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Article Reference Benthic Food Webs in Antarctica ~ Would you care for some more (micro)algae ?
The West Antarctic Peninsula (WAP) is experiencing rapid warming, which will impact ecosystem processes, particularly sympagic algae dynamics. As these ice-associated microalgae are a vital food source for primary consumers, this disruption is likely to cascade through the communities via trophic interactions. To study these effects, we sampled benthic communities along the WAP in February 2023, focusing on macroalgae forests (n=2) and soft bottoms (n=3) at Dodman Island and Blaiklock Island. Basal resources and benthic invertebrates (n=410, 49 morphospecies) were collected for carbon and nitrogen stable isotope analysis to explore differences in food webs structure between macroalgae forests and soft bottoms, addressing three questions: 1) Are sympagic algae more crucial as basal resources in one of the two habitats? 2) Is there a difference in trophic diversity between macroalgae forests and soft bottoms? 3) How does the vertical food web structure differ between the two habitats? In soft bottoms communities, consumers’ stable isotopes ratios showed a switch toward higher δ¹³C values, typical of sympagic algae in Antarctica. This may suggest a higher vulnerability of WAP soft bottoms communities to alterations of sympagic algae dynamics. Trophic diversity was generally higher in communities with a wider range of basal resources. However, significant local-scale variations in trophic diversity surpassed habitat-related differences, limiting conclusions about habitat influence on trophic diversity. Finally, soft bottoms consumers tended to occupy a higher trophic position than those in macroalgae forests, resulting in a higher mean trophic position at the community scale. This could reflect a diet shift by generalist invertebrates—common in Antarctica—towards increased consumption of more degraded organic matter or necrophagy in habitats with fewer basal resources. Overall, these results underscore the complexity of trophic dynamics in Antarctica, where both local variability and large-scale environmental changes influence food web structure and community resilience to climate change.
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 Ecology of ostracods inhabiting groundwater in Benin, West Africa, with potential use of stygobites as indicators for groundwater quality
Ostracods are significant members of groundwater ecosystems, affected by both abiotic environmental factors and biotic interactions. This study investigates the factors influencing ostracod communities in groundwater from dug wells in several regions of Benin, West Africa, which experiences chronic anthropogenic disturbances such as nutrient enrichment from sewage and fertilizer infiltration. We evaluated the presence of ostracod species in 219 wells across seven catchment areas, examining 31 predictor variables, which include a variety of water quality parameters, hydrology as well as well closure, usage and type. The influence of these variables was analyzed using distance-based linear models and redundancy analysis. Our research identified 60 ostracod species, which we classified into two ecological groups: 1) 36 stygobitic species from the family Candonidae, which represent an endemic evolutionary radiation, and 2) 24 non-stygobitic species, mostly from the family Cyprididae. Through our analysis, we identified several key factors influencing ostracod community structure, with consistent patterns observed at both species and genus levels. The primary predictors, aside from well descriptors, included water chemical and physical properties, such as electrical conductivity, pH, temperature, and bicarbonate concentration, along with NO2- concentration, a factor not previously demonstrated to be crucial for ostracod assemblages. Elevated nitrite levels in groundwater were found to significantly affect the distribution of stygobites and non-stygobites. Stygobites were notably less frequent in environments with higher NO2- concentrations, likely due to their greater vulnerability to periodic or chronic anthropogenic disturbances compared to non-stygobites. Therefore, we suggest that stygobitic ostracod species, identifiable even at the genus level, have a potential as reliable indicators of groundwater quality in the tropical regions of western Africa.
