Arzu Karahan

Biodiversity operates across multiple levels of biological organization, encompassing genes, species, and ecosystems. It plays a crucial role in sustaining ecological resilience and delivering essential services such as food and clean water. Higher biodiversity enhances the ability of ecosystems to withstand and recover from disturbances. Monitoring biodiversity is therefore vital for assessing ecosystem health, identifying imbalances, and preserving these critical services. Within the oceanic ecosystems, Marine Animal Forests (MAFs), structured by key organisms like corals and sponges, serve as biodiversity hotspots and play a vital role in regulating oceanic processes. This paper explores methodologies for studying MAFs across three levels: intra-species diversity, species diversity, and genetic diversity. Intra-species diversity focuses on variation within and between individuals, with an emphasis on phenomena like chimerism and somatic mutations. Species diversity is analyzed using taxonomic, functional, and biotic indices, while genetic diversity is examined through DNA barcoding, species delimitation analyses (SDA), metabarcoding, and microsatellite markers. Although each method provides valuable insights independently, integrating them can significantly enhance the speed and effectiveness of biodiversity assessments. Future efforts should emphasize public engagement through citizen science, ensuring biodiversity monitoring tools become more accessible, affordable, and user-friendly. Additionally, expanding server infrastructure will be key to accelerating bioinformatic workflows. Finally, strengthening global collaborations and increasing awareness of biodiversity and climate change remain essential priorities.

Sponges, comprising over 9000 recorded species, represent one of the most primitive groups of metazoans. Given the importance of species distribution records and the identification of new species in scientific research, these endeavors play a crucial role in enhancing ecological insights, conserving biodiversity, facilitating a better understanding of the relationships between various groups of organisms, advancing our knowledge of evolution, and potentially expanding biomedical implications. In this study, we used basic morphological data, mitochondrial Cytochrome Oxidase I (COI) gene, and Internal Transcribed Spacer two (ITS2) regions to evaluate the Terpios samples collected from four coastal sites along the northeastern Mediterranean Sea, covering a distance of approximately 450 km. For this purpose, 81 COI and 11 ITS2 records of the order Suberitida were mined from GenBank, and species delimitation analysis was performed using both the Automatic Barcode Gap Discovery method and the Poisson Tree Process (PTP), along with 11 samples from the present study. While we observed slight differences in spicule sizes, the overall morphology of all samples from our study was similar. Within the scope of this research, we report the first-ever presence record of T. gelatinosus in the northeastern Mediterranean Sea. Furthermore, we document evidence pointing to the potential existence of cryptic speciation in the region.

Aquatic invertebrates play a pivotal role in (eco)toxicological assessments because they offer ethical, cost‐effective and repeatable testing options. Additionally, their significance in the food chain and their ability to represent diverse aquatic ecosystems make them valuable subjects for (eco)toxicological studies. To ensure consistency and comparability across studies, international (eco)toxicology guidelines have been used to establish standardised methods and protocols for data collection, analysis and interpretation. However, the current standardised protocols primarily focus on a limited number of aquatic invertebrate species, mainly from Arthropoda, Mollusca and Annelida. These protocols are suitable for basic toxicity screening, effectively assessing the immediate and severe effects of toxic substances on organisms. For more comprehensive and ecologically relevant assessments, particularly those addressing long‐term effects and ecosystem‐wide impacts, we recommended the use of a broader diversity of species, since the present choice of taxa exacerbates the limited scope of basic ecotoxicological studies.This review provides a comprehensive overview of (eco)toxicological studies, focusing on major aquatic invertebrate taxa and how they are used to assess the impact of chemicals in diverse aquatic environments. The present work supports the use of a broad‐taxa approach in basic environmental assessments, as it better represents the natural populations inhabiting various ecosystems. Advances in omics and other biochemical and computational techniques make the broad‐taxa approach more feasible, enabling mechanistic studies on non‐model organisms. By combining these approaches with in vitro techniques together with the broad‐taxa approach, researchers can gain insights into less‐explored impacts of pollution, such as changes in population diversity, the development of tolerance and transgenerational inheritance of pollution responses, the impact on organism phenotypic plasticity, biological invasion outcomes, social behaviour changes, metabolome changes, regeneration phenomena, disease susceptibility and tissue pathologies. This review also emphasises the need for harmonised data‐reporting standards and minimum annotation checklists to ensure that research results are findable, accessible, interoperable and reusable (FAIR), maximising the use and reusability of data. The ultimate goal is to encourage integrated and holistic problem‐focused collaboration between diverse scientific disciplines, international standardisation organisations and decision‐making bodies, with a focus on transdisciplinary knowledge co‐production for the One‐Health approach.

