Emily Veltjen

Background: The Neotropics are considered one of the most biodiverse areas in the world, housing at least one third of all vascular plant species. One of the genera that has diversified in the Neotropics is Magnolia, with about 174 species of three sections (Macrophylla, Magnolia and Talauma) endemic to the Americas. In this work, we study the biogeographic history of the Neotropical Magnolia species using high-throughput sequencing data. Sequences from 39 species (38 from Magnolia and one from the sister genus Liriodendron) were assembled. The dataset contained sequences from 239 nuclear targets and complete chloroplast genomes. Phylogenomic hypotheses and the ancestral distribution range of Magnolia were reconstructed. Results: The results of the calibrated phylogenetic hypotheses and ancestral range construction suggest that the earliest arrival in the Neotropics were the ancestors of section Talauma (38 million years ago), which colonized the Pacific region. This early presence in South America suggests long-distance, overwater dispersal from North America, the presumed origin of the genus Magnolia. The analysis and the extant Talauma distribution indicate a south to north recolonization. The ancestors of the other two Neotropical sections, Magnolia and Macrophylla, migrated around 19 mya from Asia to North America, radiating southward to the Neotropics afterwards, around 11 mya. Conclusions: Our results suggest that Neotropical magnolias originated from a North American ancestor. The current sections arrived at the region independently influenced by climatic processes such as temperature drops or the Miocene Climatic Optimum. Additionally, geological processes, such as the movement of the South and North American land masses and the emergence of the Panama isthmus, facilitated the migration between continents.

The DiSSCo (Distributed System of Scientific Collections) Flanders consortium, with one of the set goals being "maturing" (i.e., optimizing the management of) and unlocking (i.e., publishing) their DNA collections, identified 1) the need for actively sharing best practices on the management of DNA collections; and 2) a need for guidance on how to bring theory into practice. During the DiSSCo Flanders project, a DNA collection working group was created. The working group is open to all biodiversity-related DNA collections associates in Belgium, including those in diverse roles such as researchers, lab technicians, collection managers and data managers. Around 50 people from 13 organizations are currently participating. Members can be passively (reading only) or actively (joining events) engaged. The strength, as well as one of the challenges, of the DiSSCo Flanders community is that the natural science collections are created and managed in different organizational contexts: universities, museum institutes and both governmental and non-governmental research organizations. This translates to a variety of collection management decisions and structures such as: decentralized or centralized; cold or room temperature storage; managed by an appointed curator or by a lab technician. The working group organizes meetings and workshops, tours of each other's collections, and shares a mailing list and an online document space. As its principal output, the group has co-created: “The key to bringing DNA collections to the next level” (Veltjen et al. 2024) with two main results: the "Challenges" and the “Key”. The "Challenges" is a list of 23 challenges applicable to DNA collection management. For example, challenge 8: "Select or customise collection management systems to meet the needs of DNA collections". They are intended to spark debate and give focus to the second output: the "Key." The "Key" lists seven yes/no questions: Do you have an up-to-date overview of all direct, internal stakeholders of the institute’s DNA collection and are you involving them in the (current) intent to “bring the DNA collection to the next level”? Is preserving a DNA collection within the scope of the institute? And is the DNA collection officially recognized within the institute? Do you have, on paper, a clear description of the scope of the DNA collection? Have you outlined the current overarching workflow of the DNA collection? Have you been able to establish your starting level on the "DNA collection maturation chart" and is the assessment properly logged? Level up, one level at a time, and log the process. Have you reached all of the goals in level 3 on the "DNA collection maturation chart"? Do you have a re-evaluation strategy for your DNA collection? Do you have an up-to-date overview of all direct, internal stakeholders of the institute’s DNA collection and are you involving them in the (current) intent to “bring the DNA collection to the next level”? Is preserving a DNA collection within the scope of the institute? And is the DNA collection officially recognized within the institute? Do you have, on paper, a clear description of the scope of the DNA collection? Have you outlined the current overarching workflow of the DNA collection? Have you been able to establish your starting level on the "DNA collection maturation chart" and is the assessment properly logged? Level up, one level at a time, and log the process. Have you reached all of the goals in level 3 on the "DNA collection maturation chart"? Do you have a re-evaluation strategy for your DNA collection? The "DNA collection maturation chart" has 11 categories (rows), three levels (columns) and 33 goals (see Table 1 in Veltjen et al. 2024). The Key provides 18 guidance chapters, which give in depth information, literature and user experiences (Suppl. material 2 in Veltjen et al. 2024). The Key is a specialized tool for DNA collections. It facilitates a standardized and holistic approach, allowing both a helicopter view of the maturation process and close-up view of specific goals. The working group aims to test the Key, whereby the process of "leveling up" is embedded in a community setting: sharing ambitions, setbacks, changes of plans and success stories. The output is ready in its first version. It is published as a reviewable publication, allowing post-publication peer review (Veltjen et al. 2024). The works are expected to evolve through time, depending on user feedback and user experiences. The working group and co-created output are positive examples of how a local community—sometimes managing smaller, or less conspicuous types of natural science collections—can work together and use their unique perspectives, experiences and needs to contribute to the international natural science collection and biobanking communities.

