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Ecology of ostracods inhabiting groundwater in Benin, West Africa, with potential use of stygobites as indicators for groundwater quality
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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.
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Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
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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.
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Ostracod radiations
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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.
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L’occupation humaine du Grognon à Namur au Mésolithique : résultats préliminaires des études archéobotaniques et archéozoologiques
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Comparing the transposon landscapes of a putative ancient asexual and a sexual non-marine ostracod (Crustacea, Arthropoda)
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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.
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Elucidating the history of the European crow hybrid zone with paleogenomics. Preliminary Program of the Society for Molecular Biology and Evolution 2024
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Observations of tidal attenuation and amplification in a mangrove forest: channels as conduits
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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.
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Contrasting saltmarsh vegetation impacts under increasing sea level rise rates
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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.
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Coastal marsh resilience: a study on the role of bio-geomorphic self-organization
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Tidal marshes are valuable coastal ecosystems that are threatened by global climate warming and the resulting sea level rise. Whether they drown or continue to exist, depends on the trapping of sediments that builds up the land surface. Tidal channel networks, which typically occur within tidal marshes, are the major supply routes for sediments towards the marshes and hence are expected to affect the capacity of marshes to keep up with sea level rise by sediment trapping. The development and evolution of tidal channel networks and the sediment trapping are locally determined by so-called bio-geomorphic interactions between plants, water flow and sediment transport. However, the effect of different environmental variables on channel network formation remains poorly understood. In this research, we investigated the impact of spatio-temporal plant colonization patterns by means of flume experiments. Four scaled landscape scale experiments were conducted in the Metronome tidal facility, a unique flume that tilts periodically to generate tidal currents. Two control experiments without vegetation, a third experiment with a channel-fringing vegetation colonization pattern, and a fourth with patchy vegetation colonization pattern. Seeds were distributed by water in the channel-fringing experiment, while a manual sowing method was used to obtain laterally expanding circular patches in the patchy experiment. Our results show that vegetation and their respective colonization pattern affect channel network formation both on a landscape scale and local scale. More extensive and effective channel networks are found in vegetation experiments. These results indicate that channel-fringing or patchy recruitment strategies might produce landscapes that are more resilient to sea level rise.
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How does landscape vegetation configuration regulate local channel initiation in rapidly expanding marsh?
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Biogeomorphic interactions between tidal channels and marsh plants play a crucial role in enhancing coastal resilience to climate change. Previous studies linking the channel formation with vegetation dynamics predominantly focused on the early initiation, characterized by local-scale plant-flow feedbacks. However, the influence of rapid changes in landscape-scale vegetation pattern on the channel initiation remains poorly understood, especially in micro-tidal system. In this study, we investigated this relationship through biogeomorphic modeling combined with the analysis of satellite images in a rapidly expanding marsh in China under Spartina alterniflora invasion. The satellite images demonstrated the increase in drainage density and the decrease in unchanneled path length following plant encroachment. Our modeling results showed that local flow acceleration between vegetation patches was insufficient to initiate channels rapidly before the merging of isolated patches under micro-tidal conditions. With plant expansion, the continuous marsh caused landscape flow diversion from homogenous platform flow to concentrated channel flow, which promoted evident tributary channel initiation in the landward marsh zone. The vegetation removal scenarios further highlighted that the flow divergence from adjacent platforms due to the spatial heterogeneity in plant configuration amplified the magnitude of local hydrodynamics and further channel incision. Our findings emphasize that the initiation of tidal channels not only depends on local plant-flow interaction but is largely driven by landscape vegetation configuration under micro-tidal conditions.
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