Differential Stage-Specific Mortality as a Mechanism for Diversification

AbstractIndividual variability in mortality is widespread in nature. The general rule is that larger organisms have a greater chance of survival than smaller conspecifics. There is growing evidence that differential mortality between developmental stages has important consequences for the ecology and evolution of populations and communities. However, we know little about how it can influence diversification. Using an eco-evolutionary model of diversification that considers individual variability in mortality, I show that commonly observed differences in mortality between juveniles and adults can facilitate adaptive diversification. In particular, diversification is expected to be less restricted when mortality is more biased toward juveniles. Additionally, I find stage-specific differences in metabolic cost and foraging capacity to further facilitate diversification when adults are slightly superior competitors, due to either a lower metabolic cost or a higher foraging capacity, than juveniles. This is because by altering the population composition, differential stage-specific mortality and competitive ability can modulate the strength of intraspecific competition, which in turn determines the outcome of diversification. These results demonstrate the strong influence that ecological differences between developmental stages have on diversification and highlight the need for integrating developmental processes into diversification theory.

Mitogenomes do not substantially improve phylogenetic resolution in a young non-model adaptive radiation of freshwater gastropods

BACKGROUND

Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups.

RESULTS

Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression.

CONCLUSIONS

This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.

A machine learning approach for modeling the occurrence of the major intermediate hosts for schistosomiasis in East Africa

Schistosomiasis, a prevalent water-borne disease second only to malaria, significantly impacts impoverished rural communities, primarily in Sub-Saharan Africa where over 90% of the severely affected population resides. The disease, majorly caused by Schistosoma mansoni and S. haematobium parasites, relies on freshwater snails, specifically Biomphalaria and Bulinus species, as crucial intermediate host (IH) snails. Targeted snail control is advisable, however, there is still limited knowledge about the community structure of the two genera especially in East Africa. Utilizing a machine learning approach, we employed random forest to identify key features influencing the distribution of both IH snails in this region. Our results reveal geography and climate as primary factors for Biomphalaria, while Bulinus occurrence is additionally influenced by soil clay content and nitrogen concentration. Favorable climate conditions indicate a high prevalence of IHs in East Africa, while the intricate connection with geography might signify either dispersal limitations or environmental filtering. Predicted probabilities demonstrate non-linear patterns, with Bulinus being more likely to occur than Biomphalaria in the region. This study provides foundational framework insights for targeted schistosomiasis prevention and control strategies in the region, assisting health workers and policymakers in their efforts.

The fossil record of freshwater Gastropoda - a global review

Gastropoda are an exceptionally successful group with a rich and diverse fossil record. They have conquered land and freshwater habitats multiple times independently and have dispersed across the entire globe. Since they are important constituents of fossil assemblages, they are often used for palaeoecological reconstruction, biostratigraphic correlations, and as model groups to study morphological and taxonomic evolution. While marine faunas and their evolution have been a common subject of study, the freshwater component of the fossil record has attracted much less attention, and a global overview is lacking. Here, I review the fossil record of freshwater gastropods on a global scale, ranging from their origins in the late Palaeozoic to the Pleistocene. As compiled here, the global fossil record of freshwater Gastropoda includes 5182 species in 490 genera, 44 families, and 12 superfamilies over a total of ~340 million years. Following a slow and poorly known start in the late Palaeozoic, diversity slowly increased during the Mesozoic. Diversity culminated in an all-time high in the Neogene, relating to diversification in numerous long-lived (ancient) lakes in Europe. I summarise well-documented and hypothesised freshwater colonisation events and compare the patterns found in freshwater gastropods to those in land snails. Furthermore, I discuss potential preservation and sampling biases, as well as the main drivers underlying species diversification in fresh water on a larger scale. In that context, I particularly highlight the importance of long-lived lakes as islands and archives of evolution and expand a well-known concept in ecology and evolution to a broader spectrum: scale-independent ecological opportunity.

Aridity, availability of drinking water and freshwater foods, and hominin and archeological sites during the Late Pliocene-Early Pleistocene in the western region of the Turkana Basin (Kenya): A review

Although the Turkana Basin is one of the driest regions of the East African Rift, its Plio-Pleistocene sediments are rich in freshwater vertebrates and invertebrates, providing evidence that freshwater resources were available to hominins in this region during the Plio-Pleistocene (4.2-0.7 Ma). Here we provide an overview of the hydroconnectivity of the Turkana Basin. We then review the period during which freshwater river and lake systems expanded into the western region of the Turkana Basin, where hominin and archeological sites have been discovered in sediments dating back to the Late Pliocene-Pleistocene. Freshwater conditions are reconstructed from river and lake sediments and the flora and micro- and macofauna they contain. Data synthesis suggests that drinking water and freshwater foods prevailed in the western region of the Turkana Basin at 4.20-3.98 Ma, 3.70-3.10 Ma, 2.53-2.22 Ma, then between 2.10 and 1.30 Ma and intermittently from 1.27 to 0.75 Ma. Milestones in hominin evolution occurred in this context, such as the first occurrence of Australopithecus anamensis (4.20-4.10 Ma) and Kenyanthropus platyops (3.50 Ma and 3.30-3.20 Ma), the presence of Paranthropus aethiopicus (2.53-2.45 Ma), early Homo (2.33 Ma), Paranthropus boisei (2.25 Ma and 1.77-1.72 Ma) and Homo ergaster/Homo erectus (1.75 Ma, 1.47-1.42 Ma and 1.10-0.90 Ma). Developments in hominin behavior also occurred during this timeframe, including the first known stone tools (3.30 Ma), the oldest Oldowan sites (2.34 Ma and 2.25 Ma) in the Turkana Basin, the earliest known evidence for the emergence of bifacial shaping in eastern Africa (1.80 Ma), and the first known Acheulean site (1.76 Ma). Our synthesis suggests that, diachronic variation in hydroconnectivity played a role on the amount of drinking water and freshwater foods available in the western region of the Turkana Basin, despite regional aridity.

Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids

Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.

Support for a radiation of free-living flatworms in the African Great Lakes region and the description of five new Macrostomum species

BACKGROUND

The African Great Lakes have long been recognized as an excellent location to study speciation. Most famously, cichlid fishes have radiated in Lake Tanganyika and subsequently spread into Lake Malawi and Lake Victoria, where they again radiated. Other taxa have diversified in these lakes, such as catfish, ostracods, gastropods, and Monegenean gill parasites of cichlids. However, these radiations have received less attention, and the process leading to their speciation in this unique region remains to be further explored. Here I present evidence that suggests a radiation of Macrostomum flatworms has occurred in the African Great Lakes region, offering a good opportunity for such investigations.

RESULTS

Recent field work has revealed a monophyletic clade of 16 Macrostomum flatworms that have, to date, only been collected from Lake Tanganyika. Additionally, a species collected from Lake Malawi was found nested within this clade. Molecular phylogenetic analysis, largely based on transcriptome data, suggests that this clade underwent rapid speciation, possibly due to a large habitat diversity in the lake. I also observed significant differences in the sperm morphology of these flatworms compared to those of species found outside Lake Tanganyika and Lake Malawi. These included the elongation of an anterior structure, a reduction in the size of the lateral sperm bristles, and changes in relative proportions. I propose functional hypotheses for these changes in sperm design, and formally describe Macrostomum gracilistylum sp. nov from Lake Malawi and its sister species Macrostomum crassum sp. nov., Macrostomum pellitum sp. nov., Macrostomum longispermatum sp. nov., and Macrostomum schäreri sp. nov., from Lake Tanganyika.

CONCLUSIONS

The available evidence is consistent with the hypothesis that Macrostomum flatworms have radiated in Lake Tanganyika and subsequently spread to Lake Malawi. However, whether this represents a bona fide adaptive radiation still needs to be determined. Therefore, the African Great Lakes are promising targets for further research into flatworm diversity and speciation.

Epidemiology of free-living amoebae infections in Africa: a review

FLA-related conditions are a rare medical occurrence. Despite their rarity, they are considered a public health concern for two reasons: the absence of a regular treatment regimen in the case of central nervous system infections and the fast progression of the symptoms leading to fatal outcomes. A total of 358 articles were retrieved from different databases (91 from PubMed, 26 from NCBI, 138 from Academia, 102 from Science Direct, and one from IJMED). 7 (46.6%) clinical cases came from Egypt, 2 (13.3%) cases of FLA infection came from Nigeria, 3 (20%) cases came from the Gambia, and 1 (6.6%) case was reported from African countries like Algeria, Tunisia, South Africa, and Zambia. Medical conditions caused by free-living amoeba are considered significant public health concerns. These ubiquitous organisms can cause both fatal and debilitating health conditions. Immediate diagnosis of cases and proper hygienic practices are necessary to provide direct medical intervention. They may be the key to reducing the morbidity and mortality rates from FLA-acquired infections. Although several government-led initiatives have been implemented to mitigate a plethora of parasitic diseases, the case of FLA-related conditions in African countries has yet to be realized.

Monitoring biodiversity loss in rapidly changing Afrotropical ecosystems: an emerging imperative for governance and research

Africa is experiencing extensive biodiversity loss due to rapid changes in the environment, where natural resources constitute the main instrument for socioeconomic development and a mainstay source of livelihoods for an increasing population. Lack of data and information deficiency on biodiversity, but also budget constraints and insufficient financial and technical capacity, impede sound policy design and effective implementation of conservation and management measures. The problem is further exacerbated by the lack of harmonized indicators and databases to assess conservation needs and monitor biodiversity losses. We review challenges with biodiversity data (availability, quality, usability and database access) as a key limiting factor that impacts funding and governance. We also evaluate the drivers of both ecosystems change and biodiversity loss as a central piece of knowledge to develop and implement effective policies. While the continent focuses more on the latter, we argue that the two are complementary in shaping restoration and management solutions. We thus underscore the importance of establishing monitoring programmes focusing on biodiversity-ecosystem linkages in order to inform evidence-based decisions in ecosystem conservation and restoration in Africa. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Meta-analysis reveals cyanotoxins risk across African inland waters

Global eutrophication and climate warming exacerbate production of cyanotoxins such as microcystins (MCs), presenting risks to human and animal health. Africa is a continent suffering from severe environmental crises, including MC intoxication, but with very limited understanding of the occurrence and extent of MCs. By analysing 90 publications from 1989 to 2019, we found that in various water bodies where MCs have been detected so far, the concentrations were 1.4-2803 times higher than the WHO provisional guideline for human lifetime exposure via drinking water (1 µg/L) in 12 of 15 African countries where data were available. MCs were relatively high in the Republic of South Africa (averaged 2803 μg/L) and Southern Africa as a whole (702 μg/L) when compared to other regions. Values were higher in reservoirs (958 μg/L) and lakes (159 μg/L) than in other water types, and much higher in temperate (1381 μg/L) than in arid (161 μg/L) and tropical (4 μg/L) zones. Highly significant positive relationships were found between MCs and planktonic chlorophyll a. Further assessment revealed high ecological risk for 14 of the 56 water bodies, with half used as human drinking water sources. Recognizing the extremely high MCs and exposure risk in Africa, we recommend routine monitoring and risk assessment of MCs be prioritized to ensure safe water use and sustainability in this region.

