Imperial College London

ProfessorTimBarraclough

Faculty of Natural SciencesDepartment of Life Sciences (Silwood Park)

Professor of Evolutionary Biology
 
 
 
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Contact

 

+44 (0)20 7594 2247t.barraclough Website

 
 
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Location

 

N2.4Silwood ParkSilwood Park

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Summary

 

Publications

Publication Type
Year
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105 results found

Schmutzer M, Barraclough T, The role of recombination, niche‐specific gene pools and flexible genomes in the ecological speciation of bacteria, Ecology and Evolution, 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.

Journal article

Kontopoulos D-G, van Sebille E, Lange M, Yvon-Durocher G, Barraclough TG, Pawar Set al., 2018, Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints, Publisher: Cold Spring Harbor Laboratory

<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 curve of growth rate of phytoplankton - a globally important functional group -, controlling for potential environmental effects. We find that thermodynamic constraints have a minor influence on the shape of the curve. In particular, we detect a very weak increase of the maximum curve height 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 detect phylogenetic signal in this as well as all other curve parameters. Our results suggest that phytoplankton thermal performance curves adapt to thermal environments largely in the absence of hard thermodynamic constraints.</jats:p>

Working paper

Schley RJ, de la Estrella M, Pérez-Escobar OA, Bruneau A, Barraclough T, Forest F, Klitgård Bet 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.

Journal article

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 [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an Article claiming to supply evidence for this idea. Debortoli et al. [18] 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. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.

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

Tang CQ, Orme CDL, Bunnefeld L, Jones FA, Powell S, Chase MW, Barraclough TG, Savolainen Vet 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.

Journal article

Humphreys AM, Rydin C, Jønsson KA, Alsop D, Callender-Crowe LM, Barraclough TG, Paradis Eet 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

Journal article

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.

Journal article

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.

Journal article

Barraclough TG, Bell TDC, Rivett D, Scheuerl T, Mombrikotb S, Culbert C, Johnstone Eet 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.

Journal article

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.

Journal article

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.

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

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.

Journal article

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

Journal article

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

Journal article

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

Journal article

Johnson LP, Walton GE, Psichas A, Frost GS, Gibson GR, Barraclough TGet 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.

Journal article

Fiegna F, Moreno-Letelier A, Bell T, Barraclough TGet al., 2015, Evolution of species interactions determines microbial community productivity in new environments, ISME JOURNAL, Vol: 9, Pages: 1235-1245, ISSN: 1751-7362

Journal article

Fujisawa T, Vogler AP, Barraclough TG, 2015, Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 282, ISSN: 0962-8452

Journal article

Fujisawa T, Vogler AP, Barraclough TG, 2015, Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles, Proceedings. Biological sciences / The Royal Society, Vol: 282

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

Journal article

Barraclough TG, 2015, How Do Species Interactions Affect Evolutionary Dynamics Across Whole Communities?, ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 46, Vol: 46, Pages: 25-48, ISSN: 1543-592X

Journal article

Tang CQ, Humphreys AM, Fontaneto D, Barraclough TGet al., 2014, Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data, Methods in Ecology and Evolution, Vol: 5, Pages: 1086-1094, ISSN: 2041-210X

1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The generalised mixed Yule coalescent (GMYC) and the Poisson tree process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such asDNAbarcodes. 2. Here, we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothingmethods.We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2000 separate species delimitation analyses across 16 empirical data sets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYCapproaches with BEAST trees for obtaining species hypotheses.

Journal article

Tang CQ, Obertegger U, Fontaneto D, Barraclough TGet al., 2014, SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS, EVOLUTION, Vol: 68, Pages: 2901-2916, ISSN: 0014-3820

Journal article

Moreno-Letelier A, Mastretta-Yanes A, Barraclough TG, 2014, Late Miocene lineage divergence and ecological differentiation of rare endemic Juniperus blancoi: clues for the diversification of North American conifers, NEW PHYTOLOGIST, Vol: 203, Pages: 335-347, ISSN: 0028-646X

Journal article

Humphreys AM, Barraclough TG, 2014, The evolutionary reality of higher taxa in mammals, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 281, ISSN: 0962-8452

Journal article

Frost GS, Walton GE, Swann JR, Psichas A, Costabile A, Johnson LP, Sponheimer M, Gibson GR, Barraclough TGet al., 2014, Impacts of Plant-Based Foods in Ancestral Hominin Diets on the Metabolism and Function of Gut Microbiota In Vitro, mBio, Vol: 5, ISSN: 2161-2129

Journal article

Fujisawa T, Barraclough TG, 2013, Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets, SYSTEMATIC BIOLOGY, Vol: 62, Pages: 707-724, ISSN: 1063-5157

Journal article

McInnes L, Jones FA, Orme CDL, Sobkowiak B, Barraclough TG, Chase MW, Govaerts R, Soltis DE, Soltis PS, Savolainen Vet al., 2013, Do Global Diversity Patterns of Vertebrates Reflect Those of Monocots?, PLOS ONE, Vol: 8, ISSN: 1932-6203

Journal article

Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, Barraclough TG, Micklem G, Tunnacliffe Aet al., 2012, Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers, PLOS GENETICS, Vol: 8, ISSN: 1553-7404

Journal article

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