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Ecosystems of Lake Victoria and riparian communities have been strongly disrupted by the introduction of the invasive Nile perch and its fishing industry. Beyond this invasion and other recent anthropogenic stressors, the Lake Victoria ecoregion also underwent phases of pronounced aridity over the Late Pleistocene, lastly during the Last Glacial Maximum (LGM). The consequences of recent and historic environmental change have been canvassed for the adaptive radiation of haplochromine cichlids occupying the ecoregion, but their effect on freshwater invertebrate diversity remains largely unknown. Here, we use 15 microsatellite loci and approximate Bayesian computation to test whether viviparid gastropods experienced a population bottleneck during the LGM, as did cichlids. Clustering analyses support three viviparid gene pools in the Lake Victoria ecoregion, gathering specimens from 1) Lake Albert and the White Nile, 2) the Victoria Nile and Lake Kyoga and 3) Lake Victoria and tributaries. The last group contains the highest genetic diversity, but all groups have a considerable number of private alleles and are inferred to predate the LGM. Examinations of demographic history reveal a 190- to 500-fold population decline that started ~ 125-150 ka ago, thus substantially before the LGM bottleneck documented in haplochromine cichlids. Population collapses in viviparids are an order of magnitude more severe than declines in cichlids and have not been halted by the re-establishment of freshwater ecosystems since the LGM. Recent anthropogenic ecosystem deterioration is causing homogenization of previously diversified microhabitats, which may contribute to (local) extinction and enhanced gene flow among species within gene pools., (© 2020 John Wiley & Sons Ltd.)

Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographical setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity., (© 2017 The Author(s).)

Background: Non-indigenous taxa currently represent a large fraction of the species and biomass of freshwater ecosystems. The accumulation of invasive taxa in combination with other stressors in these ecosystems may alter the habitats to which native taxa are adapted, which could elicit evolutionary changes in native populations and their ecological interactions. Assessing ecological and evolutionary consequences of invasions simultaneously may therefore be the most effective approach to study taxa with complex invasion histories. Here we apply such an integrated approach to the cerithioid gastropod Melanoides tuberculata, a model system in invasion biology., Results: Molecular phylogenetics and ancestral range reconstructions allowed us to identify several independent Asian invasions in Lakes Malawi and Tanganyika, the Congo River, Nigeria and Cameroon. Some invasive M. tuberculata populations display much variation in shell morphology, and overlap in morphospace with M. tuberculata populations native to Africa. Experiments confirmed great ecophenotyic plasticity in some invasive populations, which, in combination with the overlap in disparity with native populations, masks invaders and their dispersal through Africa. Finally, the results of geographic modeling indicate that cryptic M. tuberculata invasions occurred primarily in densely populated areas., Conclusions: We reveal the continental nature of invasions of Asian M. tuberculata to Africa. Several of the affected ecosystems have high endemicity in Cerithioidea: Lake Tanganyika has an unparalleled diversity in freshwater cerithioids (>10 endemic genera) and the Congo Basin and Lake Malawi are home to the two largest endemic species clusters of Melanoides in Africa (~12 and ~8 species, respectively). Cerithioids perform ecologically important functions in the benthic ecosystems of African freshwaters, but invaders and ecosystem change pose risks to their native diversity. We draw suggestions for more effective conservation strategies from our integrated approach.

