118 results found
Barraclough T, Peck L, Nowell R, 2021, Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides, BMC Genomics, ISSN: 1471-2164
Kontopoulos D-G, Smith TP, Barraclough TG, et al., 2020, Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate, PLoS Biology, Vol: 18, ISSN: 1544-9173
Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of global climate change. A key aspect of an organism's thermal performance curve (TPC)-the relationship between fitness-related trait performance and temperature-is its thermal sensitivity, i.e., the rate at which trait values increase with temperature within its typically experienced thermal range. For a given trait, the distribution of thermal sensitivities across species, often quantified as "activation energy" values, is typically right-skewed. Currently, the mechanisms that generate this distribution are unclear, with considerable debate about the role of thermodynamic constraints versus adaptive evolution. Here, using a phylogenetic comparative approach, we study the evolution of the thermal sensitivity of population growth rate across phytoplankton (Cyanobacteria and eukaryotic microalgae) and prokaryotes (bacteria and archaea), 2 microbial groups that play a major role in the global carbon cycle. We find that thermal sensitivity across these groups is moderately phylogenetically heritable, and that its distribution is shaped by repeated evolutionary convergence throughout its parameter space. More precisely, we detect bursts of adaptive evolution in thermal sensitivity, increasing the amount of overlap among its distributions in different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of 2 physiological rates underlying growth rate: net photosynthesis and respiration of plants. Furthermore, we find that these episodes of evolutionary convergence are consistent with 2 opposing forces: decrease in thermal sensitivity due to environmental fluctuations and increase due to adaptation to stable environments. Overall, our results indicate that adaptation can lead to large and relatively rapid shifts in thermal sensitivity, especially in microbes f
Kontopoulos D-G, Patmanidis I, Barraclough TG, et al., 2020, Higher temperatures worsen the effects of mutations on protein stability
<jats:title>Abstract</jats:title><jats:p>Understanding whether and how temperature increases alter the effects of mutations on protein stability is crucial for understanding the limits to thermal adaptation by organisms. Currently, it is generally assumed that the stability effects of mutations are independent of temperature. Yet, mutations should become increasingly destabilizing as temperature rises due to the increase in the energy of atoms. Here, by performing an extensive computational analysis on the essential enzyme adenylate kinase in prokaryotes, we show, for the first time, that mutations become more destabilizing with temperature both across and within species. Consistent with these findings, we find that substitution rates of prokaryotes decrease nonlinearly with temperature. Our results suggest that life on Earth likely originated in a moderately thermophilic and thermally fluctuating environment, and indicate that global warming should decrease the per-generation rate of molecular evolution of prokaryotes.</jats:p>
Nowell RW, Wilson CG, Almeida P, et al., 2020, Evolutionary dynamics of transposable elements in bdelloid rotifers
<jats:title>Abstract</jats:title><jats:p>Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates where males are thus far unknown. Contrary to expectations, we find a diverse range of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms, but we report that bdelloids share a large and unusual expansion of genes involved in RNAi-mediated TE suppression. This suggests that enhanced cellular defence mechanisms might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.</jats:p>
Schley RJ, Pennington RT, Perez-Escobar OA, et al., 2020, Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity, MOLECULAR ECOLOGY, Vol: 29, Pages: 4170-4185, ISSN: 0962-1083
Kontopoulos D, van Sebille E, Lange M, et al., 2020, Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints, Evolution, Vol: 74, Pages: 775-790, ISSN: 0014-3820
To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness‐related rates to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can—at least partly—overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta‐analysis of the thermal performance curves of growth rate of phytoplankton—a globally important functional group—, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak “hotter‐is‐better” constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.
Sheppard R, Beddis A, Barraclough T, 2020, The role of hosts, plasmids and environment in determining plasmid transfer rates: a meta-analysis, Plasmid, Vol: 108, ISSN: 0147-619X
Plasmids transfer at highly variable rates which spread over 10 orders of magnitude. While rates have been measured for decades and it is known that the rates are affected by biotic and abiotic factors, it is unclear how and to what extent these factors determine the rates of transfer. We performed a meta-analysis of 1224 published transfer rates from 33 papers (filtered to 612 transfer rates) to assess this variation. Over three quarters of the variation can be predicted, with plasmid repression and media type (solid versus liquid) identified as general variables explaining the most variation. Of the host and plasmid identities, identity of the recipient bacterium explained the most variation, up to 34% in some models, and more than any other explanatory variable. These results emphasize the role of the recipient in determining the rate of transfer, and show an improved range of transfer values and their correlates that can be used in future when modeling plasmid persistence.
