Plant and fungal identity determines pathogen protection of plant roots by arbuscular mycorrhizas

This is the peer reviewed version of the following article: BA Sikes, K Cottenie and JN Klironomos. (2009) Plant and fungal identity determines pathogen protection of plant roots by arbuscular mycorrhizas. Journal of Ecology 97: 1274-1280. http://dx.doi.org/10.1111/j.1365-2745.2009.01557.x, which has been published in final form at http://doi.org/10.1111/j.1365-2745.2009.01557.x This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.1. A major benefit of the mycorrhizal symbiosis is that it can protect plants from below-ground enemies, such as pathogens. Previous studies have indicated that plant identity (particularly plants that differ in root system architecture) or fungal identity (fungi from different families within the Glomeromycota) can determine the degree of protection from infection by pathogens. Here, we test the combined effects of plant and fungal identity to assess if there is a strong interaction between these two factors. 2. We paired one of two plants (Setaria glauca, a plant with a finely branched root system and Allium cepa, which has a simple root system) with one of six different fungal species from two families within the Glomeromycota. We assessed the degree to which plant identity, fungal identity and their interaction determined infection by Fusarium oxysporum, a common plant pathogen. 3. Our results show that the interaction between plant and fungal identity can be an important determinant of root infection by the pathogen. Infection by Fusarium was less severe in Allium (simple root system) or when Setaria (complex root system) was associated with a fungus from the family Glomeraceae. We also detected significant plant growth responses to the treatments; the fine-rooted Setaria benefited more from associating with a member of the family Glomeraceae, while Allium benefited more from associating with a member of the family Gigasporaceae. 4. Synthesis. This study supports previous claims that plants with complex root systems are more susceptible to infection by pathogens, and that the arbuscular mycorrhizal symbiosis can reduce infection in such plants – provided that the plant is colonized by a mycorrhizal fungus that can offer protection, such as the isolates of Glomus used here

Distinguishing ecological from evolutionary approaches to transposable elements

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology

Reconciling seascape genetics and fisheries science in three codistributed flatfishes

Uncertainty hampers innovative mixed‐fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species‐specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population‐specific information. We conclude that the management of fish stocks has to consider species‐specific genetic structures and may benefit from the documentation of the genetic seascape and life‐history traits.publishedVersionUnit Licence Agreemen

Reconciling seascape genetics and fisheries science in three codistributed flatfishes

Uncertainty hampers innovative mixed‐fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species‐specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population‐specific information. We conclude that the management of fish stocks has to consider species‐specific genetic structures and may benefit from the documentation of the genetic seascape and life‐history traits.publishedVersionUnit Licence Agreemen

A comparative analysis reveals weak relationships between ecological factors and beta diversity of stream insect metacommunities at two spatial levels.

The hypotheses that beta diversity should increase with decreasing latitude and increase with spatial extent of a region have rarely been tested based on a comparative analysis of multiple datasets, and no such study has focused on stream insects. We first assessed how well variability in beta diversity of stream insect metacommunities is predicted by insect group, latitude, spatial extent, altitudinal range, and dataset properties across multiple drainage basins throughout the world. Second, we assessed the relative roles of environmental and spatial factors in driving variation in assemblage composition within each drainage basin. Our analyses were based on a dataset of 95 stream insect metacommunities from 31 drainage basins distributed around the world. We used dissimilarity-based indices to quantify beta diversity for each metacommunity and, subsequently, regressed beta diversity on insect group, latitude, spatial extent, altitudinal range, and dataset properties (e.g., number of sites and percentage of presences). Within each metacommunity, we used a combination of spatial eigenfunction analyses and partial redundancy analysis to partition variation in assemblage structure into environmental, shared, spatial, and unexplained fractions. We found that dataset properties were more important predictors of beta diversity than ecological and geographical factors across multiple drainage basins. In the within-basin analyses, environmental and spatial variables were generally poor predictors of variation in assemblage composition. Our results revealed deviation from general biodiversity patterns because beta diversity did not show the expected decreasing trend with latitude. Our results also call for reconsideration of just how predictable stream assemblages are along ecological gradients, with implications for environmental assessment and conservation decisions. Our findings may also be applicable to other dynamic systems where predictability is low

