Supported Publications

Here are a few of the journal articles which have resulted from work carried out in NBAF. You can access our full bibliography: 0. NBAF Bibliography_21mar17

[2016]

          [Joint nodes]

1. Kim K-W, Griffith S, Burke T (2016) Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae). Heredity 116, 409-416. (10.1038/hdy.2015.114) [NBAF-E/S]
2. Küpper C, Stocks M, Risse JE, dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI, Kitaysky AS, Wingfield JC, Piersma T, Zeng K, Slate J, Blaxter M, Lank DB, Burke T (2016) A supergene determines highly divergent male reproductive morphs in the ruff. Nature Genetics 48, 79-83. (10.1038/ng.3443) [NBAF-E/S]
3. Meyer-Lucht Y, Mulder KP, James MC, McMahon BJ, Buckley K, Piertney SB, Hoglund J (2016) Adaptive and neutral genetic differentiation among Scottish and endangered Irish red grouse (Lagopus lagopus scotica). Conservation Genetics 17, 615-630 1–16. (10.1007/s10592-016-0810-0) [NBAF-E/S]
4. Wenzel MA, Douglas A, James MC, Redpath SM, Piertney SB (2016) The role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica). Molecular Ecology 25, 324-341. (10.1111/mec.13473) [NBAF-E/S]

          NBAF-B

1. Davidson RL, Weber RJM, Liu H, Sharma-Oates A, Viant MR (2016) Galaxy-M: A galaxy workflow for processing and analysing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. GigaScience 5, 10. (10.1186/s13742-016-0115-8)
2. Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR (2016) The time is right to focus on model organism metabolomes. Metabolites 6, 8. (10.3390/metabo6010008)
3. Hao J, Liebeke M, Sommer U, Viant MR, Bundy JG, Ebbels TMD (2016) Statistical correlations between NMR spectroscopy and direct infusion FT-ICR mass spectrometry aid annotation of unknowns in metabolomics. Analytical Chemistry 8, 2583–2589. (10.1021/acs.analchem.5b02889).
4. Molloy JC, Sommer U, Viant MR, Sinkins SP (2016) Wolbachia modulates lipid metabolism in Aedes albopictus mosquito cells. Applied and Environmental Microbiology 82, 3109-20. (10.1128/AEM.00275-16)