Scheuerl T, Hopkins M, Nowell R, et al., 2020, Bacterial adaptation is constrained in complex communities, Nature Communications, Vol: 11, ISSN: 2041-1723
A major unresolved question is how bacteria living in complex communities respond to environmental changes. In communities, biotic interactions may either facilitate or constrain evolution depending on whether the interactions expand or contract the range of ecological opportunities. A fundamental challenge is to understand how the surrounding biotic community modifies evolutionary trajectories as species adapt to novel environmental conditions. Here we show that community context can dramatically alter evolutionary dynamics using a novel approach that ‘cages’ individual focal strains within complex communities. We find that evolution of focal bacterial strains depends on properties both of the focal strain and of the surrounding community. In particular, there is a stronger evolutionary response in low-diversity communities, and when the focal species have a larger genome and are initially poorly adapted. We see how community context affects resource usage and detect genetic changes involved in carbon metabolism and inter-specific interaction. The findings demonstrate that adaptation to new environmental conditions should be investigated in the context of interspecific interactions.
Schley RJ, Pennington RT, Pérez-Escobar OA, et al., 2019, Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity
<jats:title>Abstract</jats:title><jats:p>Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (<jats:italic>Brownea</jats:italic>, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events between <jats:italic>Brownea</jats:italic> lineages and indicated that gene tree incongruence in <jats:italic>Brownea</jats:italic> is best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ∼19,000 ddRAD loci recovered a high degree of shared variation between two <jats:italic>Brownea</jats:italic> species which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization’s rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.</jats:p>
Barraclough T, 2019, Species matter for predicting the functioning of evolving microbial communities – an eco-evolutionary model, PLoS ONE, Vol: 14, ISSN: 1932-6203
Humans depend on microbial communities for numerous ecosystem services such as global nutrient cycles, plant growth and their digestive health. Yet predicting dynamics and functioning of these complex systems is hard, making interventions to enhance functioning harder still. One simplifying approach is to assume that functioning can be predicted from the set of enzymes present in a community. Alternatively, ecological and evolutionary dynamics of species, which depend on how enzymes are packaged among species, might be vital for predicting community functioning. I investigate these alternatives by extending classical chemostat models of bacterial growth to multiple species that evolve in their use of chemical resources. Ecological interactions emerge from patterns of resource use, which change as species evolve in their allocation of metabolic enzymes. Measures of community functioning derive in turn from metabolite concentrations and bacterial density. Although the model shows considerable functional redundancy, species packaging does matter by introducing constraints on whether enzyme levels can reach optimum levels for the whole system. Evolution can either promote or reduce functioning compared to purely ecological models, depending on the shape of trade-offs in resource use. The model provides baseline theory for interpreting emerging data on evolution and functioning in real bacterial communities.
