Long-term trends in trait structure of riverine communities facing predation risk increase and trophic resource decline.

Many large European rivers have undergone multiple pressures that have strongly impaired ecosystem functioning at different spatial and temporal scales. Global warming and other environmental changes have favored the success of invasive species, deeply modifying the structure of aquatic communities in large rivers. Some exogenous species could alter trophic interactions within assemblages by increasing the predation risk for potential prey species (top-down effect) and limiting the dynamics of others via resource availability limitation (bottom-up effect). Furthermore, large transboundary rivers are complex aquatic ecosystems that have often been poorly investigated so that data for assessing long-term ecological trends are missing. In this study, we propose an original approach for investigating long-term combined effects of global warming, trophic resource decrease, predation risk, and water quality variations on the trait-based structure of macroinvertebrate and fish assemblages over 26 yr (1985-2011) and 427-km stretch of the river Meuse (France and Belgium). The study of temporal variations in biological, physiological, and ecological traits of macroinvertebrate and fish allowed identifying community trends and distinguishing impacts of environmental perturbations from those induced by biological alterations. We provide evidence, for this large European river, of an increase in water temperature (close to 1°C) and a decrease in phytoplankton biomass (-85%), as well as independent effects of these changes on both invertebrate and fish communities. The reduction of trophic resources in the water column by invasive molluscs has dramatically affected the density of omnivorous fish in favor of invertebrate feeders, while scrapers became the major feeding guild among invertebrates. Macroinvertebrate and fish communities have shifted from large-sized organisms with low fecundity to prolific, small-sized organisms, with early maturity, as a response to increased predation pressure.

Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer).

BACKGROUND: African wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the "genetic health" of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites. RESULTS: The analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (A r ) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (P a ) of 11), low differentiation, and an absence of an inbreeding depression signal (mean F IS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (F IS = 0.062, mean A r = 6.160, P a = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century. CONCLUSIONS: We showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.

Genetic uniformity and long-distance clonal dispersal in the invasive androgenetic Corbicula clams.

The clam genus Corbicula is an interesting model system to study the evolution of reproductive modes as it includes both sexual and asexual (androgenetic) lineages. While the sexual populations are restricted to the native Asian areas, the androgenetic lineages are widely distributed being also found in America and Europe where they form a major aquatic invasive pest. We investigated the genetic diversity of native and invasive Corbicula populations through a worldwide sampling. The use of mitochondrial and nuclear (microsatellite) markers revealed an extremely low diversity in the invasive populations with only four, undiversified, genetic lineages distributed across Europe and America. On the contrary, in the native populations, both sexual and androgenetic lineages exhibited much higher genetic diversity. Remarkably, the most abundant and widely distributed invasive forms, the so-called form A and form R found in America and Europe respectively, are fixed for the same single COI (cytochrome c oxydase subunit I) haplotype and same multilocus genotype. This suggests that form R, observed in Europe since the 1980s, derived directly from form A found in America since the 1920s. In addition, this form shares alleles with some Japanese populations, indicating a Japanese origin for this invasive lineage. Finally, our study suggests that few androgenetic Corbicula individuals successfully invaded the non-native range and then dispersed clonally. This is one striking case of genetic paradox raising the issue of invasive and evolutionary success of genetically undiversified populations.

Time series modelling for wastewater-based epidemiology of COVID-19: A nationwide study in 40 wastewater treatment plants of Belgium, February 2021 to June 2022.