No evidence for sex chromosomes in natural populations of the cichlid fish Astatotilapia burtoni

Sex determination (SD) is not conserved among teleost fishes and can even differ between populations of the same species. Across the outstandingly species-rich fish family Cichlidae, more and more SD systems are being discovered. Still, the picture of SD evolution in this group is far from being complete. Lake Tanganyika and its affluent rivers are home to Astatotilapia burtoni, which belongs to the extremely successful East African cichlid lineage Haplochromini. Previously, in different families of an A. burtoni laboratory strain, an XYW system and an XY system have been described. The latter was also found in a second laboratory strain. In a laboratory-reared family descending from a population of the species' southern distribution, a second XY system was discovered. Yet, an analysis of sex chromosomes for the whole species distribution is missing. Here, we examined the genomes of 11 natural populations of A. burtoni, encompassing a wide range of its distribution, for sex-linked regions. We did not detect signs of differentiated sex chromosomes and also not the previously described sex chromosomal systems present in laboratory lines, suggesting different SD systems in the same species under natural and (long-term) artificial conditions. We suggest that SD in A. burtoni is more labile than previously assumed and consists of a combination of non-genetic, polygenic, or poorly differentiated sex chromosomes.

Monogeneans from Catfishes in Lake Tanganyika. II: New Infection Site, New Record, and Additional Details on the Morphology of the Male Copulatory Organ of Gyrodactylus transvaalensis Prudhoe and Hussey, 1977

The ichthyofauna of Lake Tanganyika consists of 12 families of fish of which five belong to Siluriformes (catfishes). Studies on Siluriformes and their parasites in this lake are very fragmentary. The present study was carried out to help fill the knowledge gap on the monogeneans infesting the siluriform fishes of Lake Tanganyika in general and, more particularly, Clarias gariepinus. Samples of gills of Clarias gariepinus (Clariidae) were examined for ectoparasites. We identified the monogenean Gyrodactylus transvaalensis (Gyrodactylidae). This is the first time this parasite was found infecting gills. We are the first to observe a large spine in the male copulatory organ of this species and to provide measurements of its genital spines; this completes the description of the male copulatory organ, which is important in standard monogenean identification. This is the first monogenean species reported in C. gariepinus at Lake Tanganyika and the third known species on a representative of Siluriformes of this lake. It brings the total number of species of Gyrodactylus recorded in Lake Tanganyika to four. Knowing that other locations where this species has been reported are geographically remote from Lake Tanganyika, we propose a "failure to diverge" phenomenon for G. transvaalensis.

Spatial heterogeneity in pH, body size and habitat size generates ecological opportunity in an evolutionary radiation

Much of the biological diversity we see today is thought to be the product of evolutionary radiation, the rapid proliferation of species from a single ancestor into multiple discrete forms. Spatial heterogeneity in environmental variables has been proposed as creating the necessary ecological opportunity to stimulate evolutionary radiation. Nonetheless, the ecological mechanisms generating and maintaining diversity in spatially heterogeneous environments are not fully understood. The authors investigated the role of strong spatial heterogeneity in generating ecological opportunity in an evolutionary radiation of freshwater populations of the three-spined stickleback (Gasterosteus aculeatus L.) on the island of North Uist using a spatially explicit Bayesian model. The authors identified pH, loch surface area and body size as predictors of variance in the number of lateral plates that comprise anti-predator armour in G. aculeatus. An East-West gradient of pH, a product of the distinctive environment of North Uist, generates a robust selective environment facilitating G. aculeatus evolutionary radiation. Larger lochs were associated with atypical phenotypes, possibly related to larger population sizes and greater selection efficiency. An association between pH and lateral plate number is likely an effect of body size, with a positive relationship between body size and lateral plate number that is mediated by swimming efficiency in G. aculeatus.

Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation

Background

The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9–12 million years ago (MYA) from the predecessor of the Malagarasi–Congo River and only 5–6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissatanganicae and Limnothrissamiodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids.

Results

We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S.tanganicae and L.miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissaobtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P.obtusirostris around 10.92 MYA [95% CI: 6.37–15.48].

Conclusions

These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi–Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02085-8.

Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients

Although biodiversity in East Africa is overall extremely high, species richness is not geographically uniform for fishes and mammals. We investigated the biogeographic relevance of past river activity in the Kenya Rift. We show that during a humid period 12,000 to 8,000 years ago, a river system connected currently isolated rift lakes and was partly connected to the Nile. While this river system formed pathways for the dispersal of fishes between lakes, it also acted as a barrier to the range expansion of forest mammals. This fairly recent hydrological connectivity between lakes has been a key driver of modern biodiversity patterns in East Africa. Climate-driven changes in drainage networks on multimillennial timescales are an important hypothesis in biodiversity research.

East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.

Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes

A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.