Kontopoulos D-G, Smith TP, Barraclough TG, et al., 2019, Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate, Publisher: Cold Spring Harbor Laboratory
<jats:title>Abstract</jats:title><jats:p>Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of global climate change. A key aspect of an organism’s thermal performance curve—the relationship between fitness-related trait performance and temperature—is its thermal sensitivity, i.e., the rate at which trait values increase with temperature within its typically-experienced thermal range. For a given trait, the distribution of thermal sensitivities across species, often quantified as “activation energy” values, is typically right-skewed. Currently, the mechanisms that generate this distribution are unclear, with considerable debate about the role of thermodynamic constraints vs adaptive evolution. Here, using a phylogenetic comparative approach, we study the evolution of the thermal sensitivity of population growth rate across phytoplankton (Cyanobacteria and eukaryotic microalgae) and prokaryotes (bacteria and archaea), two microbial groups that play a major role in the global carbon cycle. We find that thermal sensitivity across these groups is moderately phylogenetically heritable, and that its distribution is shaped by repeated evolutionary convergence throughout its parameter space. More precisely, we detect bursts of adaptive evolution in thermal sensitivity, increasing the amount of overlap among its distributions in different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of two physiological rates underlying growth rate: net photosynthesis and respiration of plants. Furthermore, we find that these episodes of evolutionary convergence are consistent with two opposing forces: decrease in thermal sensitivity due to environmental fluctuations and increase due to adaptation to stable environments. Overall, our results indicate that adaptation can lead to large a
Barraclough TG, 2019, Species matter for predicting the functioning of evolving microbial communities
<jats:title>ABSTRACT</jats:title><jats:p>Humans depend on microbial communities for numerous ecosystem services such as global nutrient cycles, plant growth and their digestive health. Yet predicting dynamics and functioning of these complex systems is hard, making interventions to enhance functioning harder still. One simplifying approach is to assume that functioning can be predicted from the set of enzymes present in a community. Alternatively, ecological and evolutionary dynamics of species, which depend on how enzymes are packaged among species, might be vital for predicting community functioning. I investigate these alternatives by extending classical chemostat models of bacterial growth to multiple species that evolve in their use of chemical resources. Ecological interactions emerge from patterns of resource use, which change as species evolve in their allocation of metabolic enzymes. Measures of community functioning derive in turn from metabolite concentrations and bacterial density. Although the model shows considerable functional redundancy, species packaging does matter by introducing constraints on whether enzyme levels can reach optimum levels for the whole system. Evolution can either promote or reduce functioning compared to purely ecological models, depending on the shape of trade-offs in resource use. The model provides baseline theory for interpreting emerging data on evolution and functioning in real bacterial communities.</jats:p>
Schmutzer M, Barraclough T, 2019, The role of recombination, niche‐specific gene pools and flexible genomes in the ecological speciation of bacteria, Ecology and Evolution, Vol: 9, Pages: 4544-4556, ISSN: 2045-7758
Bacteria diversify into genetic clusters analogous to those observed in sexual eukaryotes, but the definition of bacterial species is an ongoing problem. Recent work has focused on adaptation to distinct ecological niches as the main driver of clustering, but there remains debate about the role of recombination in that process. One view is that homologous recombination occurs too rarely for gene flow to constrain divergent selection. Another view is that homologous recombination is frequent enough in many bacterial populations that barriers to gene flow are needed to permit divergence. Niche-specific gene pools have been proposed as a general mechanism to limit gene flow. We use theoretical models to evaluate additional hypotheses that evolving genetic architecture, specifically the effect sizes of genes and gene gain and loss, can limit gene flow between diverging populations. Our model predicts that i) in the presence of gene flow and recombination, ecological divergence is concentrated in few loci of large effect, and ii) high rates of gene flow plus recombination promote gene loss and favor the evolution of niche-specific genes. The results show that changing genetic architecture and gene loss can facilitate ecological divergence, even without niche-specific gene pools. We discuss these results in the context of recent studies of sympatric divergence in microbes.
