Nbaf complete bibliography Please note that the list of publications for 2016 will be completed early 2017




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Theses 29


  1. Asher C (2013) PhD Thesis (University of Leeds) The dynamics of reproductive dominance in dinosaur ants (NBAF-W)

  2. Bristol R (2013) PhD thesis (University of Kent) Evolutionary genetics and reintroduction ecology of the critically-endangered Seychelles paradise flycatcher. (NBAF-S)

  3. Daly B (2014) DPhil thesis (University of Oxford) Avian malaria in the montane tropics. (NBAF-S)

  4. Dos Remedios N (2013) PhD Thesis (University of Bath) The evolutionary history of plovers, genus Charadrius: phylogeography and breeding systems. (NBAF-E /S)

  5. El Nagar A (2013) PhD Thesis (University of Nottingham) The role of parasites in the ecological speciation of three-spined sticklebacks Gasterosteus aculeatus. (NBAF-S)

  6. Ellis RP (2013) PhD Thesis (University of Plymouth). The impact of ocean acidification, increased seawater temperature and a bacterial challenge on the immune response and physiology of the blue mussel, Mytilus edulis. (NBAF-B)

  7. Farrell L (2013) PhD Thesis (Simon Fraser University) Molecular genetics of alternative reproductive morphs in ruffs. (NBAF-E /S)

  8. Farrer R (2013) PhD Thesis (Imperial College) Comparative genomics and epidemiology of the amphibian-killing fungus Batrachochytrium dendrobatidis. (NBAF-L)

  9. Fellows SA (2013) PhD Thesis (University of Sheffield) Sexual selection and the rapid evolution of reproductive genes and their products in D. pseudoobscura. (NBAF-E)

  10. Fish K (2013) PhD Thesis (University of Sheffield) The impact of hydraulic regime upon biofilms in drinking water distribution systems. (NBAF-S)

  11. Fountain T (2013) PhD Thesis (University of Sheffield) Global bedbug spread: planes, genes and insecticides. (NBAF-S)

  12. Hearn J (2013) PhD Thesis (University of Edinburgh) Exploring population history and gall induction in cynipid gallwasps using genomics and transcriptomics. (NBAF-E)

  13. Heathcote R (2013) DPhil thesis (University of Oxford) Secondary contact in the common wall lizard. (NBAF-S)

  14. Holland L (2013) PhD Thesis (University of Exeter) Genetic assessment of connectivity in the temperate octocorals eunicella verrucosa and alcyonium digitatum in the North East Atlantic. (NBAF-S)

  15. Houghton J (2013) PhD Thesis (University of Liverpool) Molecular diversity and functional composition of cellulose degrading communities in anoxic environments. (NBAF-L)

  16. Johnson B (2013) PhD Thesis (University of Birmingham) Molecular mechanisms underpinning insect diapause. (NBAF-B)

  17. Magnus C (2013) MSc thesis (University of Edinburgh) Chromosomal inversions and speciation in cactophilic Drosophila. (NBAF-E)

  18. *Morales M (2013) PhD Thesis (University of Granada, Spain) Heritability and repeatability of egg rejection behaviour in magpies. (NBAF-S)

  19. Muir AP (2013) PhD Thesis (University of Glasgow) Population genetics of the common frog (Rana temporaria) in relation to climate. (NBAF-E)

  20. Nissimov JI (2013) PhD thesis (University of Nottingham) Ecological and functional biodiversity in a marine algal-virus system : genotypes, phenotypes and their ecological significance. (NBAF-L)

  21. Phillips K (2013) PhD Thesis (UEA) Molecular ecology of hawksbill turtles Eretmochelys imbricata in the Seychelles. (NBAF-S)

  22. Poynter A (2013) PhD Thesis (University of Birmingham) Impacts of environmental stressors on the River Itchen Ranunculus community. (NBAF-B)

  23. Salmon D (2013) PhD Thesis (University of Exeter) Metabolite profiling of the coccolithophores Emiliana huxleyi to examine links between calcification and central metabolism. (NBAF-B)

  24. Sin S (2013) PhD Thesis (University of Oxford) The major histocompatibility complex, mate choice and pathogen resistance in the European badger Meles meles. (NBAF-S)

  25. Smith G (2013) PhD Thesis (University of St Andrews) Investigating the molecular basis of adaptation and speciation in divergent populations. (NBAF-L)