Filling the knowledge gap of Middle American freshwater fish parasite biodiversity: metazoan parasite fauna of Nicaragua

The heterogeneous landscape of Nicaragua harbours a large diversity of freshwater fishes. The great Nicaraguan lakes, Managua and Nicaragua, and several adjacent crater lakes harbour numerous endemic fish species. However, information about their parasite fauna is still fragmentary. Here, we surveyed the great Nicaraguan lakes and four crater lakes and provide data for 17 metazoan parasite taxa infecting seven fish host species. We also gathered all the published records from the literature on the parasites reported from Nicaraguan freshwater fishes, as well as those for Costa Rica and Panama to discuss the region of Lower Central America as a whole. With this information we built a parasite-host and a host-parasite checklist. With data from near 50% of the native and endemic freshwater fishes in Nicaragua, the parasite fauna comprises 101 taxa in 51 fish species allocated in 11 families. Cichlids are the most diverse group of fishes in this region and have been the most extensively surveyed for their metazoan parasites. Helminths are the best-represented groups of metazoan parasites, with 42 trematodes, five cestodes, 24 monogeneans, two acanthocephalans, 20 nematodes and one hirudinean. Additionally, freshwater fishes are parasitized by copepods, branchiurans and oribatid mites. Even though the inventory is not yet complete, the patterns of diversity uncovered revealed promising information about the origin, biogeography and evolutionary history of the Nicaraguan freshwater fish parasite fauna. More studies are necessary to complete our knowledge about the diversity, host association and distribution of metazoan parasites in Nicaragua and other Central American countries.

Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika

The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim‐light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in virtually the entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the environmental light with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth‐related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability and 11 sites that may be functionally important on the basis of their physicochemical properties. Among the strongest candidate sites for deep‐water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is the first comprehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.

Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii)

Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.

Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes

Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.

Social and spatial conflict drive resident aggression toward outsiders in a group-living fish

Group-living animals often experience within-group competition for resources like shelter and space, as well as for social status. Because of this conflict, residents may aggressively resist joining attempts by new members. Here, we asked whether different forms of competition mediate this response, specifically competition over 1) shelter, 2) spatial position within groups, and 3) social or sexual roles. We performed experiments on wild groups of Neolamprologus multifasciatus cichlids in Lake Tanganyika, either increasing or decreasing the number of shelters (empty snail shells) within their territories. We predicted that increases in resource abundance would reduce conflict and lower the aggression of residents toward presented conspecifics, while decreases in resources would increase aggression. We explored the effects of social conflict and spatial arrangement by introducing same or opposite sex conspecifics, at greater or lesser distances from resident subterritories. We found that changing the abundance of shells had no detectable effect on the responses of residents to presented conspecifics. Rather, aggression was strongly sex-dependent, with male residents almost exclusively aggressing presented males, and female residents almost exclusively aggressing presented females. For females, this aggression was influenced by the spatial distances between the presented conspecific and the resident female subterritory, with aggression scaling with proximity. In contrast, presentation distance did not influence resident males, which were aggressive to all presented males regardless of location. Overall, our results show that group residents respond to presented conspecifics differently depending on the type of competitive threat these potential joiners pose.

Sex-biased gene expression and recent sex chromosome turnover

Cichlids are well known for their propensity to radiate generating arrays of morphologically and ecologically diverse species in short evolutionary time. Following this rapid evolutionary pace, cichlids show high rates of sex chromosome turnover. We here studied the evolution of sex-biased gene (SBG) expression in 14 recently diverged taxa of the Lake Tanganyika Tropheini cichlids, which show different XY sex chromosomes. Across species, sex chromosome sequence divergence predates divergence in expression between the sexes. Only one sex chromosome, the oldest, showed signs of demasculinization in gene expression and potentially contribution to the resolution of sexual conflict. SBGs in general showed high rates of turnovers and evolved mostly under drift. Sexual selection did not shape the rapid evolutionary changes of SBGs. Male-biased genes evolved faster than female-biased genes, which seem to be under more phylogenetic constraint. We found a relationship between the degree of sex bias and sequence evolution driven by sequence differences among the sexes. Consistent with other species, strong sex bias towards sex-limited expression contributes to resolving sexual conflict in cichlids. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

Comparative scale morphology in the adaptive radiation of cichlid fishes (Perciformes: Cichlidae) from Lake Tanganyika

The morphology of fish scales has been investigated for > 200 years, but research on evolutionary patterns of scale morphology is scarce. Here, we study scale morphology and its evolution in the adaptive radiation of cichlid fishes from Lake Tanganyika, which are known for their exceptional diversity in habitat use, feeding ecology and morphology. Based on a geometric morphometric approach on eight scales per specimen (covering different body regions), we quantify scale types and morphology across nearly all ~240 species of the cichlid adaptive radiation in Lake Tanganyika. We first show that scale type, shape and ctenii coverage vary along the body, which is probably attributable to adaptations to different functional demands on the respective scales. Our comparative analyses reveal that flank scale size is tightly linked to phylogeny, whereas scale shape and ctenii coverage can be explained only in part by phylogenetic history and/or our proxy for ecology (stable isotopes and body shape), suggesting an additional adaptive component. We also show that our measured scale characteristics can help to assign an individual scale to a taxonomic group or ecotype. Thus, our data may serve as a valuable resource for taxonomic studies and to interpret fossil finds.