Concept mapping as means to critical thinking

This article describes a study conducted to evaluate the relationship between concept mapping and its ability to foster critical thinking in students during face-to-face and distance education classes in higher education environments. Students were introduced to the construction of concept maps at the beginning of the semester at which time a baseline score of their critical thinking (CT) was measured.  Over the course of one semester student progress was monitored and evaluated on clarity and content of subsequent mapping exercises. At the end of the semester, CT baseline scores were compared to end of semester CT scores and a significant improvement in CT scores could be observed independent of course specific map content. Rooted within constructivist thought it is believed that visually representing thoughts and relationships of past and newly gained knowledge encourages students to think critically and thus facilitate meaningful learning to take place

Improving dichotomous keys for undergraduate teaching

University of Guelph undergraduate students have been struggling to independently identify macroinvertebrates using dichotomous keys in the Biology of Polluted Waters course (BIOL*4350). The course currently uses dichotomous keys that lack definitions of complex anatomical terms and illustrations that place features in the context of the whole organism. This results in taxonomic bias, whereby some macroinvertebrate families are ignored in subsampling, especially for Ephemeroptera (mayflies). This is of particular concern to biotic assessment of stream quality that uses Ephemeroptera as biological indicators. An updated dichotomous key for Ephemeroptera with illustrations and definitions of anatomical terms integrated within the text of the key was developed at the University of Guelph in Winter 2012. The generation of the key utilized a local macroinvertebrate collection, published literature and existing keys. The effectiveness of the updated key was tested against the BIOL*4350 key by comparing the number of correct identifications produced by undergraduate student volunteers using both keys. Additionally, the number of correct identifications by student volunteers who had previously taken BIOL*4350 (n=18) and those who had not taken the course (n=40) were compared. It was predicted that students who had previously taken BIOL*4350 would produce more correct identifications than students who had not. The new key had a significantly higher proportion of correct identifications than the old key (

Applying ecological models to communities of genetic elements: the case of neutral theory

A promising recent development in molecular biology involves viewing the genome as a miniecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here we critically evaluate the prospects of Ecological Neutral Theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyze a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura’s Molecular Neutral Theory and Lynch’s Mutational Hazard Model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models which we dub ‘fitness-neutrality’ and ‘competitive neutrality’. This distinction helps to clarify the various roles for neutral models in genomics, for example, in explaining the evolution of genome size

Hidden diversity: DNA metabarcoding reveals hyper-diverse benthic invertebrate communities

Abstract Background Freshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use and recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally. Aquatic insects and other macroinvertebrates are often used as indicators of ecological condition in freshwater biomonitoring programs; however, these diverse groups can present challenges to morphological identification and coarse-level taxonomic resolution can mask patterns in community composition. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. While individual stream reaches can be very heterogenous, most community ecology studies focus on larger, landscape-level patterns of community composition. A high degree of community variability at the local scale has important implications for both biomonitoring and ecological research, and the incorporation of DNA metabarcoding into local biodiversity assessments will inform future sampling protocols. Results We sampled twenty streams in southern Ontario, Canada, for aquatic macroinvertebrates across multiple time points and assessed local community variability by comparing field replicates taken ten meters apart within the same stream. Using bulk-tissue DNA metabarcoding, we revealed that aquatic macroinvertebrate communities are highly diverse at small spatial scales with unprecedented levels of local taxonomic turnover. We detected over 1600 Operational Taxonomic Units (OTUs) from 149 families, and a single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Benthic communities were largely comprised of rare taxa detected only once per stream despite multiple biological replicates (24–94% rare taxa per site). In addition to numerous rare taxa, our species pool estimates indicated that there was a large proportion of taxa that remained undetected by our sampling regime (14–94% per site). Our sites were located across a gradient of agricultural activity, and while we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use. Within-stream dissimilarity estimates were consistently high for all levels of taxonomic resolution (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales