Population Differentiation In Daphnia Alters Community Assembly In Experimental Ponds

Most studies of community assembly ignore how genetic differentiation within species affects their colonization and extinction. However, genetic differentiation in ecologically relevant traits may be substantial enough to alter the colonization and extinction processes that drive community assembly. We measured significant molecular genetic and quantitative trait differentiation among three Daphnia pulex X pulicaria populations in southwestern Michigan ponds and investigated whether this differentiation could alter the assembly of pond zooplankton communities in experimental mesocosms. In this study, we monitored the invasion success of different D. pulex x pulicaria populations after their introduction into an established zooplankton community. We also monitored the invasion success of a diverse array of zooplankton species into different D. pulex x pulicaria populations. Zooplankton community composition depended on the D. pulex X pulicaria source population. Daphnia pulex X pulicaria from one population failed to invade zooplankton communities, while those from other populations successfully invaded similar communities. If population differentiation in other species plays a role in community assembly similar to that demonstrated in our study, assembly may be more sensitive to evolutionary processes than has been previously generally considered.Integrative Biolog

Quantifying eco-evolutionary contributions to trait divergence in spatially structured systems

Ecological and evolutionary processes can occur at similar time scales and, hence, influence one another. There has been much progress in developing metrics that quantify contributions of ecological and evolutionary components to trait change over time. However, many empirical evolutionary ecology studies document trait differentiation among populations structured in space. In both time and space, the observed differentiation in trait values among populations and communities can be the result of interactions between nonevolutionary (phenotypic plasticity, changes in the relative abundance of species) and evolutionary (genetic differentiation among populations) processes. However, the tools developed so far to quantify ecological and evolutionary contributions to trait changes are implicitly addressing temporal dynamics because they require directionality of change from an ancestral to a derived state. Identifying directionality from one site to another in spatial studies of eco-evolutionary dynamics is not always possible and often not meaningful. We suggest three modifications to existing partitioning metrics so they allow quantifying ecological and evolutionary contributions to changes in population and community trait values across spatial locations in landscapes. Applying these spatially modified metrics to published empirical examples shows how these metrics can be used to generate new empirical insights and to facilitate future comparative analyses. The possibility of applying eco-evolutionary partitioning metrics to populations and communities in natural landscapes is critical as it will broaden our capacity to quantify eco-evolutionary interactions as they occur in nature

Quantifying eco-evolutionary contributions to trait divergence in spatially structured systems

Ecological and evolutionary processes can occur at similar time scales and, hence, influence one another. There has been much progress in developing metrics that quantify contributions of ecological and evolutionary components to trait change over time. However, many empirical evolutionary ecology studies document trait differentiation among populations structured in space. In both time and space, the observed differentiation in trait values among populations and communities can be the result of interactions between nonevolutionary (phenotypic plasticity, changes in the relative abundance of species) and evolutionary (genetic differentiation among populations) processes. However, the tools developed so far to quantify ecological and evolutionary contributions to trait changes are implicitly addressing temporal dynamics because they require directionality of change from an ancestral to a derived state. Identifying directionality from one site to another in spatial studies of eco-evolutionary dynamics is not always possible and often not meaningful. We suggest three modifications to existing partitioning metrics so they allow quantifying ecological and evolutionary contributions to changes in population and community trait values across spatial locations in landscapes. Applying these spatially modified metrics to published empirical examples shows how these metrics can be used to generate new empirical insights and to facilitate future comparative analyses. The possibility of applying eco-evolutionary partitioning metrics to populations and communities in natural landscapes is critical as it will broaden our capacity to quantify eco-evolutionary interactions as they occur in nature

Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing

Background Patients with prostate cancer may present with metastatic or recurrent disease despite initial curative treatment. The propensity of metastatic prostate cancer to spread to the bone has limited repeated sampling of tumor deposits. Hence, considerably less is understood about this lethal metastatic disease, as it is not commonly studied. Here we explored whole-genome sequencing of plasma DNA to scan the tumor genomes of these patients non-invasively. Methods We wanted to make whole-genome analysis from plasma DNA amenable to clinical routine applications and developed an approach based on a benchtop high-throughput platform, that is, Illuminas MiSeq instrument. We performed whole-genome sequencing from plasma at a shallow sequencing depth to establish a genome-wide copy number profile of the tumor at low costs within 2 days. In parallel, we sequenced a panel of 55 high-interest genes and 38 introns with frequent fusion breakpoints such as the TMPRSS2-ERG fusion with high coverage. After intensive testing of our approach with samples from 25 individuals without cancer we analyzed 13 plasma samples derived from five patients with castration resistant (CRPC) and four patients with castration sensitive prostate cancer (CSPC). Results The genome-wide profiling in the plasma of our patients revealed multiple copy number aberrations including those previously reported in prostate tumors, such as losses in 8p and gains in 8q. High-level copy number gains in the AR locus were observed in patients with CRPC but not with CSPC disease. We identified the TMPRSS2-ERG rearrangement associated 3-Mbp deletion on chromosome 21 and found corresponding fusion plasma fragments in these cases. In an index case multiregional sequencing of the primary tumor identified different copy number changes in each sector, suggesting multifocal disease. Our plasma analyses of this index case, performed 13 years after resection of the primary tumor, revealed novel chromosomal rearrangements, which were stable in serial plasma analyses over a 9-month period, which is consistent with the presence of one metastatic clone. Conclusions The genomic landscape of prostate cancer can be established by non-invasive means from plasma DNA. Our approach provides specific genomic signatures within 2 days which may therefore serve as 'liquid biopsy'