Delayed adaptive radiation among New Zealand stream fishes: joint estimation of divergence time and trait evolution in a newly delineated island species flock

Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a phylogenomic data set combined with simultaneous Bayesian estimation of divergence times and trait-based speciation and extinction models, we show that the New Zealand Gobiomorphus gudgeons comprise a monophyletic assemblage, but surprisingly, the radiation did not fully occupy freshwater habitats and explosively speciate until more than 10 myr after the lineage invaded the islands. This shift in speciation rate was not accompanied by an acceleration in the rate of morphological evolution in the freshwater crown clade relative to the other species, but is correlated with a reduction in head pores and scales as well as an increase in egg size. Our results challenge the notion that clades always rapidly exploit ecological opportunities in the absence of competing lineages. Instead, we demonstrate that adaptive radiation can experience a slow start before undergoing accelerated diversification and that lineage and phenotypic diversification may be uncoupled in young radiations. [Adaptive radiation; Eleotridae; freshwater; Gobiomorphus; New Zealand.]

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Global Diversification Dynamics Since the Jurassic: Low Dispersal and Habitat-Dependent Evolution Explain Hotspots of Diversity and Shell Disparity in River Snails (Viviparidae)

The Viviparidae, commonly known as River Snails, is a dominant group of freshwater snails with a nearly worldwide distribution that reaches its highest taxonomic and morphological diversity in Southeast Asia. The rich fossil record is indicative of a probable Middle Jurassic origin on the Laurasian supercontinent where the group started to diversify during the Cretaceous. However, it remains uncertain when and how the biodiversity hotspot in Southeast Asia was formed. Here, we used a comprehensive genetic data set containing both mitochondrial and nuclear markers and comprising species representing 24 out of 28 genera from throughout the range of the family. To reconstruct the spatiotemporal evolution of viviparids on a global scale, we reconstructed a fossil-calibrated phylogeny. We further assessed the roles of cladogenetic and anagenetic events in range evolution. Finally, we reconstructed the evolution of shell features by estimating ancestral character states to assess whether the appearance of sculptured shell morphologies was driven by major habitat shifts. The molecular phylogeny supports the monophyly of the three subfamilies, the Bellamyinae, Lioplacinae, and Viviparinae, but challenges the currently accepted genus-level classification in several cases. The almost global distribution of River Snails has been influenced both by comparatively ancient vicariance and more recent founder events. In Southeast Asia, Miocene dispersal was a main factor in shaping the modern species distributions. A recurrent theme across different viviparid taxa is that many species living in lentic waters exhibit sculptured shells, whereas only one strongly sculptured species is known from lotic environments. We show that such shell sculpture is habitat-dependent and indeed evolved several times independently in lentic River Snails. Considerably high transition rates between shell types in lentic habitats probably caused the co-occurrence of morphologically distinct shell types in several lakes. In contrast, directional evolution toward smooth shells in lotic habitats, as identified in the present analyses, explains why sculptured shells are rarely found in these habitats. However, the specific factors that promoted changes in shell morphology require further work. [biogeographical analyses; fossil-calibrated phylogeny; fossil-constrained analyses; Southeast Asia; stochastic character mapping.].

Life history shifts in an exploited African fish following invasion by a castrating parasite

Evolutionary theory predicts that infection by a parasite that reduces future host survival or fecundity should select for increased investment in current reproduction. In this study, we use the cestode Ligula intestinalis and its intermediate fish host Engraulicypris sardella in Wissman Bay, Lake Nyasa (Tanzania), as a model system. Using data about infection of E. sardella fish hosts by L. intestinalis collected for a period of 10 years, we explored whether parasite infection affects the fecundity of the fish host E. sardella, and whether host reproductive investment has increased at the expense of somatic growth. We found that L. intestinalis had a strong negative effect on the fecundity of its intermediate fish host. For the noninfected fish, we observed an increase in relative gonadal weight at maturity over the study period, while size at maturity decreased. These findings suggest that the life history of E. sardella has been shifting toward earlier reproduction. Further studies are warranted to assess whether these changes reflect plastic or evolutionary responses. We also discuss the interaction between parasite and fishery-mediated selection as a possible explanation for the decline of E. sardella stock in the lake.

Research and Conservation in the Greater Gombe Ecosystem: Challenges and Opportunities

The study of chimpanzees in Gombe National Park, Tanzania, started by Jane Goodall in 1960, provided pioneering accounts of chimpanzee behavior and ecology. With funding from multiple sources, including the Jane Goodall Institute (JGI) and grants from private foundations and federal programs, the project has continued for sixty years, providing a wealth of information about our evolutionary cousins. These chimpanzees face two main challenges to their survival: infectious disease - including simian immunodeficiency virus (SIVcpz), which can cause Acquired Immune Deficiency Syndrome (AIDS) in chimpanzees - and the deforestation of land outside the park. A health monitoring program has increased understanding of the pathogens affecting chimpanzees and has promoted measures to characterize and reduce disease risk. Deforestation reduces connections between Gombe and other chimpanzee populations, which can cause loss of genetic diversity. To promote habitat restoration, JGI facilitated participatory village land use planning, in which communities voluntarily allocated land to a network of Village Land Forest Reserves. Expected benefits to people include stabilizing watersheds, improving water supplies, and ensuring a supply of forest resources. Surveys and genetic analyses confirm that chimpanzees persist on village lands and remain connected to the Gombe population. Many challenges remain, but the regeneration of natural forest on previously degraded lands provides hope that conservation solutions can be found that benefit both people and wildlife. Conservation work in the Greater Gombe Ecosystem has helped promote broader efforts to plan and work for conservation elsewhere in Tanzania and across Africa.

