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  • Journal article
    Hudson LN, Newbold T, Contu S, Hill SL, Lysenko I, De Palma A, Phillips HR, Alhusseini TI, Bedford FE, Bennett DJ, Booth H, Burton VJ, Chng CW, Choimes A, Correia DL, Day J, Echeverría-Londoño S, Emerson SR, Gao D, Garon M, Harrison ML, Ingram DJ, Jung M, Kemp V, Kirkpatrick L, Martin CD, Pan Y, Pask-Hale GD, Pynegar EL, Robinson AN, Sanchez-Ortiz K, Senior RA, Simmons BI, White HJ, Zhang H, Aben J, Abrahamczyk S, Adum GB, Aguilar-Barquero V, Aizen MA, Albertos B, Alcala EL, Del Mar Alguacil M, Alignier A, Ancrenaz M, Andersen AN, Arbeláez-Cortés E, Armbrecht I, Arroyo-Rodríguez V, Aumann T, Axmacher JC, Azhar B, Azpiroz AB, Baeten L, Bakayoko A, Báldi A, Banks JE, Baral SK, Barlow J, Barratt BI, Barrico L, Bartolommei P, Barton DM, Basset Y, Batáry P, Bates AJ, Baur B, Bayne EM, Beja P, Benedick S, Berg Å, Bernard H, Berry NJ, Bhatt D, Bicknell JE, Bihn JH, Blake RJ, Bobo KS, Bóçon R, Boekhout T, Böhning-Gaese K, Bonham KJ, Borges PA, Borges SH, Boutin C, Bouyer J, Bragagnolo C, Brandt JS, Brearley FQ, Brito I, Bros V, Brunet J, Buczkowski G, Buddle CM, Bugter R, Buscardo E, Buse J, Cabra-García J, Cáceres NC, Cagle NL, Calviño-Cancela M, Cameron SA, Cancello EM, Caparrós R, Cardoso P, Carpenter D, Carrijo TF, Carvalho AL, Cassano CR, Castro H, Castro-Luna AA, Rolando CB, Cerezo A, Chapman KA, Chauvat M, Christensen M, Clarke FM, Cleary DF, Colombo G, Connop SP, Craig MD, Cruz-López L, Cunningham SA, D'Aniello B, D'Cruze N, da Silva PG, Dallimer M, Danquah E, Darvill B, Dauber J, Davis AL, Dawson J, de Sassi C, de Thoisy B, Deheuvels O, Dejean A, Devineau JL, Diekötter T, Dolia JV, Domínguez E, Dominguez-Haydar Y, Dorn S, Draper I, Dreber N, Dumont B, Dures SG, Dynesius M, Edenius L, Eggleton P, Eigenbrod F, Elek Z, Entling MH, Esler KJ, de Lima RF, Faruk A, Farwig N, Fayle TM, Felicioli A, Felton AM, Fensham RJ, Fernandez IC, Ferreira CC, Ficetola GF, Fiera C, Filgueiras BK, Fırıncıoğlu HK, Flaspohler D, Floren A, Fonte SJ, Fournier A, Fowler RE, Franzén M, Fraseret al., 2016,

    The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project

    , Ecology and Evolution, Vol: 7, Pages: 145-188, ISSN: 2045-7758

    The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

  • 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
    Milner-Gulland EJ, Sainsbury K, Burgess N, Howe C, Sabuni F, Puis E, Killenga Ret al., 2015,

    Exploring stakeholder perceptions of conservation outcomes from alternative income generating activities in Tanzanian villages adjacent to Eastern Arc mountain forests.

    , Biological Conservation, Vol: 191, Pages: 20-28, ISSN: 0006-3207
  • Journal article
    Hui T-YJ, Burt A, 2015,

    Estimating effective population size from temporally spaced samples with a novel, efficient maximum-likelihood algorithm

    , Genetics, Vol: 200, Pages: 285-293, ISSN: 1943-2631

    The effective population size Embedded Image is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating Embedded Image have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator Embedded Image for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying Embedded Image is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator Embedded Image, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of Embedded Image to several million, hence allowing the estimation of larger Embedded Image. Finally, we demonstrate how this algorithm can cope with nonconstant Embedded Image scenarios and be used as a likelihood-ratio test to test for the equality of Embedded Image throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.