Kontopoulos D-G, van Sebille E, Lange M, et al., 2018, Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints, Publisher: Cold Spring Harbor Laboratory
<jats:title>Abstract</jats:title><jats:p>To better predict how populations and communities respond to climatic temperature variation, it is necessary to understand how the shape of the response of fitness-related traits to temperature evolves (the thermal performance curve). Currently, there is disagreement about the extent to which the evolution of thermal performance curves is constrained. One school of thought has argued for the prevalence of thermodynamic constraints through enzyme kinetics, whereas another argues that adaptation can—at least partly—overcome such constraints. To shed further light on this debate, we perform a phylogenetic meta-analysis of the thermal performance curves of growth rate of phytoplankton—a globally important functional group—, controlling for environmental effects (habitat type and thermal regime). We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of maximum performance with the temperature at which the curve peaks, suggesting a weak “hotter-is-better” constraint. Also, instead of a constant thermal sensitivity of growth across species, as might be expected from strong constraints, we find that all aspects of the thermal performance curve evolve along the phylogeny. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.</jats:p>
Schley RJ, de la Estrella M, Pérez-Escobar OA, et al., 2018, Is Amazonia a ‘museum’ for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae), Molecular Phylogenetics and Evolution, Vol: 126, Pages: 279-292, ISSN: 1055-7903
The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the ‘cradle’ or ‘museum’ model of diversification, i.e. whether species evolved rapidly over a short time period, or gradually over many millions of years. We also aimed to trace the spatio-temporal evolution of the clade by estimating ancestral biogeographical patterns in the group. We used BEAST to build a dated phylogeny of 73 Brownea clade species using three molecular markers (ITS, trnK and psbA-trnH), resulting in well-resolved phylogenetic relationships within the clade, as well as robust divergence time estimates from which we inferred diversification rates and ancestral biogeography. Our analyses revealed an Eocene origin for the group, after which the majority of diversification happened in Amazonia during the Miocene, most likely concurrent with climatic and geological changes caused by the rise of the Andes. We found no shifts in diversification rate over time, suggesting a gradual accumulation of lineages with low extinction rates. These results may help to understand why Amazonia is host to the highest diversity of tree species on Earth.
Wilson CG, Nowell R, Barraclough T, 2018, Cross-contamination explains "inter- and intraspecific horizontal genetic transfers" between asexual bdelloid rotifers, Current Biology, Vol: 28, Pages: 2436-2444.e14, ISSN: 1879-0445
A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest 17 in males [3–9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10–12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13–17]. This well-substantiated finding has invited speculation  that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex . In 2016, Current Biology published an Article claiming to supply evidence for this idea. Debortoli et al.  sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers". Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitoc hondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al.  provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.
Barraclough TG, Nowell R, Wilson C, et al., 2018, Comparative genomics of bdelloid rotifers: insights from desiccating and nondesiccating species, PLoS Biology, Vol: 16, ISSN: 1544-9173
Bdelloid rotifers are a Class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasized desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole genome sequences of three bdelloid species: Rotaria macrura and Rotaria magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccationtolerant. In combination with the published assembly of Adineta vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all four bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciaeare largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous 50 findings of high levels of horizontally transferred non-metazoan genes in both desiccating and non-desiccating bdelloid species, and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call
Tang CQ, Orme CDL, Bunnefeld L, et al., 2016, Global monocot diversification: geography better explains variation in species richness than environment or biology, Botanical Journal of the Linnean Society, Vol: 183, Pages: 1-15, ISSN: 0024-4074
Monocots account for a quarter of angiosperm species richness and are among the most economically and culturally important plants, including cereals (grasses), palms, orchids and lilies. Previous investigations of correlates of monocot species diversity have varied in scale and usually concentrated on a few drivers of diversification. Here, to disentangle the correlates of monocot diversity, we reconstructed a genus-level phylogenetic tree (1987 of the 2713 genera) and compiled an extensive database of abiotic, biotic and geographical characteristics to assess whether differences in these traits correlate with the vast asymmetrical species richness among genera present in this clade. Our results support several classical biodiversity theories, including species–area relationships, and latitudinal and elevational diversity gradients. Furthermore, interactions among these factors explain an additional 10% of the variation (compared to 36% from the main effects alone). We conclude that higher species richness among monocot genera is associated with geographical variables, especially larger ranges and lower elevations, rather than physical environment or physiology.
Humphreys AM, Rydin C, Jønsson KA, et al., 2016, Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method, Methods in Ecology and Evolution, Vol: 7, Pages: 1366-1375, ISSN: 2041-210X
1. There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade-dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade-independent approaches.2. We simulated >32 000 trees under two clade-independent models: constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs.3. The GMYC null model was rejected at a high rate on CRBD-simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD-simulated trees. These metrics could be used in future to distinguish clade-dependent and clade-independent models.4. In conclusion, detection of higher ESUs using the GMYC is robust against some clade-inde
Barraclough TG, Fujisawa T, Aswad A, 2016, A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets, Systematic Biology, Vol: 65, Pages: 759-771, ISSN: 1076-836X
Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces two new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published and newly generated data. Analyses of simulated data demonstrate that the combined method has favourable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases.