Research and Conservation in the Greater Gombe Ecosystem: Challenges and Opportunities

The study of chimpanzees in Gombe National Park, Tanzania, started by Jane Goodall in 1960, provided pioneering accounts of chimpanzee behavior and ecology. With funding from multiple sources, including the Jane Goodall Institute (JGI) and grants from private foundations and federal programs, the project has continued for sixty years, providing a wealth of information about our evolutionary cousins. These chimpanzees face two main challenges to their survival: infectious disease - including simian immunodeficiency virus (SIVcpz), which can cause Acquired Immune Deficiency Syndrome (AIDS) in chimpanzees - and the deforestation of land outside the park. A health monitoring program has increased understanding of the pathogens affecting chimpanzees and has promoted measures to characterize and reduce disease risk. Deforestation reduces connections between Gombe and other chimpanzee populations, which can cause loss of genetic diversity. To promote habitat restoration, JGI facilitated participatory village land use planning, in which communities voluntarily allocated land to a network of Village Land Forest Reserves. Expected benefits to people include stabilizing watersheds, improving water supplies, and ensuring a supply of forest resources. Surveys and genetic analyses confirm that chimpanzees persist on village lands and remain connected to the Gombe population. Many challenges remain, but the regeneration of natural forest on previously degraded lands provides hope that conservation solutions can be found that benefit both people and wildlife. Conservation work in the Greater Gombe Ecosystem has helped promote broader efforts to plan and work for conservation elsewhere in Tanzania and across Africa.

Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes

Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.

The taxonomic diversity of the cichlid fish fauna of ancient Lake Tanganyika, East Africa

Ancient Lake Tanganyika in East Africa houses the world's ecologically and morphologically most diverse assemblage of cichlid fishes, and the third most species-rich after lakes Malawi and Victoria. Despite long-lasting scientific interest in the cichlid species flocks of the East African Great Lakes, for example in the context of adaptive radiation and explosive diversification, their taxonomy and systematics are only partially explored; and many cichlid species still await their formal description. Here, we provide a current inventory of the cichlid fish fauna of Lake Tanganyika, providing a complete list of all valid 208 Tanganyikan cichlid species, and discuss the taxonomic status of more than 50 undescribed taxa on the basis of the available literature as well as our own observations and collections around the lake. This leads us to conclude that there are at least 241 cichlid species present in Lake Tanganyika, all but two are endemic to the basin. We finally summarize some of the major taxonomic challenges regarding Lake Tanganyika's cichlid fauna. The taxonomic inventory of the cichlid fauna of Lake Tanganyika presented here will facilitate future research on the taxonomy and systematics and the ecology and evolution of the species flock, as well as its conservation.

Population collapse in viviparid gastropods of the Lake Victoria ecoregion started before the Last Glacial Maximum

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.

Where Am I? Niche constraints due to morphological specialization in two Tanganyikan cichlid fish species

Food resource specialization within novel environments is considered a common axis of diversification in adaptive radiations. Feeding specializations are often coupled with striking morphological adaptations and exemplify the relation between morphology and diet (phenotype-environment correlations), as seen in, for example, Darwin finches, Hawaiian spiders, and the cichlid fish radiations in East African lakes. The cichlids' potential to rapidly exploit and occupy a variety of different habitats has previously been attributed to the variability and adaptability of their trophic structures including the pharyngeal jaw apparatus. Here we report a reciprocal transplant experiment designed to explore the adaptability of the trophic structures in highly specialized cichlid fish species. More specifically, we forced two common but ecologically distinct cichlid species from Lake Tanganyika, Tropheus moorii (rock-dweller), and Xenotilapia boulengeri (sand-dweller), to live on their preferred as well as on an unpreferred habitat (sand and rock, respectively). We measured their overall performance on the different habitat types and explored whether adaptive phenotypic plasticity is involved in adaptation. We found that, while habitat had no effect on the performance of X. boulengeri, T. moorii performed significantly better in its preferred habitat. Despite an experimental duration of several months, we did not find a shift in the morphology of the lower pharyngeal jaw bone that would be indicative of adaptive phenotypic plasticity in this trait.

Assessing the diversity and distribution of potential intermediate hosts snails for urogenital schistosomiasis: Bulinus spp. (Gastropoda: Planorbidae) of Lake Victoria

BACKGROUND

The Lake Victoria basin is one of the most persistent hotspots of schistosomiasis in Africa, the intestinal form of the disease being studied more often than the urogenital form. Most schistosomiasis studies have been directed to Schistosoma mansoni and their corresponding intermediate snail hosts of the genus Biomphalaria, while neglecting S. haematobium and their intermediate snail hosts of the genus Bulinus. In the present study, we used DNA sequences from part of the cytochrome c oxidase subunit 1 (cox1) gene and the internal transcribed spacer 2 (ITS2) region to investigate Bulinus populations obtained from a longitudinal survey in Lake Victoria and neighbouring systems during 2010-2019.

METHODS

Sequences were obtained to (i) determine specimen identities, diversity and phylogenetic positions, (ii) reconstruct phylogeographical affinities, and (iii) determine the population structure to discuss the results and their implications for the transmission and epidemiology of urogenital schistosomiasis in Lake Victoria.

