Complementary use of electric infrastructure (export cable) and maintenance may provide additional economic incentives. We discuss a number of uncertainties and negative environmental interactions that were identified during the Environmental Impact Assessment (EIA) for the first offshore energy park combining offshore wind and wave energy extraction. Assumptions on possible impacts were inferred from research and monitoring results from both WEC pilot projects and offshore wind farms separately as well as from the Environmental Impact Statement (EIS) submitted by the developer. A number of uncertainties were identified with regards to seabirds, non indigenous species, marine mammals and maritime safety which will have to be addressed prior to a full scale deployment. As a result, the environmental license that was granted includes a pilot phase during which the above mentioned environmental impacts will be quantified.
Located in Library / RBINS Staff Publications
Misc Reference Comment caractériser un assemblage de termites: un test de la méthode des transects
Located in Library / RBINS Staff Publications
Inproceedings Reference Community ecology of Tanzanian bats and their viruses
Located in Library / RBINS Staff Publications 2023
Proceedings Reference Comparing Gravettian and Epigravettian canids from Europe with Late Pleistocene canids from Yakutia
Located in Library / RBINS Staff Publications 2016
Unpublished Reference Comparing the results of four widely used automated bat identification software programs in the North Sea region
Recently a few papers were published addressing the prudency needed when using automated identification software programs to analyse recordings of bat echolocation sounds. We want to contribute to that discussion by analysing a reference dataset of bat recordings with four widely used and commercially available software programs (BatIdent, BatExplorer, Kaleidoscope and Sonochiro). The reference data were all recorded in Western-Europe with a batcorder. For most of the recordings there was a visual confirmation of the recorded species. In a few other cases certainty was obtained because the specimens were captured and released or because the recordings were made in certain areas which were outside of the range of other species (e.g. at high altitude to separate Eptesicus serotinus and Eptesicus nilssonii). After running the different programs on the reference data, we compared the outputted results. Overall, identification of the recordings to species level in this test was best with Batident (81% correct identifications), followed by Kaleidoscope (71%), Sonochiro (63%) and BatExplorer (53%). We can conclude that each of the tested programs has its own strengths and weaknesses, but none of them should be used unsupervised. Outputted results need to be checked by a trained expert. In this way, our test affirms the conclusions of previous tests in Northern Europe and the USA.
Located in Library / RBINS Staff Publications 2017
Article Reference Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
Ostracods are microscopic, bi-valved crustaceans with the best fossil record of all living arthropods. Their fossil record, starting 400 million years ago, together with a high prevalence of parthenogenetic reproduction and putative ancient asexuality, make non-marine ostracods fascinating evolutionary model organisms. In the absence of high quality ostracod reference genomes, here we compare transposon landscapes between two Illumina genome assemblies from the putative ancient asexual Darwinula stevensoni and the fully sexual ostracod Notodromas monacha. Both assemblies have around 60,000 contigs, sizes of 360-380 Mb, more than 100X coverage and BUSCO scores of 93 and 94%, respectively. Because homology-based programs are not sensitive enough to detect families of transposable elements (TEs) in species missing from Repbase or Dfam, we used three different pipelines for de novo analyses: REPET, RepeatMasker2 (RM2) and EarlGrey (RM2-based, with automated curation). TE diversity between the two genomes differs substantially regardless which pipeline was used. The Illumina assembly of N. monacha is dominated by LTR retrotransposons (6.5%) with some DNA transposons (3.7%), whereas DNA (15.5%), LINE-like (5.9%) and rolling circle Helitron elements (1.5%) were most abundant in the assembly of D. stevensoni. Our results on the dominance of DNA (Tc/mar, hAT) and LINE-like (CR1, RTE) TEs in D. stevensoni parallel earlier findings from a partial genomic library, and differ from those of other asexuals. TE copies with a low number of nucleotide substitutions are only observed with REPET (“L” shape landscape) in both genomes. Although the presented results may underestimate TE abundance, they indicate pronounced differences of the transposon landscapes and diversity between these two ostracod species. Analysis of related species should determine whether the differences are correlated with the reproductive mode or are lineage specific.