Evolutionary processes leading to adaptive radiation regularly occur too fast to be accurately recorded in the fossil record but too slowly to be readily observed in living biota. The study of evolutionary radiations is thereby confronted with an epistemological gap between the timescales and approaches used by neontologists and paleontologists. Here we report on an ongoing radiation of extant Bellamya species (n = 4) from the African Rift Lake Malawi that provides an unusual opportunity to bridge this gap. The substantial molecular differentiation in this monophyletic Bellamya clade has arisen since Late Pleistocene megadroughts in the Malawi Basin caused by climate change. Morphological time-series analysis of a high-resolution, radiocarbon-dated sequence of 22 faunas spanning the Holocene documents stasis up to the middle Holocene in all traits studied (shell height, number of whorls, and two variables obtained from geometric morphometrics). Between deposition of the last fossil fauna (~5 ka) and the present day, a drastic increase in morphological disparity was observed (3.7-5.8 times) associated with an increase in species diversity. Comparison of the rates of morphological evolution obtained from the paleontological time-series with phylogenetic rates indicates that the divergence in two traits could be reconstructed with the slow rates documented in the fossils, that one trait required a rate reduction (stabilizing selection), and the other faster rates (divergent selection). The combined paleontological and comparative approach taken here allows recognition that morphological stasis can be the dominant evolutionary pattern within species lineages, even in very young and radiating clades., Competing Interests: The authors declare no conflict of interest.

Studies on environmental changes provide important insights into modes of speciation, into the (adaptive) reoccupation of ecological niches and into species turnover. Against this background, we here examine the history of the gastropod genus Lanistes in the African Rift Lake Malawi, guided by four general evolutionary scenarios, and compare it with patterns reported from other endemic Malawian rift taxa. Based on an integrated approach using a mitochondrial DNA phylogeny and a trait-specific molecular clock in combination with insights from the fossil record and palaeoenvironmental data, we demonstrate that the accumulation of extant molecular diversity in the endemic group did not start before approximately 600,000 years ago from a single lineage. Fossils of the genus from the Malawi Rift, however, are over one million years older. We argue that severe drops in the lake level of Lake Malawi in the Pleistocene offer a potential explanation for this pattern. Our results also challenge previously established phylogenetic relationships within the genus by revealing parallel evolution and providing evidence that the endemic Lanistes species are not restricted to the lake proper but are present throughout the Malawi Rift.

A running controversy in evolutionary thought was Eldredge and Gould's punctuated equilibrium model, which proposes long periods of morphological stasis interspersed with rapid bursts of dramatic evolutionary change. One of the earliest and most iconic pieces of research in support of punctuated equilibrium is the work of Williamson on the Plio-Pleistocene molluscs of the Turkana Basin. Williamson claimed to have found firm evidence for three episodes of rapid evolutionary change separated by long periods of stasis in a high-resolution sequence. Most of the discussions following this report centered on the topics of (eco)phenotype versus genotype and the possible presence of preservational and temporal artifacts. The debate proved inconclusive, leaving Williamson's reports as one of the empirical foundations of the paradigm of punctuated equilibrium. Here we conclusively show Williamson's original interpretations to be highly flawed. The supposed rapid bursts of punctuated evolutionary change represent artifacts resulting from the invasion of extrabasinal faunal elements in the Turkana palaeolakes during wet phases well known from elsewhere in Africa.

Several methodological issues currently hamper the study of entire trematode communities within populations of their intermediate snail hosts. Here we develop a new workflow using high‐throughput amplicon sequencing to simultaneously genotype snail hosts and their infecting trematode parasites. We designed primers to amplify four snail and five trematode markers in a single multiplex PCR. While also applicable to other genera, we focused on medically and economically important snail genera within the superorder Hygrophila and targeted a broad taxonomic range of parasites within the class Trematoda. We tested the workflow using 417 Biomphalaria glabrata specimens experimentally infected with Schistosoma rodhaini, two strains of Schistosoma mansoni and combinations thereof. We evaluated the reliability of infection diagnostics, the robustness of the workflow, its specificity related to host and parasite identification, and the sensitivity to detect co‐infections, immature infections and changes of parasite biomass during the infection process. Finally, we investigated its applicability in wild‐caught snails of other genera naturally infected with a diverse range of trematodes. After stringent quality control the workflow allows the identification of snails to species level, and of trematodes to taxonomic levels ranging from family to strain. It is sensitive to detect immature infections and changes in parasite biomass described in previous experimental studies. Co‐infections were successfully identified, opening the possibility to examine parasite–parasite interactions such as interspecific competition. Together, these results demonstrate that our workflow provides a powerful tool to analyse the processes shaping trematode communities within natural snail populations. [ABSTRACT FROM AUTHOR]