          NBAF-E

1. Brennan AC, Hiscock SJ, Abbott RJ (2016) Genomic architecture of phenotypic divergence between two hybridizing plant species along an elevational gradient. AoB Plants 8, plw022. (10.1093/aobpla/plw022)
2. Brown RP, Paterson S, Risse J (2016) Genomic signatures of historical allopatry and ecological divergence in an island lizard. Genome Biology and Evolution 8, 3618-3626. (10.1093/gbe/evw268)
3. Buckley J, Kilbride E, Cevik V, Vicente JG, Holub EB, Mable BK (2016) R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system. BMC Evolutionary Biology 16, 1-17. (10.1186/s12862-016-0665-5)
4. Chapman MA, Hiscock SJ, Filatov DA (2016) The genomic bases of morphological divergence and reproductive isolation driven by ecological speciation in Senecio (Asteraceae). Journal of Evolutionary Biology 29, 98-113. (10.1111/jeb.12765)
5. Eyres I, Jaquiery J, Sugio A, Duvaux L, Legeai F, Gharbi K, Nelson M, Simon JC, Smadja CM*, Butlin RK*, Ferrari J* (2016) Differential gene expression according to race and host plant in the pea aphid. Molecular Ecology 25, 4197-4215. (10.1111/mec.13771) (*joint senior authors)
6. Fountain T, Ravinet M, Naylor R, Reinhardt K, Butlin RK (2016) A linkage map and QTL analysis for pyrethroid resistance in the bed bug Cimex lectularius. G3: Genes|Genomes|Genetics 6, 4059-4066. (10.1534/g3.116.033092)
5. Giron D, Huguet E, Stone GN, Body M (2016) Insect-induced effects on plants and possible effectors used by galling and leaf-mining insects to manipulate their host-plant. Journal of Insect Physiology 84, 70–89. (10.1016/j.jinsphys.2015.12.009)
6. Glucas GV, Younger JL, Kao D, Rogers AD, Handley J, Miller GD, Jouventin P, Nolan P, Gharbi K, Miller KJ, Hart T (2016) Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range. BMC Evolutionary Biology 16, 211. (10.1186/s12862-016-0784-z)
7. Hamilton PB, Cowx IG, Oleksiak MF, Griffiths AM, Grahn M, Stevens JR, Carvalho GR, Nicol L, Tyler CR (2016) Population-level consequences for wild fish exposed to sub-lethal concentrations of chemicals – a critical review. Fish and Fisheries Reviews 17, 545–566. (10.1111/faf.12125)
8. Hamilton PB, Rolshausen G, Webster TMU, Tyler CR (2016) Adaptive capabilities and fitness consequences associated with pollution exposure in fish. Philosophical Transactions of the Royal Society B 360, 397–413. (10.1098/rstb.2016.0042).
9. Hart ML, Forrest LL, Nicholls JA, Kidner CA (2016) Retrieval of hundreds of nuclear loci from herbarium specimens. Taxon 65, 1081-1092. (10.12705/655.9)
10. Jeffries DL, Copp GH, Lawson Handley L, Olsén KH, Sayer CD, Hänfling B (2016) Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. Molecular Ecology 25, 2997-3018. (10.1111/mec.13613)
11. Kazama Y, Ishii K, Aonuma W, Ikeda T, Kawamoto H, Koizumi A, Filatov DA, Chibalina M, Bergero R, Charlesworth D, Abe T, Kawano S (2016) A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome. Scientific Reports 6, 18917. (10.1038/srep18917)
12. Nevado B, Atchison GW, Hughes CE, Filatov DA (2016) Widespread adaptive evolution during repeated evolutionary radiations in New World lupins. Nature Communications 7, 12384. (10.1038/ncomms12384)
