Publications
99 results found
Tang CQ, Orme CDL, Bunnefeld L, et al., 2017, Global monocot diversification: geography explains variation in species richness better than environment or biology, BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Vol: 183, Pages: 1-15, ISSN: 0024-4074
Fujisawa T, Aswad A, Barraclough TG, 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: 1063-5157
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- Citations: 1
Humphreys AM, Rydin C, Jonsson 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
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- Citations: 1
Jordan SMR, Barraclough TG, Rosindell J, 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: 0962-8436
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- Citations: 2
Lawrence D, Barraclough TG, 2016, Evolution of resource use along a gradient of stress leads to increased facilitation, OIKOS, Vol: 125, Pages: 1284-1295, ISSN: 0030-1299
Lawrence D, Bell T, Barraclough TG, 2016, The Effect of Immigration on the Adaptation of Microbial Communities to Warming, AMERICAN NATURALIST, Vol: 187, Pages: 236-248, ISSN: 0003-0147
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- Citations: 2
Rivett DW, Scheuerl T, Culbert CT, et al., 2016, Resource-dependent attenuation of species interactions during bacterial succession, ISME JOURNAL, Vol: 10, Pages: 2259-2268, ISSN: 1751-7362
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- Citations: 2
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
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- Citations: 10
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
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- Citations: 9
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
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- Citations: 8
Fiegna F, Moreno-Letelier A, Bell T, et al., 2015, Evolution of species interactions determines microbial community productivity in new environments, ISME Journal, Vol: 9, Pages: 1235-1245, ISSN: 1751-7362
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- Citations: 20
Fiegna F, Scheuerl T, Moreno-Letelier A, et al., 2015, Saturating effects of species diversity on life-history evolution in bacteria, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 282, ISSN: 0962-8452
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
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- Citations: 1
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
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- Citations: 5
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.
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
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- Citations: 5
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
Frost GS, Walton GE, Swann JR, et 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: 2150-7511
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- Citations: 6
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
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- Citations: 17
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
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- Citations: 6
Tang CQ, Humphreys AM, Fontaneto D, et 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.
Tang CQ, Obertegger U, Fontaneto D, et al., 2014, SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS, EVOLUTION, Vol: 68, Pages: 2901-2916, ISSN: 0014-3820
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- Citations: 10
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
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- Citations: 226
McInnes L, Jones FA, Orme CDL, et al., 2013, Do Global Diversity Patterns of Vertebrates Reflect Those of Monocots?, PLOS ONE, Vol: 8, ISSN: 1932-6203
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- Citations: 5
Barraclough TG, Balbi KJ, Ellis RJ, 2012, Evolving Concepts of Bacterial Species, EVOLUTIONARY BIOLOGY, Vol: 39, Pages: 148-157, ISSN: 0071-3260
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- Citations: 13
Bergsten J, Bilton DT, Fujisawa T, et al., 2012, The Effect of Geographical Scale of Sampling on DNA Barcoding, SYSTEMATIC BIOLOGY, Vol: 61, Pages: 851-869, ISSN: 1063-5157
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- Citations: 156
Boschetti C, Carr A, Crisp A, et al., 2012, Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers, PLOS GENETICS, Vol: 8, ISSN: 1553-7404
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- Citations: 55
Eyres I, Frangedakis E, Fontaneto D, et al., 2012, Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers, BMC EVOLUTIONARY BIOLOGY, Vol: 12, ISSN: 1471-2148
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- Citations: 4
Fontaneto D, Tang CQ, Obertegger U, et al., 2012, Different Diversification Rates Between Sexual and Asexual Organisms, EVOLUTIONARY BIOLOGY, Vol: 39, Pages: 262-270, ISSN: 0071-3260
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- Citations: 14
Kisel Y, Moreno-Letelier AC, Bogarin D, et al., 2012, TESTING THE LINK BETWEEN POPULATION GENETIC DIFFERENTIATION AND CLADE DIVERSIFICATION IN COSTA RICAN ORCHIDS, EVOLUTION, Vol: 66, Pages: 3035-3052, ISSN: 0014-3820
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- Citations: 11
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