RESULTS

Phylogenies, species delimitation methods (SDMs) and statistical parsimony networks revealed the presence of two main groups of Bulinus species occurring in Lake Victoria; B. truncatus/B. tropicus complex with three species (B. truncatus, B. tropicus and Bulinus sp. 1), dominating the lake proper, and a B. africanus group, prevalent in banks and marshes. Although a total of 47 cox1 haplotypes, were detected within and outside Lake Victoria, there was limited haplotype sharing (only Haplotype 6 was shared between populations from Lake Victoria open waters and neighbouring aquatic systems) - an indication that haplotypes are specific to habitats.

CONCLUSIONS

The Bulinus fauna of Lake Victoria consists of at least B. truncatus, B. tropicus, Bulinus sp. 1 (B. trigonus?) and B. ugandae. The occurrence and wide distribution of Bulinus species in Lake Victoria potentially implies the occurrence of urogenital schistosomiasis in communities living along the shores and on islands of the lake who depend solely on the lake for their livelihood. More in-depth studies are needed to obtain a better picture of the extent of the disease in the Lake Victoria basin.

Checklist of the fresh and brackish water snails (Mollusca, Gastropoda) of Bénin and adjacent West African ecoregions

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.

Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers

In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that generated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual “patterns” of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.

Structural manipulations of a shelter resource reveal underlying preference functions in a shell-dwelling cichlid fish

Many animals can modify the environments in which they live, thereby changing the selection pressures they experience. A common example of such niche construction is the use, creation or modification of environmental resources for use as nests or shelters. Because these resources often have correlated structural elements, it can be difficult to disentangle the relative contribution of these elements to resource choice, and the preference functions underlying niche-construction behaviour remain hidden. Here, we present an experimental paradigm that uses 3D scanning, modelling and printing to create replicas of structures that differ with respect to key structural attributes. We show that a niche-constructing, shell-dwelling cichlid fish, Neolamprologus multifasciatus, has strong open-ended preference functions for exaggerated shell replicas. Fish preferred shells that were fully intact and either enlarged, lengthened or had widened apertures. Shell intactness was the most important structural attribute, followed by shell length, then aperture width. We disentangle the relative roles of different shell attributes, which are tightly correlated in the wild, but nevertheless differentially influence shelter choice and therefore niche construction in this species. We highlight the broad utility of our approach when compared with more traditional methods (e.g. two-choice tasks) for studying animal decision-making in a range of contexts.

Uncharted digenean diversity in Lake Tanganyika: cryptogonimids (Digenea: Cryptogonimidae) infecting endemic lates perches (Actinopterygii: Latidae)

BACKGROUND

Lake Tanganyika is considered a biodiversity hotspot with exceptional species richness and level of endemism. Given the global importance of the lake in the field of evolutionary biology, the understudied status of its parasite fauna is surprising with a single digenean species reported to date. Although the most famous group within the lake's fish fauna are cichlids, the pelagic zone is occupied mainly by endemic species of clupeids (Actinopterygii: Clupeidae) and lates perches (Actinopterygii: Latidae, Lates Cuvier), which are an important commercial source for local fisheries. In this study, we focused on the lake's four lates perches and targeted their thus far unexplored endoparasitic digenean fauna.

METHODS

A total of 85 lates perches from four localities in Lake Tanganyika were examined. Cryptogonimid digeneans were studied by means of morphological and molecular characterisation. Partial sequences of the nuclear 28S rRNA gene and the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene were sequenced for a representative subset of the specimens recovered. Phylogenetic analyses were conducted at the family level under Bayesian inference.

RESULTS

Our integrative approach revealed the presence of six species within the family Cryptogonimidae Ward, 1917. Three out of the four species of Lates were found to be infected with at least one cryptogonimid species. Two out of the three reported genera are new to science. Low interspecific but high intraspecific phenotypic and genetic diversity was found among Neocladocystis spp. Phylogenetic inference based on partial 28S rDNA sequences revealed a sister group relationship for two of the newly erected genera and their close relatedness to the widely distributed genus Acanthostomum Looss, 1899.

CONCLUSIONS

The present study provides the first comprehensive characterisation of the digenean diversity in a fish family from Lake Tanganyika which will serve as a baseline for future explorations of the lake's digenean fauna. Our study highlights the importance of employing an integrative approach for revealing the diversity in this unique host-parasite system.

Diversification dynamics of freshwater bivalves (Unionidae: Parreysiinae: Coelaturini) indicate historic hydrographic connections throughout the East African Rift System

Invertebrates are exceptionally diverse, but many are in decline because of anthropogenic changes to their habitat. This situation is particularly problematic for taxa that are not well monitored or taxonomically poorly understood, because the lack of knowledge hampers conservation. Despite their important functional role in freshwater ecosystems, African bivalves of the family Unionidae remain poorly studied compared to their highly threatened relatives in Europe, the U.S.A. and Canada. To resolve relationships and to study diversification dynamics in space and time, we performed time-calibrated phylogenetic studies and biogeographical modeling on the unionids from the East African Rift System and surroundings, including representatives of all currently recognized Afrotropical genera except for Brazzaea (and Unio from southern Africa). Our analyses indicate that all sampled Afrotropical unionids belong to the tribe Coelaturini (subfamily Parreysiinae), as does the genus Moncetia from Lake Tanganyika, which is currently attributed to the family Iridinidae. Colonization of Africa from Eurasia by Parreysiinae occurred ~17 Ma ago, and the subsequent diversification of Coelaturini in Africa continued at a steady pace, although net diversification decreased over time as more niches and ecoregions became occupied. Clades in Coelaturini largely reflect drainage basins, with the oldest lineages and highest regional diversity occurring in Lake Tanganyika, followed by the Congo Basin watershed in general. The species assemblage of Lake Tanganyika reflects multiple independent events of colonization and intralacustrine diversification since the Late Miocene or Early Pliocene. The clades of other regions, including that containing the species from Lake Malawi, are comparatively young. Biogeographical analyses indicate that the colonization history was mainly driven by cladogenesis in sympatry, whereas few anagenetic events contributed to the modern distribution of Coelaturini. Ancestral range estimations demonstrate that Coelaturini originated in the Victoria and/or Tanganyika ecoregions, and that the Congo Basin played an essential role in the colonization of Africa by Coelaturini.