  26. Toseland A (2013) PhD Thesis (University of East Anglia) Computational analysis of eukaryotic metatranscriptomes from diverse marine environments. (NBAF-E)

  27. Tyler F (2013) PhD Thesis (University of Exeter) Behavioural and genomic studies of sexual selection in wild field crickets. (NBAF-S)

  28. Yang G (2013) PhD Thesis (University of Aberdeen) Intersexuality and endocrine disruption in the amphipod Echinogrammarus marinus: from genes to physiology. (NBAF-L)

  29. Walkup J (2013) PhD Thesis (University of Aberdeen) Small scale genetic and morphological structure in an island population of European starlings (Sturnus vulgaris). (NBAF-S)

[2012]
[Joint nodes] 5


  1. *Hansson B, Tarka M, Dawson DA, Horsburgh GJ (2012) Hybridization but no evidence for backcrossing and introgression in a sympatric population of great reed warblers and clamorous reed warblers. Plos One 7, e31667. [NBAF-E/L/S]

  2. Hegarty MJ, Abbott RJ, Hiscock SJ (2012) Allopolyploid speciation in action: the origins and evolution of Senecio cambrensis. Chapter in Soltis D & Soltis P (Eds.) Polyploidy in Plants. Springer, New York. [NBAF E/L/S]

  3. Kuepper C, Edwards S, Kosztolanyi A, Alrashidi M, Burke T, Herrmann P, Argüelles-Tico A, Amat JA, Amezian M, Rocha A, Hötker H, Ivanov A, Chernicko J, Szekely T High gene flow on a continental scale in the polyandrous Kentish plover Charadrius alexandrinus. Molecular Ecology 21, 5864–5879. [NBAF-E/L/S]

  4. McMahon BJ, Johansson MP, Piertney SB, Buckley K, Höglund J (2012) Genetic variation among endangered Irish red grouse (Lagopus lagopus hibernicus) populations: Implications for conservation and management. Conservation Genetics 13, 639-647. (10.1007/s10592-011-0314-x) NBAF E/S

  5. Short S, Yang G, Kille P, Ford AT (2012) A Widespread and Distinctive Form of Amphipod Intersexuality Not Induced by Known Feminising Parasites. Sexual Development 6, 320–324. [NBAF-E/L]

[NBAF-B] 4




  1. Dove ADM, Leisen J, Zhou M, Byrne JJ, Lim-Hing K, Webb HD, Gelbaum L, Viant MR, Kubanek J, Fernández FM (2012) Biomarkers of whale shark health: a metabolomic approach. PLOS One 7, e49379.

  2. Freitag S, Feldmann J, Raab A, Crittenden PD, Hogan EJ, Squier AH, Boyd KG, Thain S (2012) Metabolite profile shifts in the heathland lichen Cladonia portentosa in response to N deposition reveal novel biomarkers. Plant Physiology 146, 160-172.

  3. Liebeke M, Bundy JG (2012) Tissue disruption and extraction methods for metabolic profiling of an invertebrate sentinel species. Metabolomics 8, 819-830.

  4. Ludwig C, Easton JM, Lodi A, Tiziani S, Manzoor SE, Southam AD, Byrne JJ, Bishop LM, He S, Arvanitis TN, Günther UL, Viant MR (2012) Birmingham Metabolite Library: a publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR). Metabolomics 8, 8-18.

[NBAF-E] 17



  1. Amin SA, Green DH, Waheeb DA, Gärdes A, Carrano CJ (2012) Iron transport in the genus Marinobacter. Biometals 25, 135-147.

  2. Halliday AM, Lainson FA, Yaga R, Inglis NF, Bridgett S, Nath M, Knox DP (2012) Transcriptional changes in Teladorsagia circumcincta upon encountering host tissue of differing immune status. Parasitology. 139, 387-405. (10.1017/S0031182011002010)

  3. Haudry A, Zha HG, Stift M, Mable BK (2012) Disentangling the effects of breakdown of self-incompatibility and transition to selfing in North American Arabidopsis lyrata. Molecular Ecology 21, 1130–1142. (10.1111/j.1365-294X.2011.05435.x)

  4. Kelly LJ, Leitch AR, Fay MF, Renny-Byfield S, Pellicer J, Macas J, Leitch IJ (2012) Why size really matters when sequencing plant genomes. Plant Ecology & Diversity 5, 415-425.