Members of the tunicates, a subphylum of marine filter-feeder chordates, inhabit all marine and oceanic habitats from the subtidal to the abyssal. Considered the closest relatives to the vertebrates, the tunicates are widely used as model organisms for evo-devo, allorecognition, senescence, and whole-body regeneration studies. However, species boundaries are poorly understood due to the high morphological and genetic plasticity that characterizes many tunicate taxa. Here, we present findings on seven tunicate species (Botrylloides israeliense, Botrylloides sp., Botryllus humilis, Botryllus schlosseri, Symplegma brakenhielmi, Polyclinum constellatum and Didemnum perlucidum) sampled from six Turkish sites at the North Eastern Mediterranean Sea and employed the mitochondrial barcoding marker (COI) for evaluating the relationships among geographically restricted and widely spread ascidian species. Species delimitation was conducted using sequences generated in the current study in addition to sequences obtained from GenBank. General morphological features and colors of colonies were recorded at sampling sites. Then, all Styelidae colonies were attached and cultured on slides in an aquaculture room, enabling the study of other features, such as zooid distributions and sizes, oral tentacle numbers, and life cycles, using stereo and light microscopes. The spicules of formalin-fixed Didemnum perlucidum samples were examined under a light microscope. Then, scientific names were assigned to all species based on the results of the species delimitation and on comparisons of the obtained COI sequences with GenBank sequences. A putative new Botrylloides species (Botrylloides sp.) from the Antalya region was revealed, with a 99% match with the COI gene of another specimen from Saudi Arabia; further waiting for detailed traditional taxonomy.

Summary: I completed my undergraduate education in Atatürk University, Education Faculty, Biology Department. Then pursued my graduate education at the Biology Department of Mersin University. Both my master's and PhD theses were on the biological and population genetics features of various fish species. My initial encounter with tunicates dates back to my Postdoc at Israel Oceanographic and Limnologic Research Institute (IOLR) in 2011, where I was working on a DNA barcoding project. During that time, the entire institute was actively engaged in research on tunicates, and discussions during lunchtime often revolved around this fascinating group of organisms. Prof. Rinkevich usually only spoke seriously about tunicate biology but 1 day he told me “You know Botryllus schlosseri is riding horse in Black Sea coasts of Turkiye.” I was totally surprised and was trying to understand the meaning of this comment from a scientific perspective. He then showed me the picture of a B. schlosseri colony attached to a seahorse. Following several more Postdoc experiences, I began working as a Principal Investigator at Institute of Marine Sciences, Middle East Technical University (IMS‐METU) in 2017. Since then, my team and I have been working on tunicate biodiversity, evolutionary biology, genomics, DNA barcoding, metabarcoding, metabolomics, whole‐body regeneration (WBR) and aging related pathways.