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 Ostracod radiations
Ostracods presently occur in almost all aquatic habitats, be they freshwater, brackish or marine, surface or groundwater, stagnant or flowing, in large lakes and small phytothelmata, in permanent or temporary pools, as well as in (semi-) terrestrial habitats. Some of these habitats are species-poor, other habitats harbour large numbers of species. Some of these species can be wide-spread (cosmopolitan and even ubiquitous), but others are endemic to a single lake or watershed. Why did speciation in certain ostracod lineages lead to large numbers of species in certain habitats, while other “ostracod lineage vs habitat type” combinations did not lead to such, often spectacular, morphological speciation events? A speciose lineage of ostracods which derived from a single ancestor is called a species flock. In ancient lakes such as Lake Baikal (Siberia, Russia), Lake Tanganyika and Lake Malawi (East Africa), several such ostracod species flocks exist side by side. These ancient lakes are excellent examples where ostracod radiations, including several species flocks, can be studied in situ, in the cradle in which they originated, namely in ostracod lineages such as Cyprideis s.l.and Cytherissa (Cytherideinae) (in Tanganyika and Baikal, respectively) , Gomphocythere (Timiriaseviinae) and Cypridopsis s.l., (Cypridopsinae) (in both Tanganyika and Malawi) to name only a few. Other examples of ostracod radiations are in the subfamily Candonidae in groundwaters in Pilbara (Australia), Texas (USA) and in Benin (West Africa). Several lineages in the family Cyprididae radiated in temporary water bodies on various continents, for example the genus Bennelongia (Cyprididae) in Australia, the genus Sclerocypris in the Megalocypridjnae in Africa and Cypretta and Strandesia in the southern Hemisphere (excluding Antarctica) as a whole. A special case are the species of the genus Elpidium (Timiriaseviinae) occurring in bromeliad phytothelmata in South and Central America. A new field of diversity discovery is in the identification of genetic species, which might not be identifiable based on the phenotype, aka “cryptic species”. Various intrinsic (pertaining to the specific biology) or extrinsic (habitat-related) factors can contribute to large speciation events resulting in ostracod radiations and species flocks. Yet, in some habitats where at least some of the extrinsic factors are present, no vast ostracod species flocks can be found. This is mostly due to historic events, such as in the African lakes Kivu and Turkana.
Located in Library / RBINS Staff Publications 2024
Inproceedings Reference L’occupation humaine du Grognon à Namur au Mésolithique : résultats préliminaires des études archéobotaniques et archéozoologiques
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, 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
Webpublished Reference audio/x-realaudio Elucidating the history of the European crow hybrid zone with paleogenomics. Preliminary Program of the Society for Molecular Biology and Evolution 2024
Located in Library / RBINS Staff Publications 2024
Webpublished Reference Observations of tidal attenuation and amplification in a mangrove forest: channels as conduits
Mangroves are increasingly recognized as an effective nature-based coastal defence strategy. Mangrove trees are proven to reduce the height of propagating long-period waves such as storm tides and extreme sea levels. Existing empirical studies, however, are limited to small scales (~10²-10³ m) or only cover continuous belts of mangroves. Here we present water level measurements along a 20 km channel and in the surrounding mangrove forests for regular neap- and spring tides in a natural mangrove forest in the Guayas Delta, Ecuador. For tides with peak water levels which are high enough to flood the surrounding mangroves, inundation levels reached 45 cm with attenuation rates up to 40 cm/km. Along the entire 20 km channel, however, no attenuation occurred. Instead, we measured amplification with rates varying between 4.3 and 4.6 cm/km. Amplification rates increased with peak water level until water levels were high enough to flood the surrounding mangroves, upon which amplification rates decreased with peak water level. The latter implies that with higher peak levels, such as during an extreme sea level event, the capacity of mangroves to dampen amplification or even attenuate increases.
Located in Library / RBINS Staff Publications 2024
Webpublished Reference Contrasting saltmarsh vegetation impacts under increasing sea level rise rates
The resilience of saltmarshes mainly depends on their ability to gain elevation by sediment accretion to keep pace with sea level rise. While vegetation is known to facilitate sediment accretion at the plant scale by trapping mineral sediments and producing organic matter, the long-term impact at the landscape scale is still poorly understood. Here we use the biogeomorphic model Demeter to reveal contrasting vegetation impacts on spatial patterns of sediment accretion under different sea level rise regimes. Under contemporary sea level rise rates (2-10 mm/yr), vegetation inhibits sediment transport from tidal channels to platform interiors and creates levee-depression patterns. Hence, intertidal platforms accrete slower with vegetation than without, but this trend attenuates with increasing sea level rise rate, as water depth increases, and vegetation drag decreases. Under extreme sea level rise rate (20 mm/yr), platform interiors don’t keep up and turn into open water, while vegetation allows to preserve intertidal levees. Our results help to better understand some basic biophysical mechanisms that will control the fate of coastal wetlands under global climate change.
Located in Library / RBINS Staff Publications 2024