  5. Kumar S, Koutsovoulos G, Kaur G, Blaxter M (2012) Toward 959 nematode genomes. Worm 1, 42-50.

  6. Leitch AR, Leitch IJ (2012) Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytologist 194, 629-646.

  7. Lohse K, Barton NH, Melika G and Stone GN (2012) A likelihood-based comparison of population histories in a parasitoid guild. Molecular Ecology 21, 4605-4617.

  8. Marsden CD, Woodroffe R, Mills MGL, McNutt JW, Creel S, Groom R, Emmanuel M, Cleaveland S, Kat P, Rasmussen GSA, Ginsberg J, Lines R, André J-M, Begg C, Wayne RK, Mable BK (2012) Spatial and temporal patterns of neutral and adaptive genetic variation in the endangered African wild dog (Lycaon pictus). Molecular Ecology 21, 1379-1393.

  9. Marsden CD, Wayne RK, Mable BK (2012) Inferring the ancestry of African wild dogs that returned to the Serengeti-Mara. Conservation Genetics 13, 525-533.

  10. Mazard S, Ostrowski M, Partensky F, Scanlan DJ (2012) Multilocus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus. Environmental Microbiology 14, 372-386.

  11. Nadeau NJ, Whibley A, Jones RT, Davey JW, Dasmahapatra KK, Baxter SW, Quail MA, Joron M, ffrench-Constant RH, Blaxter ML, Mallet J, Jiggins CD (2012) Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philosophical Transactions of the Royal Society B 367, 343–353.

  12. Nicholls JA, Challis RJ, Mutun S and Stone GN (2012) Mitochondrial barcodes are diagnostic of shared refugia but not species in hybridising oak gallwasps. Molecular Ecology 21, 4051-4062.

  13. Odee DW, Telford A, Wilson J, Gaye A, Cavers S (2012) Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion. Heredity 109, 372-382.

  14. Smadja CM, Canbäck B, Vitalis R, Gautier M, Ferrari J, Zhou JJ, Butlin RK (2012) Large-scale candidate gene scan reveals the role of chemoreceptor genes in host plant specialisation and speciation in the pea aphid. Evolution 66, 2723-2738.

  15. Smith DB, McFadden N, Blundell RJ, Meredith A, Simmonds P (2012) Diversity of murine norovirus in wild rodent populations: species-specific associations suggest an ancient divergence. Journal of General Virology 93, 259-266.

  16. Stone GN, Lohse K, Nicholls JA, Fuentes-Utrilla P, Sinclair F, Schönrogge K, Csóka G, Melika G, Nieves-Aldrey J-L, Pujade-Villar J, Tavakoli M, Askew RR and Hickerson MJ (2012) Reconstructing community assembly in time and space reveals enemy escape in a western palearctic insect community. Current Biology 22, 1-6.

  17. Tyson T, O'Mahony Zamora G, Wong S, Skelton M, Daly B, Jones JT, Mulvihill ED, Elsworth B, Phillips M, Blaxter M, Burnell AM (2012) A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags. BMC Research Notes 5, 68.

[NBAF-L] 15




  1. Bik H, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK (2012) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution 27, 233-243.

  2. Christin PA, Edwards EJ, Besnard G, Boxall SF, Gregory R, Kellogg EA, Hartwell J, Osborne CP, (2012) Adaptive evolution of C4 photosynthesis through recurrent lateral gene transfer. Current Biology 22, 445-449.

  3. Canbäck B, André C, Galindo J, Johannesson K, Johansson T, Panova M, Tunlid A, Butlin RK (2012) The Littorina Sequence Database (LSD) – an online resource for genomic data. Molecular Ecology Resources 12, 142–148.

  4. Fonseca VG, Nichols B, Lallias D, Quince C, Carvalho GR, Power DM, Creer S (2012) Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research 40, 9.