  • 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
    Samani P, Low-Decarie E, McKelvey K, Bell T, Burt A, Koufopanou V, Landry CR, Bell Get al., 2015,

    Metabolic variation in natural populations of wild yeast

    , ECOLOGY AND EVOLUTION, Vol: 5, Pages: 722-732, ISSN: 2045-7758
  • 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
    Igea J, Bogarin D, Papadopulos AST, Savolainen Vet al., 2015,

    A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation

    , Evolution, Vol: 69, Pages: 482-491, ISSN: 0014-3820

    Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy-based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation.

  • Journal article
    Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arca B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VLM, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DST, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MKN, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon NF, Sharakhova MV, Shea T, Simao FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GWC, Tojo M, Topalis P, Tubio JMC, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu Y-C, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MAT, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJet al., 2015,

    Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

    , Science, Vol: 347
  • Journal article
    Gill RJ, Raine NE, 2014,

    Chronic impairment of bumblebee natural foraging behaviour induced by sublethal pesticide exposure

    , FUNCTIONAL ECOLOGY, Vol: 28, Pages: 1459-1471, ISSN: 0269-8463
  • Journal article
    Lim J, Crawley MJ, De Vere N, Rich T, Savolainen Vet al., 2014,

    A phylogenetic analysis of the British flora sheds light on the evolutionary and ecological factors driving plant invasions

    , ECOLOGY AND EVOLUTION, Vol: 4, Pages: 4258-4269, ISSN: 2045-7758
  • 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
    Papadopulos AST, Kaye M, Devaux C, Hipperson H, Lighten J, Dunning LT, Hutton I, Baker WJ, Butlin RK, Savolainen Vet al., 2014,

    Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

    , PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 369, ISSN: 0962-8436
  • Journal article
    Harrison E, MacLean RC, Koufopanou V, Burt Aet al., 2014,

    Sex drives intracellular conflict in yeast

    , JOURNAL OF EVOLUTIONARY BIOLOGY, Vol: 27, Pages: 1757-1763, ISSN: 1010-061X
  • Journal article
    Lakeman-Fraser P, Ewers RM, 2014,

    Untangling interactions: do temperature and habitat fragmentation gradients simultaneously impact biotic relationships?

    , PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 281, ISSN: 0962-8452
  • Journal article
    Morfopoulos C, Sperlich D, Penuelas J, Filella I, Llusia J, Medlyn BE, Niinemets U, Possell M, Sun Z, Prentice ICet al., 2014,

    A model of plant isoprene emission based on available reducing power captures responses to atmospheric CO2

    , New Phytologist, Vol: 203, Pages: 125-139, ISSN: 0028-646X

    We present a unifying model for isoprene emission by photosynthesizing leaves based on the hypothesis that isoprene biosynthesis depends on a balance between the supply of photosynthetic reducing power and the demands of carbon fixation.We compared the predictions from our model, as well as from two other widely used models, with measurements of isoprene emission from leaves of Populus nigra and hybrid aspen (Populus tremula × P. tremuloides) in response to changes in leaf internal CO2 concentration (Ci) and photosynthetic photon flux density (PPFD) under diverse ambient CO2 concentrations (Ca).Our model reproduces the observed changes in isoprene emissions with Ci and PPFD, and also reproduces the tendency for the fraction of fixed carbon allocated to isoprene to increase with increasing PPFD. It also provides a simple mechanism for the previously unexplained decrease in the quantum efficiency of isoprene emission with increasing Ca.Experimental and modelled results support our hypothesis. Our model can reproduce the key features of the observations and has the potential to improve process‐based modelling of isoprene emissions by land vegetation at the ecosystem and global scales.