Jordan S, Barraclough T, Rosindell JL, 2016, Quantifying the effects of the break up of Pangaea on global terrestrial diversification with neutral theory, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 371, ISSN: 1471-2970
The historic richness of most taxonomic groups increases substantially over geological time. Explanations for this fall broadly into two categories: bias in the fossil record and elevated net rates of diversification in recent periods. For example, the break up of Pangaea and isolation between continents might have increased net diversification rates. In this study, we investigate the effect on terrestrial diversification rates of the increased isolation between land masses brought about by continental drift. We use ecological neutral theory as a means to study geologically complex scenarios tractably. Our models show the effects of simulated geological events that affect all species equally, without the added complexity of further ecological processes. We find that continental drift leads to an increase in diversity only where isolation between continents leads to additional speciation through vicariance, and where higher taxa with very low global diversity are considered. We conclude that continental drift by itself is not sufficient to account for the increase in terrestrial species richness observed in the fossil record.
Barraclough TG, Bell TDC, Rivett D, et al., 2016, Resource-dependent attenuation of species interactions during bacterial succession, ISME Journal, Vol: 10, Pages: 2259-2268, ISSN: 1751-7362
Bacterial communities are vital for many economically and ecologically important processes. The role of bacterial community composition in determining ecosystem functioning depends critically on interactions among bacterial taxa. Several studies have shown that, despite a predominance of negative interactions in communities, bacteria are able to display positive interactions given the appropriate evolutionary or ecological conditions. We were interested in how interspecific interactions develop over time in a naturalistic setting of low resource supply rates. We assembled aquatic bacterial communities in microcosms and assayed the productivity (respiration and growth) and substrate degradation while tracking community composition. The results demonstrated that while bacterial communities displayed strongly negative interactions during the early phase of colonisation and acclimatisation to novel biotic and abiotic factors, this antagonism declined over time towards a more neutral state. This was associated with a shift from use of labile substrates in early succession to use of recalcitrant substrates later in succession, confirming a crucial role of resource dynamics in linking interspecific interactions with ecosystem functioning.
Lawrence D, Barraclough TG, 2016, Evolution of resource use along a gradient of stress leads to increased facilitation, Oikos, ISSN: 1600-0706
The stress-gradient hypothesis (SGH) posits that the relative importance of facilitative interactions versus negative interactions increases as levels of abiotic stress increase. Originally formulated in empirical studies of plant populations, in recent years the SGH has been found to describe how interactions change in response to stress in a wide range of species including algae, mussels and moths. However, there has been little theory attempting to predict patterns from first principles in relation to different types of interactions. Here, we use mathematical models of microbial populations to investigate whether patterns consistent with the SGH arise when species interact through resource use and allelopathy. Evolution alters the degree to which competition for resource use versus facilitation (cross-feeding) occurs. Our results are consistent with the SGH; species interactions evolve to be more facilitative as average stress intensifies. This occurs because at greater stress the species evolve to become specialists on either of the two resources thereby decreasing overlap in resource use and increasing facilitation through cross-feeding. In addition, the production of toxic allelopathic compounds decreases as stress intensifies due to density-dependent effects. Our results suggest that the SGH could arise through fundamental interactions that are common to many organisms and therefore that the SGH could be a more widespread phenomenon than previously recognised.
Barraclough TG, Lawrence D, Bell T, 2015, The effect of immigration on the adaptation of microbial communities to warming, American Naturalist, Vol: 187, ISSN: 1537-5323
Theory predicts that immigration can either enhance or impair the rate at which species and whole communities adapt to environmental change, depending on the traits of genotypes and species in the source pool relative to local conditions. These responses in turn will determine how well whole communities function in changing environments. We tested the effects of immigration and experimental warming on microbial communities during an 81 day field experiment. The effects of immigration depended on the warming treatment. In warmed communities immigration was detrimental to community growth whereas in ambient communities it was beneficial. This result is explained if colonists came from a local species pool pre-adapted to ambient conditions. Loss of metabolic diversity, however, was buffered by immigration in both environments. Communities showed increasing local adaptation to temperature conditions during the experiment and this was independent of whether or not they received immigration. Genotypes that comprised the communities were not locally adapted, however, indicating that community local adaptation can be independent of adaptation of component genotypes. Our results are consistent with a greater role for species interactions rather than adaptation of constituent species in determining local adaptation of whole communities, and confirm that immigration can either enhance or impair community responses to environmental change depending on the environmental context.