Stability and Fluctuations in Complex Ecological Systems

From 08-12 August, 2022, 32 individuals participated in a workshop, Stability and Fluctuations in Complex Ecological Systems, at the Lorentz Center, located in Leiden, The Netherlands. An interdisciplinary dialogue between ecologists, mathematicians, and physicists provided a foundation of important problems to consider over the next 5-10 years. This paper outlines eight areas including (1) improving our understanding of the effect of scale, both temporal and spatial, for both deterministic and stochastic problems; (2) clarifying the different terminologies and definitions used in different scientific fields; (3) developing a comprehensive set of data analysis techniques arising from different fields but which can be used together to improve our understanding of existing data sets; (4) having theoreticians/computational scientists collaborate closely with empirical ecologists to determine what new data should be collected; (5) improving our knowledge of how to protect and/or restore ecosystems; (6) incorporating socio-economic effects into models of ecosystems; (7) improving our understanding of the role of deterministic and stochastic fluctuations; (8) studying the current state of biodiversity at the functional level, taxa level and genome level.Comment: 22 page

The interface between metacommunity ecology and microevolution in freshwater zooplankton

textIn many habitats, species’ traits correspond strongly to local environmental conditions. The cause of this pattern may be in-situ evolution, where initially mal-adapted resident species evolved traits that increased their fitness. Alternatively, species with suitable traits may have colonized the focal habitat and replaced resident species. Since theories in the fields of evolutionary biology and community ecology developed independently, few guidelines tell us when to expect evolutionary adaptation or ecological species replacement as the primary driver of species and trait composition in a given habitat. The goal of my dissertation research was to explain how evolutionary adaptation and ecological species replacement together determine the composition of pond zooplankton communities. I combined theoretical models with thorough surveys of natural pond communities and manipulative experiments. I discovered that one particular zooplankton species, Daphnia pulex, evolved to have different trait values in ponds with different environments. The evolutionary divergence within D. pulex profoundly affected its ecological interactions with other zooplankton species. D. pulex populations diverged from one another so much that they differed in their ability to successfully colonize ponds full of competing zooplankton species. I also used a computer simulation model to determine when a community’s trait changes were explained by evolutionary adaptation or ecological species replacement. The dispersal rate of species among habitats and the amount of genetic variance within these species both influenced adaptive trait change in a community. The group of research studies that indicate evolutionary and ecological processes operate on a similar time scale is small but growing. My dissertation research provides another crucial demonstration that evolution within individual species, such as D. pulex, influences their community ecological interactions with other species. I also identified key parameters (dispersal rate among and genetic variance within species) that may help biologists predict whether evolution or ecological species replacement explained adaptive trait change. My projects mostly concern the community and trait distributions that result from the assembly of species in new habitats. However, this framework may inform studies of community response to environmental changes such as invasive species or habitat destruction.Biological Sciences, School o

Strong spatial turnover in cichlid fish assemblages in the upper río Madera (Amazon basin) despite the absence of hydrological barriers

In freshwater ecosystems, spatial turnover in fish assemblages is often attributed to dispersal limitation imposed by fragmentation of water bodies. Other factors like environmental properties or biotic interactions have often been assumed to be minute relative to dispersal limitation when hydrogeological barriers are abundant. This study aims to describe the spatial differentiation of cichlid fish assemblages in the upper río Madera in Bolivia, Brazil and Perú, a large drainage ystem characterized by the absence of significant hydrogeological barriers. We assessed the relative importance of spatial, climatic and geological predictors in the observed biogeographic structure using an integrative combination of cluster analyses, elements of metacommunity structure analysis, variation partitioning, and network analysis. Our results show that distinct assemblages of cichlid fish species replace each other across the landscape and that this turnover is partially determined by climate and geological gradients. A considerable fraction of the cichlid assembly structure could not be assigned to either space, climate or geology and might be explained by unmeasured parameters such as habitat structure or biotic interactions. Incorporating knowledge on spatial turnover of species assemblages into conservation strategies will be essential for the biodiversity management of the diverse aquatic fauna of the upper río Madera.status: publishe

Eco-evolutionary dynamics in freshwater systems

There is an increasing recognition that evolutionary dynamics may occur at timescales that are sufficiently rapid to impact ecological responses to environmental change and influence ecological dynamics. In the development of the emerging paradigm of eco-evolutionary dynamics, studies of freshwater organisms have been very important. Here we highlight a number of key observations and achievements, and point to remaining challenges.status: publishe

Niche use and co-occurrence patterns of zooplankton along a strong urbanization gradient

Community composition in a given landscape is a complex product of the constituent species' niche requirements, geographic connectivity, environmental properties, species interactions and drift. In this study, we examined niche use of 16 cladoceran species in 81 zooplankton communities that inhabit environmentally variable sites along a strong urbanization gradient. We tested to what extent niche shifts occurred along the urbanization gradient. We also quantified to what extent niche overlap can explain co-occurrence patterns and tested whether alternative processes such as dispersal limitation or environmental heterogeneity impact co-occurrence patterns. Niche use in the study region was size-mediated, with larger species preferring nutrient-rich environments while smaller species were more specialized on distinct niche axes. Our analyses also revealed that mainly generalist species were able to establish in urban sites. While the average niche position for most species was conserved from rural to urban sites, the niches of those species occurring in both rural and urban areas remain partly unfilled in the urban populations. We observed that a relatively small proportion (13%) of species pairs co-occurred more or less often than expected by chance, but also that niche overlap was the only predictor that was strongly and significantly associated with co-occurrence scores in our study. While most of these species pairs showed evidence for a role of environmental filtering, a few common, generalist species pairs displayed segregated co-occurrence patterns and high niche overlap, suggesting a role of limiting similarity relationships as well. Our study highlights the damaging effects on biodiversity of urbanization through biotic homogenization benefitting generalist species, as well as the difficulty species may face in occupying available niche space in urbanized habitats