  • 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
    Burt A, 2014,

    Heritable strategies for controlling insect vectors of disease

    , PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 369, ISSN: 0962-8436
  • Journal article
    Galizi R, Doyle LA, Menichelli M, Bernardini F, Deredec A, Burt A, Stoddard BL, Windbichler N, Crisanti Aet al., 2014,

    A synthetic sex ratio distortion system for the control of the human malaria mosquito

    , Nature Communications, Vol: 5, ISSN: 2041-1723

    It has been theorized that inducing extreme reproductive sex ratios could be a method to suppress or eliminate pest populations. Limited knowledge about the genetic makeup and mode of action of naturally occurring sex distorters and the prevalence of co-evolving suppressors has hampered their use for control. Here we generate a synthetic sex distortion system by exploiting the specificity of the homing endonuclease I-PpoI, which is able to selectively cleave ribosomal gene sequences of the malaria vector Anopheles gambiae that are located exclusively on the mosquito’s X chromosome. We combine structure-based protein engineering and molecular genetics to restrict the activity of the potentially toxic endonuclease to spermatogenesis. Shredding of the paternal X chromosome prevents it from being transmitted to the next generation, resulting in fully fertile mosquito strains that produce >95% male offspring. We demonstrate that distorter male mosquitoes can efficiently suppress caged wild-type mosquito populations, providing the foundation for a new class of genetic vector control strategies.

  • 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
    Garcia RA, Cabeza M, Rahbek C, Araujo MBet al., 2014,

    Multiple Dimensions of Climate Change and Their Implications for Biodiversity

    , SCIENCE, Vol: 344, Pages: 486-+, ISSN: 0036-8075
  • Journal article
    Saslis-Lagoudakis CH, Hawkins JA, Greenhill SJ, Pendry CA, Watson MF, Tuladhar-Douglas W, Baral SR, Savolainen Vet al., 2014,

    The evolution of traditional knowledge: environment shapes medicinal plant use in Nepal

    , PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 281, ISSN: 0962-8452
  • Journal article
    Garcia RA, Araujo MB, Burgess ND, Foden WB, Gutsche A, Rahbek C, Cabeza Met al., 2014,

    Matching species traits to projected threats and opportunities from climate change

    , JOURNAL OF BIOGEOGRAPHY, Vol: 41, Pages: 724-735, ISSN: 0305-0270
  • Journal article
    O'Loughlin SM, Magesa S, Mbogo C, Mosha F, Midega J, Lomas S, Burt Aet al., 2014,

    Genomic Analyses of Three Malaria Vectors Reveals Extensive Shared Polymorphism but Contrasting Population Histories

    , MOLECULAR BIOLOGY AND EVOLUTION, Vol: 31, Pages: 889-902, ISSN: 0737-4038
  • Journal article
    Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JMC, Werner EI, Allen J, De Nardi AB, Donelan EM, Marino G, Fassati A, Campbell PJ, Yang F, Burt A, Weiss RA, Stratton MRet al., 2014,

    Transmissable Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage

    , SCIENCE, Vol: 343, Pages: 437-440, ISSN: 0036-8075
  • Journal article
    Heuertz M, Duminil J, Dauby G, Savolainen V, Hardy OJet al., 2014,

    Comparative Phylogeography in Rainforest Trees from Lower Guinea, Africa

    , PLOS ONE, Vol: 9, ISSN: 1932-6203
  • Journal article
    Valente LM, Britton AW, Powell MP, Papadopulos AST, Burgoyne PM, Savolainen Vet al., 2014,

    Correlates of hyperdiversity in southern African ice plants (Aizoaceae)

    , BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Vol: 174, Pages: 110-129, ISSN: 0024-4074
  • Journal article
    Dyer RJ, Pellicer J, Savolainen V, Leitch IJ, Schneider Het al., 2013,

    Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae)

    , BMC PLANT BIOLOGY, Vol: 13, ISSN: 1471-2229

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