  5. Guler Y, Short S, Kile P, Ford AT (2012) Integrating field and laboratory evidence for environmental sex determination in the amphipod, Echinogammarus marinus. Marine Biology 159, 2885-2890. (10.1007/s00227-012-2042-2)

  6. Kazama Y, Nishihara K, Bergero R, Fujiwara MT, Abe T, Charlesworth D, Kawano S (2012) SlWUS1; An X-linked Gene Having No Homologous Y-Linked Copy in Silene latifolia. G3 (Bethesda) 2, 1269-1278. (10.1534/g3.112.003749)

  7. Larsen PE, Field D, Gilbert JA (2012) Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods 9, 621-625 doi:10.1038/nmeth.1975

  8. Lewis C, Ford AT (2012) Infertility in male aquatic invertebrates: a review. Aquatic Toxicology 120, 79-89. (10.1016/j.aquatox.2012.05.002)

  9. Matyasek R, Renny-Byfield S, Fulnecek J, Macas J, Grandbastien M-A, Nichols R, Leitch A, Kovarik A (2012) Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 13, 722.

  10. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012) Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. Journal of Virology 86, 2896-7.

  11. Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012) Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. Journal of Virology 86, 2380-1.

  12. Renny-Byfield S, Kovařík A, Chester M, Nichols RA, Macas J, Novák P, Leitch AR (2012) Independent, rapid and targeted loss of highly repetitive DNA in natural and synthetic allopolyploids of Nicotiana tabacum. PLoS One 7, e36963.

  13. Rooks D, McDonald JE, McCarthy AJ (2012) Metagenomics approaches to the discovery of cellulases. Methods in Enzymology 510, 375-394.

  14. Short S, Guler Y, Yang G, Kille P, Ford AT (2012) Paramyxean–microsporidian co-infection in amphipods: is the consensus that Microsporidia can feminise their hosts presumptive? International Journal for Parasitology 42, 683-691. (10.1016/j.ijpara.2012.04.014)

  15. Turner AK, Begon M, Jackson JA and Paterson S (2012) Evidence for selection at cytokine loci in a natural population of field voles (Microtus agrestis). Molecular Ecology 21, 1632-1646.

[NBAF-S] 23




  1. *Barratt CD, Horsburgh GJ, Dawson DA, Gower DJ, Wilkinson M, Loader SP, Jehle R (2012) Characterisation of nine microsatellite loci in the ceacilian amphibian Boulengerula uluguruensis (Gymnophiona), and their cross-species utility in three congeneric species. Conservation Genetics Resources 4, 225-229.

  2. Bicknell AWJ, Knight ME, Bilton D, Reid JB, Burke T, Votier SC (2012) Population genetic structure and long-distance dispersal among seabird populations: Implications for colony persistence. Molecular Ecology 21, 2863-2876.

  3. Brekke P, Wang J, Bennett PM, Cassey P, Dawson DA, Horsburgh GJ, Ewen JG (2012) Post-copulatory mechanisms of inbreeding avoidance in the island endemic hihi (Notiomystis cincta). Behavioural Ecology 23, 278-284.

  4. Buckley J, Butlin RK, Bridle J (2012) Evidence for evolutionary change associated with the recent range expansion of the UK brown argus butterfly in response to climate change. Molecular Ecology 21, 267–280.

  5. *Dawson DA, Horsburgh GJ, Krupa AK, Stewart IRK, Skjelseth S, Jensen H, Ball AD, Spurgin LG, Mannarelli M-E, Nakagawa S, Schroeder S, Vangestel C, Hinten GN, Burke T (2012) Microsatellite resources for Passeridae species: a predicted microsatellite map of the house sparrow Passer domesticus. Molecular Ecology Resources 12, 501-523.

  6. *Ekblom R, Slate J, Horsburgh GJ, Birkhead T, Burke T (2012) Comparison between normalised and un-normalised 454-sequencing libraries for small-scale RNA-seq studies. Comparative and Functional Genomics 281693, 1-8.

  7. Farrell LL, Dawson DA, Horsburgh GJ, Burke T, Lank DL (2012) Isolation, characterisation and predicted genome locations of ruff (Philomachus pugnax, AVES) microsatellite loci. Conservation Genetic Resources 4, 763-771.

  8. Frantz AC, Massei G, Burke T (2012) Genetic evidence for past hybridisation between domestic pigs and English wild boars. Conservation Genetics 13, 1355-1364.

  9. Jan C, Dawson DA, Altringham JD, Burke T, Butlin R (2012) Development of conserved microsatellite markers of high cross-species utility in bat species (Vespertilionidae, Chiroptera, Mammalia). Molecular Ecology Resources 12, 532-548.