Aim: The roles of geodynamics, climatic variability and landscape evolution in shaping aquatic biodiversity patterns on the African continent remain poorly understood. We studied the geographical origin and phylogenetic relationships of an Afrotropical freshwater snail genus to examine the role of drainage evolution on diversification and range evolution. The relevance of fish provinces in bio‐regionalization of invertebrates was explored, as well as the evolution of habitat specificity. Location: Africa including Madagascar. Taxon: Lanistes (Gastropoda: Ampullariidae). Methods: Based on a sampling covering the entire geographical range, we reconstructed a fossil‐calibrated multi‐locus molecular phylogeny using maximum likelihood and Bayesian inference approaches. After applying species delimitation methods, we estimated ancestral areas and habitats and examined rates of diversification through time using lineage through time plots. Results: RAxML and MrBayes analyses resulted in highly congruent topologies and a strongly supported phylogeny. Our BEAST analysis indicate that Lanistes probably originated in the Eocene about 50 Ma and the most recent common ancestor (MRCA) of all 23 Lanistes OTUs in our study may have inhabited an area including the Central African and adjacent Lower Guinean biogeographical regions. A steeper increase in species accumulation from the middle Miocene (c. 15 to 10 Ma), followed by a decrease towards the present was found. Sympatry and jump dispersal were the common cladogenetic events and only a single anagenetic dispersal event was detected. The biogeographical analyses further suggest that Madagascar was colonized from East Africa and that the Zambezi River was colonized at least twice independently. Seven species are confined to rivers and three live exclusively in lakes. The estimation of ancestral habitats suggested that the MRCA of all Lanistes probably evolved in a riverine habitat. Main conclusions: The diversification of Lanistes started in the Eocene and occurred at a constant pace apart from a possible climate‐related increase in the Miocene. This study highlights the significance of temporal geographical isolation of river systems and subsequent reconnection in clade diversification and of jump dispersal in range evolution. More comparative analyses across various taxa are needed to obtain a better understanding of African freshwater biodiversity. [ABSTRACT FROM AUTHOR]

Currently no comprehensive checklist of fresh and brackish water gastropods from Bénin exists, and those for adjacent West African areas are outdated. Yet, such checklists provide essential biodiversity information and a consistent taxonomic and nomenclatural framework for that biodiversity. Here a first checklist of the fresh and brackish water gastropods from Bénin and adjacent West African ecoregions is presented, based on an extensive literature review and field surveys between September 2014 and June 2019 in six major fresh and brackish water ecosystems in Bénin. This inventory includes information on synonymy, species distribution in West Africa, habitats, and conservation status. The fresh and brackish water gastropod fauna includes 60 species, belonging to 28 genera and 16 families. Pachychilidae, Ampullariidae, Neritidae, and Bulinidae were the most diverse families with 9, 8, 7, and 7 species, respectively. However, literature and field data indicated that 23 species observed in West African basins that extend to Bénin do not occur in the territory of Bénin. These species were not detected in our field surveys, most likely because they are rare at collecting sites. Of the 60 species included, five are classified as "Data Deficient", 43 as "Least Concern", two as "Nearly Threatened", one as "Vulnerable", and six as "Endangered" by the IUCN, whereas the remaining three species were not evaluated. Because the taxonomy of fresh and brackish water gastropods in West Africa is still largely based on morphology, comparative molecular and taxonomic studies may result in substantial revisions of this checklist over the coming years. [ABSTRACT FROM AUTHOR]