African climate response to orbital and glacial forcing in 140,000-y simulation with implications for early modern human environments

A climate/vegetation model simulates episodic wetter and drier periods at the 21,000-y precession period in eastern North Africa, the Arabian Peninsula, and the Levant over the past 140,000 y. Large orbitally forced wet/dry extremes occur during interglacial time, ∼130 to 80 ka, and conditions between these two extremes prevail during glacial time, ∼70 to 15 ka. Orbital precession causes high seasonality in Northern Hemisphere (NH) insolation at ∼125, 105, and 83 ka, with stronger and northward extended summer monsoon rains in North Africa and the Arabian Peninsula and increased winter rains in the Mediterranean Basin. The combined effects of these two seasonally distinct rainfall regimes increase vegetation and narrow the width of the Saharan-Arabian desert and semidesert zones. During the opposite phase of the precession cycle (∼115, 95, and 73 ka), NH seasonality is low, and decreased summer insolation and increased winter insolation cause monsoon and storm track rains to decrease and the width of the desert zone to increase. During glacial time (∼70 to 15 ka), forcing from large ice sheets and lowered greenhouse gas concentrations combine to increase winter Mediterranean storm track precipitation; the southward retreat of the northern limit of summer monsoon rains is relatively small, thereby limiting the expansion of deserts. The lowered greenhouse gas concentrations cause the near-equatorial zone to cool and reduce convection, causing drier climate with reduced forest cover. At most locations and times, the simulations agree with environmental observations. These changing regional patterns of climate/vegetation could have influenced the dispersal of early humans through expansions and contractions of well-watered corridors.

Characteristics, Main Impacts, and Stewardship of Natural and Artificial Freshwater Environments: Consequences for Biodiversity Conservation

In this overview (introductory article to a special issue including 14 papers), we consider all main types of natural and artificial inland freshwater habitas (fwh). For each type, we identify the main biodiversity patterns and ecological features, human impacts on the system and environmental issues, and discuss ways to use this information to improve stewardship. Examples of selected key biodiversity/ecological features (habitat type): narrow endemics, sensitive (groundwater and GDEs); crenobionts, LIHRes (springs); unidirectional flow, nutrient spiraling (streams); naturally turbid, floodplains, large-bodied species (large rivers); depth-variation in benthic communities (lakes); endemism and diversity (ancient lakes); threatened, sensitive species (oxbow lakes, SWE); diverse, reduced littoral (reservoirs); cold-adapted species (Boreal and Arctic fwh); endemism, depauperate (Antarctic fwh); flood pulse, intermittent wetlands, biggest river basins (tropical fwh); variable hydrologic regime—periods of drying, flash floods (arid-climate fwh). Selected impacts: eutrophication and other pollution, hydrologic modifications, overexploitation, habitat destruction, invasive species, salinization. Climate change is a threat multiplier, and it is important to quantify resistance, resilience, and recovery to assess the strategic role of the different types of freshwater ecosystems and their value for biodiversity conservation. Effective conservation solutions are dependent on an understanding of connectivity between different freshwater ecosystems (including related terrestrial, coastal and marine systems).

Adaptive divergence in shell morphology in an ongoing gastropod radiation from Lake Malawi

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.

Old lake versus young taxa: a comparative phylogeographic perspective on the evolution of Caspian Sea gastropods (Neritidae: Theodoxus)

The Caspian Sea has been a highly dynamic environment throughout the Quaternary and witnessed major oscillations in lake level, which were associated with changes in salinity and habitat availability. Such environmental pressures are considered to drive strong phylogeographic structures in species by forcing populations into suitable refugia. However, little is actually known on the effect of lake-level fluctuations in the Caspian Sea on its aquatic biota. We compared the phylogeographic patterns of the aquatic Neritidae snail genus Theodoxus across the Pontocaspian region with refugial populations in southern Iran. Three gene fragments were used to determine relationships and divergence times between the sampled populations in both groups. A dated phylogeny and statistical haplotype networks were generated in conjunction with the analyses of molecular variance and calculations of isolation by distance using distance-based redundancy analyses. Extended Bayesian skyline plots were constructed to assess demographic history. Compared with the southern Iranian populations, we found little phylogeographic structure for the Pontocaspian Theodoxus group, with more recent diversification, homogeneity of haplotypes across the Pontocaspian region and a relatively stable demographic history since the Middle Pleistocene. Our results argue against a strong influence of Caspian Sea low stands on the population structure post the early Pleistocene, whereas high stands may have increased the dispersal possibilities and homogenization of haplotypes across the Pontocaspian region during this time. However, during the early Pleistocene, a more dramatic low stand in the Caspian Sea, around a million years ago, may have caused the reduction in Theodoxus diversity to a single lineage in the region. In addition, our results provide new insights into Theodoxus taxonomy and outlooks for regional conservation.