BACKGROUND: Wastewater-based epidemiology (WBE) has been implemented to monitor surges of COVID-19. Yet, multiple factors impede the usefulness of WBE and quantitative adjustment may be required. AIM: We aimed to model the relationship between WBE data and incident COVID-19 cases, while adjusting for confounders and autocorrelation. METHODS: This nationwide WBE study includes data from 40 wastewater treatment plants (WWTPs) in Belgium (02/2021-06/2022). We applied ARIMA-based modelling to assess the effect of daily flow rate, pepper mild mottle virus (PMMoV) concentration, a measure of human faeces in wastewater, and variants (alpha, delta, and omicron strains) on SARS-CoV-2 RNA levels in wastewater. Secondly, adjusted WBE metrics at different lag times were used to predict incident COVID-19 cases. Model selection was based on AICc minimization. RESULTS: In 33/40 WWTPs, RNA levels were best explained by incident cases, flow rate, and PMMoV. Flow rate and PMMoV were associated with -13.0 % (95 % prediction interval: -26.1 to +0.2 %) and +13.0 % (95 % prediction interval: +5.1 to +21.0 %) change in RNA levels per SD increase, respectively. In 38/40 WWTPs, variants did not explain variability in RNA levels independent of cases. Furthermore, our study shows that RNA levels can lead incident cases by at least one week in 15/40 WWTPs. The median population size of leading WWTPs was 85.1 % larger than that of non­leading WWTPs. In 17/40 WWTPs, however, RNA levels did not lead or explain incident cases in addition to autocorrelation. CONCLUSION: This study provides quantitative insights into key determinants of WBE, including the effects of wastewater flow rate, PMMoV, and variants. Substantial inter-WWTP variability was observed in terms of explaining incident cases. These findings are of practical importance to WBE practitioners and show that the early-warning potential of WBE is WWTP-specific and needs validation.

SARS-CoV-2 Surveillance in Belgian Wastewaters.

Wastewater-based surveillance was conducted by the national public health authority to monitor SARS-CoV-2 circulation in the Belgian population. Over 5 million inhabitants representing 45% of the Belgian population were monitored throughout 42 wastewater treatment plants for 15 months comprising three major virus waves. During the entire period, a high correlation was observed between the daily new COVID-19 cases and the SARS-CoV-2 concentration in wastewater corrected for rain impact and covered population size. Three alerting indicators were included in the weekly epidemiological assessment: High Circulation, Fast Increase, and Increasing Trend. These indicators were computed on normalized concentrations per individual treatment plant to allow for a comparison with a reference period as well as between analyses performed by distinct laboratories. When the indicators were not corrected for rain impact, rainy events caused an underestimation of the indicators. Despite this negative impact, the indicators permitted us to effectively monitor the evolution of the fourth virus wave and were considered complementary and valuable information to conventional epidemiological indicators in the weekly wastewater reports communicated to the National Risk Assessment Group.

Phylogeny and androgenesis in the invasive Corbicula clams (Bivalvia, Corbiculidae) in Western Europe.

BACKGROUND: The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with American and Asian Corbicula clams. We studied several populations from West European river basins (Meuse, Seine, Rhine and Rhône) through an "integrative taxonomy" approach. We combined morphology, partial mitochondrial COI and cyt b sequences and eleven microsatellite loci. Furthermore, we looked for discrepancies between mtDNA and nrDNA/morphology, indicative of androgenesis between lineages. RESULTS: There are three Corbicula morphotypes in Western Europe associated to three mitochondrial lineages and three genotypes. Form R shares the same COI haplotype as the American form A and the Japanese C. leana. Form S and the American form C have the same haplotype, although their morphologies seem divergent. The European form Rlc belongs to the same mitochondrial lineage as both the American form B and the Asian C. fluminea.Interestingly, within each haplotype/genotype or lineage, no genetic diversity was found although their invasive success is high. Moreover, we detected rare mismatches between mtDNA and nrDNA/morphology, indicative of androgenesis and mitochondrial capture between form R and form S and therefore challenging the phylogenetic relatedness and the species status within this genus. The global phylogenetic analysis revealed that the sexual Corbicula lineages seem restricted to the native areas while their androgenetic relatives are widespread and highly invasive. CONCLUSIONS: We clarified the discrepancies and incongruent results found in the literature about the European morphotypes of Corbicula and associated mitochondrial lineages. The three West European morphotypes belong to three distinct nuclear and mitochondrial lineages. However mitochondrial capture occurs in sympatric populations of forms R and S. The species status of the morphotypes therefore remains doubtful. Moreover the androgenetic lineages seem widely distributed compared to their sexual relatives, suggesting that androgenesis and invasive success may be linked in the genus Corbicula.

A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species.

The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.

Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia).

The zebra mussel (Dreissena polymorpha) and the quagga mussel (Dreissena rostriformis bugensis) are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit I mitochondrial gene (COI) is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals.