Publications
146 results found
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: 23
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: 97
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: 34
Moreno-Letelier A, Mastretta-Yanes A, Barraclough TG, 2014, Late Miocene lineage divergence and ecological differentiation of rare endemic <i>Juniperus blancoi</i>: clues for the diversification of North American conifers, NEW PHYTOLOGIST, Vol: 203, Pages: 335-347, ISSN: 0028-646X
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- Citations: 22
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: 55
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: 2161-2129
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: 1080
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: 9
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: 107
Tang CQ, Leasi F, Obertegger U, et al., 2012, The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 16208-16212, ISSN: 0027-8424
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- Citations: 245
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: 347
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: 25
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: 11
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: 26
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: 28
Perron GG, Lee AEG, Wang Y, et al., 2012, Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 279, Pages: 1477-1484, ISSN: 0962-8452
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- Citations: 54
Lawrence D, Fiegna F, Behrends V, et al., 2012, Species interactions alter evolutionary responses to a novel environment., PLoS Biol, Vol: 10
Studies of evolutionary responses to novel environments typically consider single species or perhaps pairs of interacting species. However, all organisms co-occur with many other species, resulting in evolutionary dynamics that might not match those predicted using single species approaches. Recent theories predict that species interactions in diverse systems can influence how component species evolve in response to environmental change. In turn, evolution might have consequences for ecosystem functioning. We used experimental communities of five bacterial species to show that species interactions have a major impact on adaptation to a novel environment in the laboratory. Species in communities diverged in their use of resources compared with the same species in monocultures and evolved to use waste products generated by other species. This generally led to a trade-off between adaptation to the abiotic and biotic components of the environment, such that species evolving in communities had lower growth rates when assayed in the absence of other species. Based on growth assays and on nuclear magnetic resonance (NMR) spectroscopy of resource use, all species evolved more in communities than they did in monocultures. The evolutionary changes had significant repercussions for the functioning of these experimental ecosystems: communities reassembled from isolates that had evolved in polyculture were more productive than those reassembled from isolates that had evolved in monoculture. Our results show that the way in which species adapt to new environments depends critically on the biotic environment of co-occurring species. Moreover, predicting how functioning of complex ecosystems will respond to an environmental change requires knowing how species interactions will evolve.
Pio DV, Broennimann O, Barraclough TG, et al., 2011, Spatial Predictions of Phylogenetic Diversity in Conservation Decision Making, CONSERVATION BIOLOGY, Vol: 25, Pages: 1229-1239, ISSN: 0888-8892
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- Citations: 37
McInnes L, Baker WJ, Barraclough TG, et al., 2011, Integrating ecology into macroevolutionary research, BIOLOGY LETTERS, Vol: 7, Pages: 644-646, ISSN: 1744-9561
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- Citations: 10
Claremont M, Williams ST, Barraclough TG, et al., 2011, The geographic scale of speciation in a marine snail with high dispersal potential, JOURNAL OF BIOGEOGRAPHY, Vol: 38, Pages: 1016-1032, ISSN: 0305-0270
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- Citations: 58
Schnitzler J, Barraclough TG, Boatwright JS, et al., 2011, Causes of Plant Diversification in the Cape Biodiversity Hotspot of South Africa, SYSTEMATIC BIOLOGY, Vol: 60, Pages: 343-357, ISSN: 1063-5157
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- Citations: 178
Pons J, Fujisawa T, Claridge EM, et al., 2011, Deep mtDNA subdivision within Linnean species in an endemic radiation of tiger beetles from New Zealand (genus <i>Neocicindela</i>), MOLECULAR PHYLOGENETICS AND EVOLUTION, Vol: 59, Pages: 251-262, ISSN: 1055-7903
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- Citations: 33
Schaefer H, Hardy OJ, Silva L, et al., 2011, Testing Darwin's naturalization hypothesis in the Azores, ECOLOGY LETTERS, Vol: 14, Pages: 389-396, ISSN: 1461-023X
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- Citations: 122
Fontaneto D, Iakovenko N, Eyres I, et al., 2011, Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach, HYDROBIOLOGIA, Vol: 662, Pages: 27-33, ISSN: 0018-8158
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- Citations: 57
Swanstrom J, Chen K, Castillo K, et al., 2011, Testing for evidence of inefficient selection in bdelloid rotifers: do sample size and habitat differences matter?, HYDROBIOLOGIA, Vol: 662, Pages: 19-25, ISSN: 0018-8158
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- Citations: 15
Waterman RJ, Bidartondo MI, Stofberg J, et al., 2011, The effects of above- and belowground mutualisms on orchid speciation and coexistence, American Naturalist, Vol: 177, Pages: E54-E68
Barraclough TG, 2010, Evolving entities: towards a unified framework for understanding diversity at the species and higher levels, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 365, Pages: 1801-1813, ISSN: 0962-8436
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- Citations: 50
Valente LM, Reeves G, Schnitzler J, et al., 2010, DIVERSIFICATION OF THE AFRICAN GENUS <i>PROTEA</i> (PROTEACEAE) IN THE CAPE BIODIVERSITY HOTSPOT AND BEYOND: EQUAL RATES IN DIFFERENT BIOMES, EVOLUTION, Vol: 64, Pages: 745-759, ISSN: 0014-3820
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- Citations: 109
Kisel Y, Barraclough TG, 2010, Speciation Has a Spatial Scale That Depends on Levels of Gene Flow, AMERICAN NATURALIST, Vol: 175, Pages: 316-334, ISSN: 0003-0147
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- Citations: 342
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