Biology subjects

Kochzius, M.

Publications and source records attributed to Kochzius, M..

7 recordsLinked to original sources

bioRxiv2026

WIO-ReefFish: A High-Resolution Dataset for Taxon-Aware Coral Reef Fish Detection in the Western Indian Ocean

Coral reef fish assemblages are widely used as indicators of ecosystem condition, yet manual annotation of underwater video remains a major bottleneck for scalable biodiversity monitoring. Despite rapid progress in automated detection, ecologically realistic and publicly available datasets remain scarce, particularly for the Western Indian Ocean. Here, we present WIO-ReefFish, a reef fish detection dataset derived from diver-operated line-intercept transects and designed for ecological monitoring under natural survey conditions. WIO-ReefFish comprises 1,000 ultra-high-definition images (3840 $\times$ 2160 pixels) and 6,768 exhaustive bounding-box annotations spanning 24 taxonomic categories, thereby preserving full-frame assemblage structure in complex reef scenes. We also establish a standardized benchmark across nine object detection models under two complementary protocols: class-aware detection and class-agnostic fish localization. Detection performance was consistently higher under the class-agnostic protocol. The best-performing model (RT-DETR) improved from 0.48 mAP50 in the class-aware setting to 0.70 mAP50 when taxonomic constraints were removed, indicating that taxonomic discrimination remains substantially more challenging than fish localisation in reef imagery. Spatially independent evaluation revealed a pronounced generalisation gap, particularly for taxonomic detection, whereas class-agnostic fish localisation remained substantially more robust across transects and countries. Together, these results establish WIO-ReefFish as a realistic benchmark for automated reef fish detection and provide a foundation for more robust computer-vision tools in coral reef biodiversity monitoring. The WIO-ReefFish dataset and associated benchmarking resources are publicly available.

ecology↗

bioRxiv2025

Proteomic insights into the photobiology of the Hawaiian rice coral Montipora capitata in response to decreased light intensity

Reef-building corals are sessile marine organisms that inhabit a wide range of light habitats along depth gradients. As coral biology is often studied in the context of global change and changing temperatures, knowledge gaps persist in our understanding of the molecular and cellular pathways involved in the responses to other factors than temperature, such as light intensity, which decreases exponentially in the water column and gradually changes the environment. To fill this gap, we tested the response of the Hawaiian rice coral Montipora capitata to decreased light intensity in a field experiment in K[a]neohe Bay, Oahu, Hawaii, using Data-Independent Acquisition (DIA) proteomics. There was a significant effect of light intensity on both the coral and zooxanthellae proteomes. In the M. capitata host, 69 proteins differed significantly in abundance between light levels after two years. The 50 proteins identified as significantly more abundant in the control condition were mostly involved in mRNA and RNA processing, pointing toward a positive correlation between metabolic activity, growth rates and increased light levels. The 19 proteins identified as significantly more abundant in the shade treatment were associated with calcium transport and with the structure of key cellular components, such as cell membrane and cytoskeleton. By contrast, zooxanthellae showed only minor changes in protein abundances, with photosynthesis proteins more abundant in the shade treatment and enzymes involved in fatty acid metabolism more abundant in the control treatment. Overall, these findings establish a baseline for our understanding of the cellular and metabolic processes driving Montipora capitatas acclimatization potential to different light intensities.

ecology↗

bioRxiv2025

Nature vs nurture? Light availability drives phenotypic plasticity within a reef coral species

Scleractinian corals exhibit wide intra-specific phenotypic variations. However, the extent to which these variations are explained by genotypic variation or phenotypic plasticity remains unclear. To elucidate this question, we devised a replicated experiment in which nine Montipora capitata coral colonies were cut into six pieces each, three of which were placed in shaded conditions (with a 73% reduction in light intensity) whereas the other three were kept in natural conditions as a control. After one year, we detected statistically significant morphological differences between corals of the same genotypes grown in different light environments, but no significant change in symbiont community structure. Colonies kept in control conditions exhibited high surface complexity and converged towards more digitate or corymbose morphs compared to shaded corals, which exhibited planar-like surfaces and converged toward laminar and foliose forms. Our data demonstrate the high level of light-driven phenotypic plasticity of Montipora capitata and suggest a trade-off between the amount of biomass per space area and the amount of absorption of incident light.