  10. Kuepper C, Augustin J, Edwards S, Szekely T, Kosztolanyi A, Burke T, Janes DE Triploid plover female provides support for a role of the W chromosome in avian sex determination. Biology Letters 8, 787-789.

  11. Raisin C, Frantz AC, Kundu S, Greenwood AG, Jones CG, Zuel N, Groombridge JJ (2012) Genetic consequences of intensive conservation management for the Mauritius parakeet. Conservation Genetics 13, 707-715.

  12. Rossiter SJ, Zubaid A, Mohd-Adnan A, Struebig MJ, Kunz TH, Gopal S, Petit EJ, Kingston T (2012) Social organisation and genetic structure: insights from co-distributed bat populations. Molecular Ecology 21, 647-661.

  13. *Salmona J, Salamolard M, Fouillot D, Ghestemme T, Larose J, Centon J-F, Sousa V, Dawson DA, Thebaud C, Chikhi L (2012) Signature of a pre-human population decline in the critically endangered Reunion Island endemic forest bird Coracina newtoni. PLOS One 7, e43524.

  14. *Schroeder J, Burke T, Mannarelli M-E, Dawson DA, Nakagawa S (2012) Maternal effects and heritability of annual productivity. Journal of Evolutionary Biology 25, 149–156.

  15. Sin YW, Dugdale H, Newman C, Macdonald DW, Burke T (2012) MHC class II genes in the European badger (Meles meles): characterization, patterns of variation, and transcription analysis. Immunogenetics 64, 313-327.

  16. Sin YW, Buesching CD, Burke T, Macdonald DW (2012) Molecular characterization of the microbial communities in the subcaudal gland secretion of the European badger (Meles meles). FEMS Microbiology Ecology 81, 648-659.

  17. Sin YW, Dugdale HL, Newman C, Macdonald DW, Burke T (2012) Evolution of MHC class I genes in the European badger (Meles meles). Ecology and Evolution 2, 1644-1662.

  18. Smith JA, Dawson DA, Horsburgh GJ, Reynolds SJ (2012) Characterisation of blue tit Cyanistes caeruleus microsatellite loci, and assessment of sequence homology among species to predict cross-species utility and chromosome locations. Conservation Genetics Resources 4, 605-612.

  19. Spurgin LG, Illera JC, Padilla D, Richardson DS (2012) Biogeographical patterns and co-occurrence of pathogenic infection across island populations of Berthelot’s pipit. Oecologia 168, 691-701.

  20. *Vangestel C, Mergeay J, Dawson DA, Callens T, Vandomme V, Lens L (2012) Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient. Heredity 109, 163-172.

  21. Wright LI, Fuller WJ, Godley BJ, McGowan A, Tregenza T, Broderick AC (2012) Reconstruction of paternal genotypes over multiple breeding seasons reveals male green turtles do not breed annually. Molecular Ecology 21, 3625-3635

  22. Wright LI, Stokes KL, Fuller WJ, Godley BJ, McGowan A, Snape R, Tregenza T, Broderick AC (2012) Turtle mating patterns buffer against disruptive effects of climate change. Proceedings of the Royal Society B 279, 2122-2127.

  23. Young EF, Rock Meredith MP, Belchier M, Murphy EJ, Carvalho GR (2012) Physical and behavioural influences on larval fish retention: contrasting patterns in two Antarctic fishes. Marine Ecology Progress Series 465, 201–215.

[NBAF-W] 4



  1. Bowes MJ, Ings NL, McCall SJ, Warwick A, Barrett C, Wickham HD, Harman SA, Armstrong LK, Scarlett PM, Roberts C, Lehmann K, Singer AC (2012) Nutrient and light limitation of periphyton in the River Thames: Implications for catchment management. Science of The Total Environment 434, 201-212. 10.1039/c2em30705g

  2. Holcombe M, Adra S, Bicak M, Chin S, Coakley S, Graham AI, Green J et al. (2012) Modelling complex biological systems using an agent-based approach. Integrated Biology 4, 53-64. 10.1039/c1ib00042j

  3. Krampis K, Booth T, Chapman B, Tiwari B, Bicak M, Field D, Nelson KE (2012) Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics 13, 42. 10.1186/1471-2105-13-42

  4. Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, et al. (2012) Diversity of bifidobacteria within the infant gut microbiota. PLoS One 7, e36957. 10.1371/journal.pone.0036957



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