Background: Ecological speciation is a prominent mechanism of diversification but in many evolutionary radiations, particularly in invertebrates, it remains unclear whether supposedly critical ecological traits drove or facilitated diversification. As a result, we lack accurate knowledge on the drivers of diversification for most evolutionary radiations along the tree of life. Freshwater mollusks present an enigmatic example: Putatively adaptive radiations are being described in various families, typically from long-lived lakes, whereas other taxa represent celebrated model systems in the study of ecophenotypic plasticity. Here we examine determinants of shell-shape variation in three nominal species of an ongoing ampullariid radiation in the Malawi Basin (Lanistes nyassanus, L. solidus and Lanistes sp. (ovum-like)) with a common garden experiment and semi-landmark morphometrics. Results: We found significant differences in survival and fecundity among these species in contrasting habitats. Morphological differences observed in the wild persisted in our experiments for L. nyassanus versus L. solidus and L. sp. (ovum-like), but differences between L. solidus and L. sp. (ovum-like) disappeared and re-emerged in the F1 and F2 generations, respectively. These results indicate that plasticity occurred, but that it is not solely responsible for the observed differences. Our experiments provide the first unambiguous evidence for genetic divergence in shell morphology in an ongoing freshwater gastropod radiation in association with marked fitness differences among species under controlled habitat conditions. Conclusions: Our results indicate that differences in shell morphology among Lanistes species occupying different habitats have an adaptive value. These results also facilitate an accurate reinterpretation of morphological variation in fossil Lanistes radiations, and thus macroevolutionary dynamics. Finally, our work testifies that the shells of freshwater gastropods may retain signatures of adaptation at low taxonomic levels, beyond representing an evolutionary novelty responsible for much of the diversity and disparity in mollusks altogether. [ABSTRACT FROM AUTHOR]

Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographical setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity. [ABSTRACT FROM AUTHOR]

Biotic invasions can have far-reaching effects in isolated, eco-insular systems such as the African Great Lakes, certainly in synergy with other anthropogenic stressors that affect ecosystem stability. Interactions between invasive and indigenous taxa across trophic levels often tend to propagate throughout the ecosystem, but also those at the same trophic level may affect biodiversity. Here, we examine faunal interactions between an invasive Asian morph of the cerithioidean gastropod Melanoides tuberculata and indigenous gastropods in long-lived Lake Malawi. Studying quantitative samples, we document a negative spatial correlation between the established invader and endemic Melanoides species, and positive ones between invasive and native M. tuberculata, and between native Melanoides and schistosome-transmitting Bulinus. Comparison of modern and fossil samples indicates that Melanoides communities have changed since the middle Holocene from consisting predominantly of endemic taxa (~95%) toward a dominance by non-endemics (~80%). External evidence suggests that ecosystem change, such as increased sedimentation and eutrophication, and interactions between the invasive and endemic Melanoides species are the most likely causes for these changes. More in-depth study of the benthic ecosystem is required to document interaction mechanisms better, but the invasive taxon is playing an important role in reshaping communities and diversity in Lake Malawi. [ABSTRACT FROM AUTHOR]

1. Ancient, deep lakes have traditionally been considered as stable, ecological islands, well buffered from environmental change because of their great depth. However, they are not immune to anthropogenic and climatic stress. Ecosystems of the permanently stratified warm Lakes Malawi and Tanganyika in the Great East African Rift are particularly delicate. Their stratification regime has historically limited the distribution of benthic biota to a 'bathtub ring of biodiversity', namely substrata in the upper, oxygenated water layer. 2. We use historical data on the endemic deep-water molluscs of these lakes to assess present-day stress on their benthic ecosystems. During the 20th century, these molluscs have probably decreased in abundance and migrated to shallower water. 3. These apparent trends have a significance beyond species-based conservation, foremost because deep-water organisms heavily rely on the position and temporal stability of the oxycline and therefore provide an early warning of large-scale changes in the distribution of dissolved oxygen. Oxygen demands have increased in the East African Great Lakes over the last century whereas ventilation of deep water has remained the same or declined. 4. The combination of these factors is resulting in a narrowing of the ring of biodiversity and a changed nutrient flux through this ring. Reduction in the habitat available inevitably puts biota at risk, whereas changes in nutrient flux may cause shifts in the entire ecosystem or the collapse of parts of it. 5. Considering the socioeconomic value of these lakes and the potentially grave implications for their faunal biodiversity and entire ecosystems, existing evidence of faunal decline, especially in taxa that depend strongly on the stratification regime, is of great concern. Moreover, because the factors responsible are widespread and include surface-water warming, increased run-off and eutrophication, respiration stress may also develop in other tropical and subtropical lakes. [ABSTRACT FROM AUTHOR]