13. Nürnberger B, Lohse K, Fijarczyk A, Szymura JM, Blaxter M (2016) Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): inference from transcriptome-wide coalescence analyses. Evolution 70, 1803–1818. (10.1111/evo.12978)
14. Lohse K, Chmelik M, Frantz L, Barton NH (2016) Efficient strategies for calculating likelihoods under the coalescent. Genetics 202, 775-786. (10.1534/genetics.115.183814)
15. Mallon EB, Amarasinghe HE, Ott SR (2016) Acute and chronic gregarisation are associated with distinct DNA methylation fingerprints in desert locusts. Scientific Reports 6, 35608 (10.1038/srep35608)
16. Nicholls JA, Melika G, Stone GN (2016) Sweet tetra-trophic interactions: multiple evolutions of nectar secretion, a defensive extended phenotype in cynipid gallwasps. The American Naturalist 189, 67-77. (10.1086/689399)
17. Ouvrard P, Hicks DM, Mouland M, Nicholls JA, Baldock KCR, Goddard MA, Kunin WE, Potts SG, Thieme T, Veromann E, Stone GN (2016) Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae; Meligethinae), and the population structure of Brassicogethes aeneus. Genome 59, 1101-1116. (10.1139/gen-2016-0020)
18. Pascoal S, Mendrok M, Mitchell C, Wilson AJ, Hunt J, Bailey NW (2016) Sexual selection and population divergence I. The influence of socially flexible cuticular hydrocarbon expression in male field crickets (Teleogryllus oceanicus). Evolution 70, 82-97. (10.1111/evo.12839)
19. Porcelli D, Westram AM, Pascual M, Gaston KJ, Butlin RK, Snook RR (2016) Gene expression clines reveal local adaptation and associated trade-offs at a continental scale. Scientific Reports 6, 32975. (10.1038/srep32975)
20. Qiu S, Bergero R, Guirao-Rico S, Campos JL, Cezard T, Gharbi K, Charlesworth D (2016) RAD-mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region. Molecular Ecology 25, 414-430. (10.1111/mec.13297)
21. Szitenberg A, Cha S, Opperman CH, Bird DM, Blaxter ML, Lunt DH (2016) Genetic drift, not life history or RNAi, determine long term evolution of transposable elements. Genome biology and evolution 8, 2964-2978. (10.1093/gbe/evw208)
22. Truebano M, Tills O, Spicer JI (2016) Embryonic transcriptome of the brackishwater amphipod Gammarus chevreuxi. Marine Genomics 28, 5-6. (10.1016/j.margen.2016.02.002)
23. Vallejo-Marín M, Cooley AM, Lee MYQ, Folmer MR, McKain MR, Puzey JR (2016) Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. American Journal of Botany 103, 1-17. (10.3732/ajb.1500471)
24. Vallejo-Marin M, Hiscock SJ (2016) Hybridization and hybrid speciation under global change. New Phytologist 211, 1170-1187. (10.1111/nph.14004)
25. Wallbank RWR, Baxter SW, Pardo-Diaz C, Hanly JJ, Martin SH, Mallet J, Dasmahapatra KK, Salazar C, Joron M, Nadeau N, McMillan WO, Jiggins CD (2016) Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling. PLoS Biology 14, e1002353. (10.1371/journal.pbio.1002353)
26. Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA (2016) Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by RAD markers. Molecular Ecology 25, 2413–2426. (10.1111/mec.13644)

