101 results found
Nowell RW, Almeida P, Wilson CG, et al., 2018, Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species., PLoS Biol, Vol: 16
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 emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. 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 4 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. ricciae are 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 findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer.
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
© 2018 Elsevier Inc. 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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Barraclough TG, Balbi KJ, Ellis RJ, 2012, Evolving Concepts of Bacterial Species, EVOLUTIONARY BIOLOGY, Vol: 39, Pages: 148-157, ISSN: 0071-3260
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
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
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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