Eyres I, Boschetti C, Crisp A, et al., 2015, Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats, BMC Biology, Vol: 13, ISSN: 1741-7007
Background: Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer inmulticellular eukaryotes. Bdelloids rotifers are microscopic animals that contain a higherproportion of horizontally transferred, non-metazoan genes in their genomes than typical ofanimals. It has been hypothesized that bdelloids incorporate foreign DNA when they repairtheir chromosomes following double-strand breaks caused by desiccation. HGT might therebycontribute to species divergence and adaptation, as in prokaryotes. If so, we expect thatspecies should differ in their complement of foreign genes, rather than sharing the same set offoreign genes inherited from a common ancestor. Furthermore, there should be more foreigngenes in species that desiccate more frequently. We tested these hypotheses by surveyingHGT in four congeneric species of bdelloids from different habitats: two from permanentaquatic habitats and two from temporary aquatic habitats that desiccate regularly.Results: Transcriptomes of all four species contain many genes with a closer match to nonmetazoangenes than to metazoan genes. Whole genome sequencing of one species confirmedthe presence of these foreign genes in the genome. Nearly half of foreign genes are sharedbetween all four species and an outgroup from another family, but many hundreds are uniqueto particular species, which indicates that HGT is ongoing. Using a dated phylogeny, weestimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years.Consistent with the desiccation hypothesis, the level of HGT is higher in the species thatexperience regular desiccation events than those that do not. However, HGT still contributedhundreds of foreign genes to the species from permanently aquatic habitats. Foreign geneswere mainly enzymes with various annotated functions that include catabolism of complexpolysaccharides and stress responses. We found evidence of differential loss of ancestralforeign genes previously associated with desic
Barraclough TG, Bell T, Scheuerl T, 2015, Saturating effects of species diversity on life-history evolution in bacteria, Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol: 282, ISSN: 0080-4649
Species interactions can play a major role in shaping evolution in new environments. In theory, species interactions can either stimulate evolution by promoting coevolution or inhibit evolution by constraining ecological opportunity. The relative strength of these effects should vary as species richness increases, and yet there has been little evidence for evolution of component species in communities. We evolved bacterial microcosms containing between 1 and 12 species in three different environments. Growth rates and yields of isolates that evolved in communities were lower than those that evolved in monocultures, consistent with recent theory that competition constrains species to specialize on narrower sets of resources. This effect saturated or reversed at higher levels of richness, consistent with theory that directional effects of species interactions should weaken in more diverse communities. Species varied considerably, however, in their responses to both environment and richness levels. Mechanistic models and experiments are now needed to understand and predict joint evolutionary dynamics of species in diverse communities.
Moreno-Letelier A, Barraclough TG, 2015, Mosaic genetic differentiation along environmental and geographic gradients indicate divergent selection in a white pine species complex, EVOLUTIONARY ECOLOGY, Vol: 29, Pages: 733-748, ISSN: 0269-7653
Fontaneto D, Barraclough TG, 2015, Do Species Exist in Asexuals? Theory and Evidence from Bdelloid Rotifers, INTEGRATIVE AND COMPARATIVE BIOLOGY, Vol: 55, Pages: 253-263, ISSN: 1540-7063
Barraclough TG, Humphreys AM, 2015, The evolutionary reality of species and higher taxa in plants: a survey of post-modern opinion and evidence, NEW PHYTOLOGIST, Vol: 207, Pages: 291-296, ISSN: 0028-646X
Johnson LP, Walton GE, Psichas A, et al., 2015, Prebiotics modulate the effects of antibiotics on gut microbial diversity and functioning in vitro, Nutrients, Vol: 7, Pages: 4480-4497, ISSN: 2072-6643
Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs), which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation—another method used to modulate gut composition and function—could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre), inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria) or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.
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