          NBAF-L

1. Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL (2016) Prophages mediate defense against phage infection through diverse mechanisms. ISME Journal 10, 2854-2866. (10.1038/ismej.2016.79)
2. Chabas H, van Houte S, Høyland-Kroghsbo NM, Buckling A, Westra ER (2016) Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies. Proceedings of the Royal Society B 283, 20160721. (10.1098/rspb.2016.0721)
3. Cox F, Newsham KK, Bol R, Dungait JAJ, Robinson CH (2016) Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic. Ecology Letters, 19, 528-536. (10.1111/ele.12587)
4. Cunliffe M (2016) Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3. FEMS Microbiology Ecology 92, fiv150. (10.1093/femsec/fiv150)
5. Farrant GK, Doré H, Cornejo-Castillo FM, Partensky F, Ratin M, Ostrowski M, Pitt FD, Wincker P, Scanlan DJ, Iudicone D, Acinas SG, Garczarek L (2016) Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria. Proceedings of the National Academy of Sciences of the United States of America E3365-E3374. (10.1073/pnas.1524865113)
6. Gomez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, (…) Buckling A (2016) Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nature Communications 7, 12453. (10.1038/ncomms12453)
7. Gonzalez-Quevedo C, Davies RG, Phillips KP, Spurgin LG, Richardson DS (2016) Landscape-scale variation in an anthropogenic factor shapes immune gene variation within a wild population. Molecular Ecology 25, 4234–4246. (10.1111/mec.13759)
8. Hargreaves KR, Thanki AM, Jose BR, Oggioni MR, Clokie MRJ (2016) Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078. BMC Genomics 17, 1020. (10.1186/s12864-016-3346-2)
9. Harrison E, Dytham C, Hall JPJ, Guymer D, Spiers AJ, Paterson S, Brockhurst MA (2016) Rapid compensatory evolution promotes the survival of conjugative plasmids. Mobile Genetic Elements 6, e1179074. (10.1080/2159256x.2016.1179074)
10. Hiscox J, Savoury M, Johnston SR, Parfitt D, Müller CT, Rogers HJ, Boddy L (2016) Location, location, location: priority effects in wood decay communities may vary between sites. Environmental Microbiology 18, 1954-1969. (10.1111/1462-2920.13141)
11. King KC, Brockhurst MA, Vasieva O, Paterson S, Betts A, Ford S, Frost CL, Horsburgh MJ, Haldenby S, Hurst GDD (2016) Rapid evolution of microbe-mediated protection against pathogens in a worm host. ISME Journal 10, 1915–1924. (10.1038/ismej.2015.259)
12. Lappin FM, Shaw RL, Macqueen DJ (2016) Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis. Marine Genomics 30, 15-26 (10.1016/j.margen.2016.06.003)
13. Newsham KK, Hopkins DW, Carvalhais LC, Fretwell PT, Rushton SP, O’Donell AG, Dennis PG (2016) Relationship between soil fungal diversity and temperature in the maritime Antarctic. Nature Climate Change 6, 182–186. (10.1038/nclimate2806)
14. Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C (2016) Ecological coherence and phylogenetic congruence in Thaumarchaeota. ISME Journal 10, 85-96. (10.1038/ismej.2015.101)
15. Palmer WH, Obbard DJ (2016) Variation and evolution in the glutamine-rich repeat region of Drosophila Argonaute-2. Genes, Genomes, Genetics 6, 2563-2572. (10.1534/g3.116.031880)
16. Pascoal S, Liu X, Ly T, Fang Y, Rockliffe N, Paterson S, Shirran SL, Botting CH, Bailey NW (2016) Rapid evolution and gene expression: a rapidly-evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression. Journal of Evolutionary Biology 29, 1234-1246. (10.1111/jeb.12865)
17. Perez Sepulveda B, Redgwell T, Rihtman B, Pitt F, Scanlan DJ, Millard A (2016) Marine phage genomics: the tip of the iceberg. FEMS Microbiology Letters 363, fnw158. (10.1093/femsle/fnw158)
18. Pitt FD, Millard A, Ostrowski M, Dervish S, Mazard S, Paulsen IT, Zubkov MV, Scanlan DJ (2016) A sample-to-sequence protocol for genus targeted transcriptomic profiling: application to marine Synechococcus. Frontiers in Microbiology 7, 1592. (10.3389/fmicb.2016.01592)
19. Price SJ, Garner TWJ, Cunningham AA, Langton TES, Nichols RA (2016) Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans. Proceedings of the Royal Society B 283, 20160952. (10.1098/rspb.2016.0952)
20. Strittmatter M, Grenville-Briggs LJ, Breithut L, van West P, Gachon CMM, Küpper FC (2016) Infection of the brown alga Ectocarpus siliculosus by the oomycete Eurychasma dicksonii induces oxidative stress and halogen metabolism. Plant, Cell & Environment 39, 259-271. (10.1111/pce.12533)
21. van Houte S, Ekroth AK, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, Gandon S, Boots M, Paterson S, Buckling A, Westra ER (2016) The diversity-generating benefits of a prokaryotic adaptive immune system. Nature 532, 385-8. (10.1038/nature17436)
22. Van’t Hof AE, Campagne P, Rigden DJ, Yung CJ, Lingley J, Quail MA, Hall N, Darby AC, Saccheri IJ (2016) The industrial melanism mutation in British peppered moths is a transposable element. Nature 534, 102-105. (10.1038/nature17951)
23. Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A (2016) Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 125, 683–699 (10.1007/s00412-015-0556-3)

          NBAF-S

1. Almathen F, Charruau P, Mohandesan E, Mwacharo JM, Orozco-terWengel P, Pitt D, Abdussamad AM, Uerpmann M, Uerpmann HP, De Cupere B, Magee P, Alnaqeeb MA, Salim B, Raziq A, Dessie T, Abdelhadi OM, Banabazi MH, Al-Eknah M, Walzer C, Faye B, Michael Hofreiter M, Peters J, Hanotte O, Burger PA (2016) Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary. Proceedings of the National Academy of Sciences of the United States of America 113, 6707-6712. (10.1073/pnas.1519508113)
2. Bi G, dos Remedios N, Dawson DA, Kingma SA, Schroeder J, Dugdale HL (2016) A multiplex set for microsatellite typing and sexing of the European bee-eater (Merops apiaster). European Journal of Wildlife Research 62, 501. (10.1007/s10344-016-1012-2)
3. Dawson DA, dos Remedios N, Horsburgh GJ (2016) A new marker based on the avian spindlin gene that is able to sex most birds, including species problematic to sex with CHD markers. Zoo Biology 35, 533-545. (10.1002/zoo.21326)
4. Diao W, Mousset M, Horsburgh GJ, Vermeulen CJ, Johannes F, van de Zande L, Ritchie MG, Schmitt T, Beukeboom LW (2016) Quantitative Trait Locus analysis of mating behavior and male sex pheromones in Nasonia wasps. G3 Genes Genomes Genetics 6, 1549-1562. (10.1534/g3.116.029074)
5. El Nagar A, MacColl ADC (2016) Parasites contribute to ecologically dependent postmating isolation in the adaptive radiation of three-spined stickleback. Proceedings of the Royal Society B 283, 20160691. (10.1098/rspb.2016.0691)
6. Engler JO, Secondi J, Dawson DA, Elle O, Hochkirch A (2016) Range expansion and retraction along a moving contact zone has no effect on the genetic diversity of two passerine birds. Ecography 38, 1-10. (10.1111/ecog.01520)
7. Field J, Leadbeater E (2016) Cooperation between non-relatives in a primitively eusocial paper wasp, Polistes dominula. Philosophical Transactions of the Royal Society of London Series B. 371, 20150093. (10.1098/rstb.2015.0093)
8. Giraldo-Perez P, Herrera P, Campbell A, Taylor ML, Skeats A, Aggio R, Wedell N, Price TAR (2016) Winter is coming: hibernation reverses the outcome of sperm competition in a fly. Journal of Evolutionary Biology 29, 371–379. (10.1111/jeb.12792)
9. Green J, RP Freckleton, BJ Hatchwell (2016) Variation in helper investment among cooperatively breeding bird species is consistent with Hamilton’s rule. Nature Communications 7, 12663. (10.1038/ncomms12663)
10. Heathcote R, MacGregor H, Sciberras J, While GM, D’Ettorre P, Uller T (2016) Male behaviour drives assortative reproduction during the initial stage of secondary contact. Journal of Evolutionary Biology 29, 1003-1015. (10.1111/jeb.12840)
11. Levy HJ, Clucas GV, Rogers AD, Leaché AD, Ciborowski K, Polito MJ, Lynch HJ, Dunn M, Hart T (2016) Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc. Ecology and Evolution 6, 1834–1853. (10.1002/ece3.1929)
12. Lindholm AK, Dyer KA, Firman RC, Fishman L, Forstmeier W, Holman L, Johannesson H, Knief U, Kokko H, Larracuente AM, Manser A, Montchamp-Moreau C, Petrosyan VG, Pomiankowski A, Presgraves DC, Safronova LD, Sutter A, Unckless RL, Verspoor RL, Wedell N, Wilkinson GS, Price TAR (2016) The ecology and evolutionary dynamics of meiotic drive. Trends in Ecology and Evolution 31, 315-326. (10.1016/j.tree.2016.02.001)
13. Mundy NI, Stapley J, Bennison C, Tucker R, Twyman H, Kim K-W, Burke TA, Birkhead TR, Andersson S, Slate J (2016) Red carotenoid coloration in the zebra finch is controlled by a cytochrome P450 gene cluster. Current Biology 26, 1435-1440. (10.106/j.cub.2016.04.047)
14. Napper CJ & BJ Hatchwell (2016) Social dynamics in non-breeding flocks of a cooperatively breeding bird: causes and consequences of kin associations. Animal Behaviour 122, 23-35. (10.1016/j.anbehav.2016.09.008)
15. Preston SA, JV Briskie & BJ Hatchwell (2016) The fitness consequences of helping in the cooperatively breeding rifleman. Behavioral Ecology 27, 1617-1626. (10.1093/beheco/arw087)
16. Quinn LR, Meharg AA, van Franeker JA, Graham IM, Thompson PM (2016) Validating the use of intrisic markers in body feathers to identify inter-individual differences in non-breeding areas of northern fulmars. Marine Biology 163, 64. (10.1007/s00227-016-2822-1)
17. Saether BE, V Grøtan, S Engen, T Coulson, P Grant, ME Visser, JE Brommer, R Grant, L Gustaffson, BJ Hatchwell, K Jerstad, P Karell, H Pietiainen, A Roulin, OW Røstad, H Weimerskirch (2016) Demographic routes to variability and regulation in bird populations. Nature Communications 7, 12001. (10.1038/ncomms12001)
18. Sin YW, Newman C, Dugdale HL, Buesching C, Mannarelli M-E, Annavi G, Burke T, Macdonald DW (2016) No compensatory relationship between the innate and adaptive immune system in wild-living European badgers. PLoS One 11, e0163773. (10.1371/journal.pone.0163773)
19. Wright DJ, Brouwer L, Mannarelli ME, Burke T, Komdeur J, Richardson DS (2016) Social pairing of Seychelles warblers under reduced constraints: MHC, neutral heterozygosity, and age. Behavioral Ecology 27, 295-303. (10.1093/beheco/arv150)

          NBAF-W

Lehmann K, Bell T, Bowes MJ, Amos GCA, Gaze WH, Wellington EMH, Singer AC (2016) Trace levels of sewage effluent are sufficient to increase class 1 integron prevalence in freshwater biofilms without changing the core community, Water Research 106, 163–170. (10.1016/j.watres.2016.09.035).

          Chapter

Buesching CD, Tinnesand HV, Sin YW, Rosell F, Burke T, Macdonald DW (2016) Coding of group odor in the subcaudal gland secreation of the European badger Meles meles: chemical composition and pouch microbiota. In Chemical Signals in Vertebrates, Part II, Chapter 13, 45–62. Springer International Publishing, Switzerland. (10.1007/978-3-319-22026-0_5) (NBAF-S)