Background: Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) are globally distributed in tropical and subtropical freshwater ecosystems and many species are ecologically and economically important. Ampullariids exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including the biogeography of native and invasive populations. The limited availability of genomic data, however, hinders in-depth ecological and evolutionary studies of these non-model organisms. Results: Using Illumina Hiseq platforms, we sequenced 1220 million reads for seven species of apple snails. Together with the previously published RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species that belong to five genera of Ampullariidae, two of which represent Old World lineages and the other three New World lineages. There were 20,730 to 35,828 unigenes with predicted open reading frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1320 to 1803 bp. 69.7% to 80.2% of these unigenes were functionally annotated by searching against NCBI’s non-redundant, Gene Ontology database and the Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST functionality for DNA/protein sequences, keyword searching for unigenes/functional terms, and download functions for sequences and whole transcriptomes. Conclusions: In summary, we have generated comprehensive transcriptome data for multiple ampullariid genera and species, and created a publicly accessible database with a user-friendly interface to facilitate future basic and applied studies on ampullariids, and comparative molecular studies with other invertebrates. [ABSTRACT FROM AUTHOR]

• Mollusc community ecology analysis using SOM and machine learning models. • SOM in conjunction with IndVal, LDA and RF models are effective tools. • Mollusc assemblages are structured by physicochemical variables related to the river–estuary continuum. • Progressively downstream ward habitats faced to increasing anthropogenic stress. • Our approach can likely be applied for a variety of freshwater systems. The poor understanding of changes in mollusc ecology along rivers, especially in West Africa, hampers the implementation of management measures. We used a self–organizing map, indicator species analysis, linear discriminant analysis and a random forest model to distinguish mollusc assemblages, to determine the ecological preferences of individual mollusc species and to associate major physicochemical variables with mollusc assemblages and occurrences in the Sô River Basin, Benin. We identified four mollusc assemblages along an upstream–downstream gradient. Dissolved oxygen (DO), biochemical oxygen demand (BOD), salinity, calcium (Ca), total nitrogen (TN), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd) and mercury (Hg) were the major physicochemical variables responsible for structuring these mollusc assemblages. However, the physicochemical factors responsible for shaping the distribution of individual species varied per species. Upstream sites (assemblage I) showed high DO and low BOD and mineral compounds (i.e., TN, salinity, and Ca), which are primarily responsible for structuring the occurrences of bivalves (Afropisidium pirothi , Etheria elliptica , Sphaerium hartmanni) and the gastropod Lanistes varicus. Sites along the middle reach (assemblage II) were characterised by a high degree of organic pollution but low heavy metal pollution; we detected no specific mollusc indicator species. Downstream sites (assemblage III) displayed high mineral and heavy metal concentrations and a fauna without specific indicator species. Finally, downstream sites associated with brackish water (assemblage IV) displayed important levels of organic and heavy metal pollution. These sites are dominated by diverse gastropods (i.e., Bulinus spp., Gabbiella africana , Indoplanorbis exustus , Pachymelania fusca , Radix natalensis , Stenophysa marmorata and Tympanotonos fuscatus). Our results highlight that mollusc communities in the Sô River Basin are structured by key physicochemical variables related to the river–estuary continuum. Habitats that are progressively more downstream are confronted with increasing anthropogenic stress. Conservation and management plans should focus on downstream habitats. [ABSTRACT FROM AUTHOR]