Imperial College London


Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Research Associate



thomas.smith1 Website




Unit CSilwood ParkSilwood Park





Publication Type

10 results found

Smith TP, Flaxman S, Gallinat AS, Kinosian SP, Stemkovski M, Unwin HJT, Watson OJ, Whittaker C, Cattarino L, Dorigatti I, Tristem M, Pearse WDet al., 2021, Temperature and population density influence SARS-CoV-2 transmission in the absence of nonpharmaceutical interventions., Proc Natl Acad Sci U S A, Vol: 118

As COVID-19 continues to spread across the world, it is increasingly important to understand the factors that influence its transmission. Seasonal variation driven by responses to changing environment has been shown to affect the transmission intensity of several coronaviruses. However, the impact of the environment on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains largely unknown, and thus seasonal variation remains a source of uncertainty in forecasts of SARS-CoV-2 transmission. Here we address this issue by assessing the association of temperature, humidity, ultraviolet radiation, and population density with estimates of transmission rate (R). Using data from the United States, we explore correlates of transmission across US states using comparative regression and integrative epidemiological modeling. We find that policy intervention ("lockdown") and reductions in individuals' mobility are the major predictors of SARS-CoV-2 transmission rates, but, in their absence, lower temperatures and higher population densities are correlated with increased SARS-CoV-2 transmission. Our results show that summer weather cannot be considered a substitute for mitigation policies, but that lower autumn and winter temperatures may lead to an increase in transmission intensity in the absence of policy interventions or behavioral changes. We outline how this information may improve the forecasting of COVID-19, reveal its future seasonal dynamics, and inform intervention policies.

Journal article

Smith TP, Mombrikotb S, Ransome E, Kontopoulos D-G, Pawar S, Bell Tet al., 2021, Latent functional diversity may accelerate microbial community responses to environmental fluctuations, Publisher: Cold Spring Harbor Laboratory

Whether and how whole ecological communities can respond to climate change remains an open question. With their fast generation times and abundant functional diversity, microbes in particular harbor great potential to exhibit community-level adaptation through a combination of strain-level adaptation, phenotypic plasticity, and species sorting. However, the relative importance of these mechanisms remains unclear. Here, through a novel laboratory experiment, we show that bacterial communities can exhibit a remarkable degree of community-level adaptability through a combination of phenotypic plasticity and species sorting alone. Specifically, by culturing soil communities from a single location at six temperatures between 4°C and 50°C, we find that multiple strains well adapted to different temperatures can be isolated from the community, without immigration or strain-level adaptation. This is made possible by the ability of strains with different physiological and life history traits to “switch on” under suitable conditions, with phylogenetically distinct K-specialist taxa favoured under cooler conditions, and r-specialist taxa in warmer conditions. Our findings provide new insights into microbial community adaptation, and suggest that microbial community function is likely to respond rapidly to climatic fluctuations, through changes in species composition during repeated community assembly dynamics.

Working paper

Smith TP, Dorigatti I, Mishra S, Volz E, Walker PGT, Ragonnet-Cronin M, Tristem M, Pearse WDet al., 2021, Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission intensity

<jats:title>Abstract</jats:title><jats:p>Previous work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that, like other SARS-CoV-2 strains, lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of England. However, we also find evidence of B.1.1.7 having a transmission advantage at warmer temperatures compared to other strains. This implies that spring and summer conditions are unlikely to slow B.1.1.7’s invasion in Europe and across the Northern hemisphere - an important consideration for public health interventions.</jats:p>

Journal article

Kontopoulos D-G, Smith TP, Barraclough TG, Pawar Set 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

Journal article

Smith TP, Flaxman S, Gallinat AS, Kinosian SP, Stemkovski M, Unwin HJT, Watson OJ, Whittaker C, Cattarino L, Dorigatti I, otherset al., 2020, Environment influences SARS-CoV-2 transmission in the absence of non-pharmaceutical interventions, medRxiv

Journal article

Smith T, Thomas TJH, Garcia-Carreras B, Sal S, Yvon-Durocher G, Bell T, Pawar Set al., 2019, Community-level respiration of prokaryotic microbes may rise with global warming, Nature Communications, Vol: 10, ISSN: 2041-1723

Understanding how the metabolic rates of prokaryotes respond to temperature is fun-damental to our understanding of how ecosystem functioning will be altered by climatechange, as these micro-organisms are major contributors to global carbon efflux. Ecologicalmetabolic theory suggests that species living at higher temperatures evolve higher growthrates than those in cooler niches due to thermodynamic constraints. Here, using a globalprokaryotic dataset, we find that maximal growth rate at thermal optimum increases withtemperature for mesophiles (temperature optima.45◦C), but not thermophiles (&45◦C).Furthermore, short-term (within-day) thermal responses of prokaryotic metabolic rates aretypically more sensitive to warming than those of eukaryotes. Because climatic warmingwill mostly impact ecosystems in the mesophilic temperature range, we conclude that asmicrobial communities adapt to higher temperatures, their metabolic rates and therefore,biomass-specific CO2production, will inevitably rise. Using a mathematical model, weillustrate the potential global impacts of these findings.

Journal article

Papadopulos AST, Igea J, Smith TP, Hutton I, Baker WJ, Butlin RK, Savolainen Vet al., 2019, Ecological speciation in sympatric palms: 4. Demographic analyses support speciation of Howea in the face of high gene flow, Evolution, Vol: 73, Pages: 1996-2002, ISSN: 0014-3820

The idea that populations must be geographically isolated (allopatric) to evolve into separate species has persisted for a long time. It is now clear that new species can also diverge despite ongoing genetic exchange, but few accepted cases of speciation in sympatry have held up when scrutinised using modern approaches. Here, we examined evidence for speciation of the Howea palms of Lord Howe Island, Australia, in light of new genomic data. We used coalescence-based demographic models combined with double digest restriction-site associated DNA sequencing of multiple individuals and provide support for previous claims by Savolainen et al. (Nature 441: 210–213, 2006) that speciation in Howea did occur in the face of gene flow.

Journal article

Barraclough TG, Nowell R, Wilson C, Smith Tet 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

Journal article

Kontopoulos DG, García-Carreras B, Sal S, Smith TP, Pawar Set al., 2018, Use and misuse of temperature normalisation in meta-analyses of thermal responses of biological traits, PeerJ, Vol: 6, ISSN: 2167-8359

There is currently unprecedented interest in quantifying variation in thermal physiologyamong organisms, especially in order to understand and predict the biological impactsof climate change. A key parameter in this quantification of thermal physiologyis the performance or value of a rate, across individuals or species, at a commontemperature (temperature normalisation). An increasingly popular model for fittingthermal performance curves to data—the Sharpe-Schoolfield equation—can yieldstrongly inflated estimates of temperature-normalised rate values. These deviationsoccur whenever a key thermodynamic assumption of the model is violated, i.e., whenthe enzyme governing the performance of the rate is not fully functional at the chosenreference temperature. Using data on 1,758 thermal performance curves across awide range of species, we identify the conditions that exacerbate this inflation. Wethen demonstrate that these biases can compromise tests to detect metabolic coldadaptation, which requires comparison of fitness or rate performance of differentspecies or genotypes at some fixed low temperature. Finally, we suggest alternativemethods for obtaining unbiased estimates of temperature-normalised rate values formeta-analyses of thermal performance across species in climate change impact studies.

Journal article

Eyres I, Boschetti C, Crisp A, Smith TP, Fontaneto D, Tunnacliffe A, Barraclough TGet 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

Journal article

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