Botrylloides niger (class Ascidiacea) is an invasive marine filter-feeding invertebrate that is believed to originate from the West Atlantic region. This species of colonial tunicate has been observed in several locations along the coasts of Israel and around the Suez Canal, but it has not yet been reported on the coasts of the Northeastern Mediterranean Sea (NEMS), suggesting an ongoing Lessepsian migration. However, the extent of this invasion might be concealed by reports of other potentially misidentified species of Botrylloides, given that the strong morphological similarities within this genus renders taxonomical identification particularly challenging. In this study, we performed a phylogeographic and morphological analysis of B. niger in the NEMS. We collected 238 samples from 8 sampling stations covering 824 km of the coastlines of NEMS. We reported 14 different morphotypes, of which the orange-brown, orange, and brown-striped morphs were the most abundant. Using the mitochondrial cytochrome C oxidase I (COI) as a DNA barcode marker, we identified 4 haplotypes. The COI haplotypes clustered with the reference B. niger sequences from GenBank and differed significantly from the sister Botrylloides species. We confirmed our identification using three additional barcoding markers (Histone 3, 18S rRNA, and 28S rRNA), which all matched with over 99% similarity to reference sequences. In addition, we monitored a station for a year and conducted a temporal analysis of the collected colonies. The colonies were absent during the winter and spring, while new colonies were established in the summer and expanded during autumn. We performed demographic population analysis on our spatial data that identified a possible population subdivision at a sampling site, which might have been caused by local freshwater input. Herein, we present the first report on the presence of Botrylloides niger in the NEMS. This study represents a key step toward understanding the diversity and the propagation of this highly invasive species of colonial ascidians, both within the Mediterranean basin as well as globally.

Members of the tunicates, a subphylum of marine filter-feeder chordates, inhabit all marine and oceanic habitats from the subtidal to the abyssal. Considered as the closest relatives to the vertebrates, the tunicates are widely used as model organisms for evo-devo, allorecognition, senescence, and whole-body regeneration studies. Yet, species boundaries are poorly understood due to high morphological and genetic plasticity that characterize many tunicates taxa. Here we study taxonomy and the distribution of eight tunicate species ( Botrylloides niger Herdman, 1886/ aff. leachii, Botrylloides israeliense Brunetti, 2009, Botrylloides sp., Botrylloides anceps (Herdman, 1891), Botryllus schlosseri (Pallas, 1766), Didemnum perlucidum Monniot F., 1983, Symplegma brakenhielmi (Michaelsen, 1904) and Polyclinum constellatum Savigny, 1816) sampled from six Turkish North Eastern Mediterranean Sea sites and employed the mitochondrial barcoding marker (COI) for evaluating the relationships among geographically restricted and widely spread ascidian species. Species delimitation analysis was conducted using NCBI and the present study sequences. Morphological examinations were first done in the field and then, styelide colonies were cultured in the laboratory and studied using stereo and light microscopes. A putative new Botrylloides species ( Botrylloides sp .) from the Antalya region was revealed, with 99% matching on the COI gene from Saudi Arabia, further awaiting for detailed traditional taxonomy.

Botrylloides niger is an invasive marine filter-feeding invertebrate that is believed to originate from the West Atlantic region. This species of colonial tunicate has been observed on several locations along the coasts of Israel and around the Suez Canal but it has not yet been reported on the coasts of the northeastern Mediterranean Sea (NEMS), suggesting an ongoing Lessepsian migration. However, the extent of this invasion might be concealed by reports of other potentially misidentified species of Botrylloides , given that the strong morphological similarities within this genus renders taxonomical identification particularly challenging. In this study, we performed a phylogeographic and morphological analysis of B. niger in the NEMS. We collected 241 samples from 8 sampling stations covering 824 km of coastlines of NEMS. We reported 14 different morphotypes, of which the orange-brown, orange and brown-striped morphs were the most abundant. Using the mitochondrial cytochrome C oxidase I (COI), one of the four most commonly used DNA barcoding marker, we identified 4 haplotypes with the Konacık (H4) and the Mezitli (H3) ones being the most diverged. The COI haplotypes clustered with the reference B. niger sequences from GenBank and separated from sister Botrylloides species with high confidence. We confirmed our identification using the three additional barcoding markers (Histone 3, 18S rRNA and 28S rRNA), which all matched with over 99% similarity to the reference sequences. In addition, we monitored the Kızkalesi station for a year and applied temporal analysis to the colonies collected. The colonies regressed during winter while resettled and expanded during summer. We performed gene flow analysis on our spatial data that identified a possible population subdivision at the sampling site of Side, which might be caused by a local freshwater input. Overall, we here present the first report on the presence of Botrylloides niger in the NEMS, we show that this species is commonly present throughout this region and with a particularly high morphological as well as genomic diversity.