DNA collections are a valuable type of Natural Science collection, enabling the validation of past research, serving as a source for new genomic studies and supporting ex situ conservation. The DiSSCo Flanders DNA collection working group, aiming to advance and "unlock" their DNA collections, identified the need for: 1) actively sharing best practices regarding the management of DNA collections; and 2) providing guidance on how to bring theory into practice. By combining best practice examples from within the working group with available literature and brainstorming ideas, the working group co-created two outputs, referred to as: the "Challenges" and the "Key". The Challenges are a list of obstacles to DNA collection management, which shape the structure of the linked Key and can also be used to spark discussion amongst stakeholders. The Key is a tool that guides users through the maturation process of their DNA collection in a standardised way. It stimulates holistic growth, breaks down the needed work into manageable steps and helps to decide priorities during the process. Furthermore, the Key facilitates communication with both internal stakeholders and external DNA collection managers. The Key distinguishes itself from other self-assessment tools in several ways: it includes (re)investigation of the collection’s purpose and context; it is specialised for DNA collections; it delivers concrete goals linked to relevant information and shared experience; and it is inclusive, targeting all Natural Science DNA collections, regardless of their context or size.

On the island of Hispaniola, five endemic species of Magnolia occur, all of which are threatened with extinction. Little is known about their distribution and genetic health, hampering targeted conservation actions. The objective of this study is to assess the potential distribution and the genetic health of the Magnolias of Hispaniola, to inform concrete guidelines for effective conservation management. Using species distribution modelling (SDM), we predict habitat suitability for the Magnolias of Hispaniola by analysing 21 variables, describing climate and landscape features, on 635 occurrences. We genotyped 417 individuals using 16 microsatellite markers, to test for genetic structure and degree of inbreeding. The SDM and genetic data confirm the recognition of the four studied Magnolia species. The known individuals of the three Dominican Magnolias are structured into five populations which show ample genetic diversity and little inbreeding overall. For conservation management, we propose to focus on exploration using the SDM results, and protection and reinforcement using the genetic and occurrence data. The genetic results guide prioritization of species and populations. The SDM results guide spatial prioritization. Installing and/or protecting habitat corridors between populations, starting with the two species with the lowest genetic diversity and relatively nearby populations, is recommended as a durable conservation strategy. Meanwhile, reinforcement efforts can be undertaken to artificially increase gene flow for which we appoint sink and source population pairs, using the genetic data.

An accurate taxa delimitation, based on a full understanding of evolutionary processes involved in taxa differentiation, can be gained from a combination of ecological, morphological, and molecular approaches. The taxonomy of Magnolia subsect. Talauma in Cuba has long been debated and exclusively based on traditional morphological study of a limited number of individuals. A more accurate description of leaf morphology variation using geometric morphometrics combined with genetic data could bring consistency to taxa delimitation in this group. Leaf samples for the morphological (243) and genetic (461) analyses were collected throughout the entire distribution range. The variability of each taxon was analyzed through multivariate and geometric morphometry, and 21 genetic markers (SSR). The observed leaf morphological variability was higher than previously described. Morphological and genetic classifications were highly congruent in two out of four taxa. Our data brought evidence that Magnolia orbiculata can be considered a true species with very clear genetic and morphological limits. The main taxonomic issues concern the north-eastern Cuban populations of Magnolia subsect. Talauma. The data supported the existence of two clear groups: corresponding mainly to M. minor-M. oblongifolia and T. ophiticola. However, these two groups cannot be considered fully delimited since genetic markers provided evidence of genetic admixture between them. Due to the likely absence of, at least strong, reproductive barriers between these three taxa, we propose therefore to consider them as a species complex.