Located in Library / RBINS Staff Publications 2024
Article Reference Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
Ostracods are microscopic, bi-valved crustaceans with the best fossil record of all living arthropods. Their fossil record, starting 400 million years ago, together with a high prevalence of parthenogenetic reproduction and putative ancient asexuality, make non-marine ostracods fascinating evolutionary model organisms. In the absence of high quality ostracod reference genomes, we here compare transposon landscapes between two Illumina genome assemblies from the putative ancient asexual Darwinula stevensoni and the fully sexual ostracod Notodromas monacha. Both assemblies have around 60,000 contigs, sizes of 360-380 Mb, more than 100X coverage and BUSCO scores of 93 and 94%, respectively. Because homology-based programs are not sensitive enough to detect families of transposable elements (TEs) in species missing from Repbase or Dfam, we used three different pipelines for de novo analyses: REPET, RepeatMasker2 (RM2) and EarlGrey (RM2-based, with automated curation). TE diversity between the two genomes differs substantially regardless which pipeline was used. The Illumina assembly of N. monacha is dominated by LTR retrotransposons (6.5%) with some DNA transposons (3.7%), whereas DNA (15.5%), LINE-like (5.9%) and rolling circle Helitron elements (1.5%) were most abundant in the assembly of D. stevensoni. Our results on the dominance of DNA (Tc/mar, hAT) and LINE-like (CR1, RTE) TEs in D. stevensoni parallel earlier findings from a partial genomic library, and differ from those of other asexuals. TE copies with a low number of nucleotide substitutions are only observed with REPET (“L” shape landscape) in both genomes. Although the presented results may underestimate TE abundance, they indicate pronounced differences of the transposon landscapes and diversity between these two ostracod species. Analysis of related species should determine whether the differences are correlated with the reproductive mode or are lineage specific. We are currently curating TEs in an Oxford Nanopore draft assembly of D. stevensoni to further confirm our initial results.
Located in Library / RBINS Staff Publications 2024
Article Reference Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
Ostracods are microscopic, bi-valved crustaceans with the best fossil record of all living arthropods. Their fossil record, starting 400 million years ago, together with a high prevalence of parthenogenetic reproduction and putative ancient asexuality, make non-marine ostracods fascinating evolutionary model organisms. In the absence of high quality ostracod reference genomes, we here compare transposon landscapes between two Illumina genome assemblies from the putative ancient asexual Darwinula stevensoni and the fully sexual ostracod Notodromas monacha. Both assemblies have around 60,000 contigs, sizes of 360-380 Mb, more than 100X coverage and BUSCO scores of 93 and 94%, respectively. Because homology-based programs are not sensitive enough to detect families of transposable elements (TEs) in species missing from Repbase or Dfam, we used three different pipelines for de novo analyses: REPET, RepeatMasker2 (RM2) and EarlGrey (RM2-based, with automated curation). TE diversity between the two genomes differs substantially regardless which pipeline was used. The Illumina assembly of N. monacha is dominated by LTR retrotransposons (6.5%) with some DNA transposons (3.7%), whereas DNA (15.5%), LINE-like (5.9%) and rolling circle Helitron elements (1.5%) were most abundant in the assembly of D. stevensoni. Our results on the dominance of DNA (Tc/mar, hAT) and LINE-like (CR1, RTE) TEs in D. stevensoni parallel earlier findings from a partial genomic library, and differ from those of other asexuals. TE copies with a low number of nucleotide substitutions are only observed with REPET (“L” shape landscape) in both genomes. Although the presented results may underestimate TE abundance, they indicate pronounced differences of the transposon landscapes and diversity between these two ostracod species. Analysis of related species should determine whether the differences are correlated with the reproductive mode or are lineage specific. We are currently curating TEs in an Oxford Nanopore draft assembly of D. stevensoni to further confirm our initial results.
Located in Library / RBINS Staff Publications 2024