ecology↗

bioRxiv2024

Shading does not lower thermal tolerance in the coral Montipora capitata: implications for conservation intervention

Marine heatwaves trigger severe coral bleaching events that result in dramatic losses of coral reefs worldwide. An increasingly common method used to mitigate coral bleaching is to shade portions of reefs. However, as shaded corals become less exposed to environmental stress, shading has also been hypothesized to lower their thermal tolerance, which would be detrimental for their survival. Here, we investigated how long-term shading modifies the response of Montipora capitata to both light and temperature stressors. After two years of growth, we used the Coral Bleaching Automated Stress System (CBASS) to compare responses of 73% shaded and unshaded corals during 1) temperature stress under ambient light, 2) temperature stress under low light, and 3) ambient temperature with light stress. Results show that shaded corals are less resistant than control ones to light stress and to heat stress under high light, but not to heat stress under low light, where no difference was detected. We further demonstrate that low light intensity during heat stress reduces the decline of photosynthetic efficiency when compared to heat stress at ambient light, regardless of the light history of the coral colonies. Our data support light-mediated stress, both independent of and synergistic with heat-induced stress, and suggest that light and heat stresses trigger different molecular and cellular pathways. We hereby confirm the benefits of coral shading under both short- and long-term temperature stress, and underline the importance of light acclimation in the conservation and restoration of coral reefs.

ecology↗

bioRxiv2023

Recurrent gene flow events shaped the diversification of the clownfish skunk complex

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which was shown to have triggered the adaptive radiation of the group. Within clownfishes, the skunk complex is particularly interesting as, besides ecological speciation, gene flow between species and hybrid speciation are suggested to have shaped the diversification of the group. We investigated, for the first time, the mechanisms underlying the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole-genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined the population structure, genomic divergence patterns and introgression signals, and performed demographic modeling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation, of hybrid origin of A. sandaracinos, and ruled out the presence of extensive gene flow in sympatry. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo-Australian Archipelago throughout the diversification process of the group. We identified introgressed regions in A. sandaracinos and detected two large regions of high divergence in A. perideraion, likely maintained by the disruption of recombination. Altogether, our results show that ancestral hybridization events shaped the groups diversification. However, more recent gene flow is less pervasive than initially thought and suggests a role of host repartition or behavioral barriers in maintaining the genetic identity of the species in sympatry.

evolutionary biology↗

bioRxiv2021

Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

genomics↗

bioRxiv2021

Strong genetic structure and limited connectivity among populations of Clark's Anemonefish (Amphiprion clarkii) in the centre of marine biodiversity

Populations of anemonefish species often show signs of local isolation due limited dispersal potential and oceanographic conditions. Additionally, anthropogenic pressure, such as overharvesting and coral reef exploitation causes reduced population size, eventually leading to local extinction. The understanding of the genetic population structure, as well as the influence of both historical and current connectivity, is required to design effective marine protected area (MPA) networks. In this study, the genetic structure of Clarks Anemonefish (Amphiprion clarkii) populations of the Indo-Malay Archipelago (IMA) is assessed through mitochondrial control region (mtCR) sequences and nuclear microsatellites. Results provided evidence of a significant genetic structure (mtCR: {Phi}st = 0.42039, {Phi}ct = 0.63852; microsatellites: Fst = 0.01449, Fct = 0.05199). Genetic breaks were identified among Western (Padang Karimunjawa), Central (Sulawesi, Borneo, Bali, Komodo, Timor), and Eastern (Biak) IMA populations, which matches with patterns obtained for congeneric and other coral reef taxa. Due to the restricted connectivity among these three regions, it is suggested to consider them as separate management areas in the design of MPA networks.

molecular biology↗