Aim: Islands are ‘nature's laboratories of evolution’. Most island biogeographical studies have focussed on remote volcanic island chains. Here, we challenge island biogeographical patterns using a slowly evolving recent colonist present on five islands in a nonlinear chronosequence island chain.Location: The Lesser Antilles (Caribbean).Taxon: Magnolia dodecapetala (Magnoliaceae).Methods: Genetic diversity was characterised using Sanger sequencing of 21 individuals amplified for 11 DNA markers, plus microsatellite data of 195 individuals genotyped with 19 simple sequence repeat (SSR) markers. Sanger sequencing data were used to construct a Bayesian phylogenetic hypothesis, while SSR markers were used to run approximate Bayesian computation (ABC) demographic analyses and calculate population statistics.Results: Both types of molecular data support stepwise colonisation, decoupled from known island ages. The ABC analyses support a north to south migration while the Sanger sequencing data indicate a mixture of island progression rule and stepping stone dispersal. The SSR data show strong genetic structuring per island and significant inbreeding in all populations except in Saint Lucia. The lowest genetic diversity is found in the population from Saint Vincent. A high amount of genetic linkage occurs in a subpopulation from Dominica.Main Conclusions: Biogeographical patterns in the complex geological setting of the Lesser Antilles are uncovered using a slowly evolving study species. All genetic data support treating each island as distinct Management Units for conservation and call for a re‐evaluation of the species limits. Inbreeding threatens the survival of island populations and the populations of Saint Vincent and Dominica represent conservation priorities.

DiSSCo Flanders aims at developing a standardised natural science collections management infrastructure, ensuring proper long-term conservation, and future re-usage of the collections. Meise Botanic Garden coordinates the Flemish consortium. This four-year project, funded by the FWO (Research Foundation – Flanders), started in January 2021. The consortium brings together both the more classical ‘museum’ collections (Meise Botanic Garden, Ghent University Museum), with research collections (Research Institute for Nature and Forest, Flanders Research Institute for Agriculture, Fisheries and Food, Flanders Marine Institute, universities), and living collections (Belgian Association of Botanic Gardens and Arboreta, Zoo of Antwerp (Poo 2022)). Many of the research collections are smaller orphan collections, lacking a (full-time) curator, for which collection management is not the core business of the hosting institute. The Belgian federal DiSSCo members are associated with the project, allowing close collaboration between European, national and regional (digital) collection management inititatives. Building on the expertise of the European DiSSCo-related projects, an initial high-level inventory and assessment of the collections has been made and will provide a better understanding of the collections landscape in Flanders (Van Baelen 2022). This step in the digitization will increase the findability of the diverse regional collections and highlight the available knowledge to the research community. Close collaboration with the TDWG Collections Descriptions interest group and the development of the Latimer Core standard (Woodburn 2021) will ensure maximal interoperability of the collection data. In order to be relevant for research, the Flemish collections need to be more interconnected and linked to other data sources. To ensure that collection data is adhering to the FAIR principles (Findable, Accessible, Interoperable and Resuable) and ready to connect to the DiSSCo research infrastructure, DiSSCo Flanders will have a large focus on the collection(s) management system (CMS). Depending on the needs and specificities of each collection, a strategy will be chosen to implement and/or collection data will be migrated to (an) optimised system(s). Parallel to the digital inventory and CMS choice, the consortium addresses specific themes in the format of working groups. Most of the institutes have identified that their molecular collection (DNA, tissues) has not been properly acknowledged as a separate long-term collection. Challenges such as the storage and curation of e-DNA and environmental samples (e.g., soil) have been identified. Very often it will only be feasible to add basic data in the CMS and essential data is not available to the researchers. DiSSCo Flanders invests in the enrichment of specimen data to ensure that a maximal amount of information becomes available to the community. This can be accomplished either through the use of citizen science/crowdsourcing using the DoeDat platform (Groom 2018), or by using machine learning techniques performed by the IDLab at Ghent University (Thirukokaranam Chandrasekar 2021). Besides the technical aspects of the DiSSCo research infrastructure, the consortium is covering topics such as data publication, legal aspects of collections, standard operating procedures, etc. through knowledge sharing and active dialog.

Chloroplast genomes are considered to be highly conserved. Nevertheless, differences in their sequences are an important source of phylogenetically informative data. Chloroplast genomes are increasingly applied in evolutionary studies of angiosperms, including Magnoliaceae. Recent studies have focused on resolving the previously debated classification of the family using a phylogenomic approach and chloroplast genome data. However, most Neotropical clades and recently described species have not yet been included in molecular studies. We performed sequencing, assembly, and annotation of 15 chloroplast genomes from Neotropical Magnoliaceae species. We compared the newly assembled chloroplast genomes with 22 chloroplast genomes from across the family, including representatives from each genus and section. Family-wide, the chloroplast genomes presented a length of about 160 kb. The gene content in all species was constant, with 145 genes. The intergenic regions showed a higher level of nucleotide diversity than the coding regions. Differences were higher among genera than within genera. The phylogenetic analysis in Magnolia showed two main clades and corroborated that the current infrageneric classification does not represent natural groups. Although chloroplast genomes are highly conserved in Magnoliaceae, the high level of diversity of the intergenic regions still resulted in an important source of phylogenetically informative data, even for closely related taxa.