Publications
Pdf versions are either the open access published version or the accepted version of the manuscript, depending on publisher open-access policy. Final versions can be supplied upon request.
2025
Owens, J.B., Wüster, W., Mulley, J., Graham, S., Morgan, R., Barlow, A., Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium, 2025. ‘The genome sequence of the common adder, Vipera berus (Linnaeus, 1758)’. Wellcome Open Research, 10, p.11. [Link]
Major, T., Jeffrey, L., Limia Russel, G., Bracegirdle, R., Gandini, A., Morgan, R., Marshall, B.M., Mulley, J.F. and Wüster, W., 2024. ‘A reliance on human habitats is key to the success of an introduced predatory reptile’. PLoS One, 20(2), p.e0310352. [Link]
2024
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Mayeur, H., Leyhr, J., Mulley, J., Nicolas, L., Michel, L., Sharma, K., … & Debiais-Thibaud, M. (2024). ‘The sensory shark: high-quality phenotypic, genomic and transcriptomic data for the small spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates’. Molecular Biology and Evolution 41 (12): msae246 [Link]
2023
Mulley, J.F., Lees, D.C., Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium, 2023. ‘The genome sequence of Ashworth’s Rustic, Xestia ashworthii (Doubleday, 1855).’ Wellcome Open Research 8: 578. [Link]
Boyes, D., Mulley, J.F., University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium (2023). ‘The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795)’. Wellcome Open Research 8: 441. [Link]
Boyes, D., Mulley, J.F., University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium (2023). ‘The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809)’. Wellcome Open Research 8: 399. [Link]
Falk, S., Mulley, J.F., University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium (2023). ‘The genome sequence of the short-fringed mining bee, Andrena dorsata (Kirby, 1802)’. Wellcome Open Research 8:373 [Link].
Brekke, T.D., Shier, L., Hegarty, M. J., Mulley, J. F. (2023) ‘Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles’ Conservation Genetics Resources 15: 117–124. [Link]
Brekke, T.D., Papadopulos, A.S., Julià, E., Fornas, O., Fu, B., Yang, F., de la Fuente, R., Page, J., Baril, T., Hayward, A. and Mulley, J.F. (2023) ‘A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome’. Molecular Biology and Evolution, p.msad115. [Link]
Rogerson, G., Bock, S., Loera, Y., Parrott, B., Mulley, J.F. (2023) ‘Incubation temperature alters stripe formation and head colouration in American alligator hatchlings and is unaffected by E2-induced sex reversal.’ Journal of Experimental Biology 226 (6), jeb245219. [Link] [ECR Spotlight – Grace Rogerson]
Crowley, L.M., Mulley, J.F., University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium, (2023). ‘The genome sequence of the Tawny Mining Bee, Andrena fulva (Müller, 1766)’. Wellcome Open Research 8: 258. [Link]
Falk, S., Mulley, J.F., University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective and Darwin Tree of Life Consortium (2023). The genome sequence of the variegated flesh fly, Sarcophaga variegata (Scopoli, 1763). Wellcome Open Research 8: 234. [Link]
Crowley, L.M., Telfer, M., Geiser, M., Mulley, J.F. and Darwin Tree of Life Consortium, (2023) ‘The genome sequence of Philonthus cognatus (Stephens, 1832) (Coleoptera, Staphylinidae), a rove beetle.’ Wellcome Open Research 8: 169. [Link]
Boyes, D., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).’ Wellcome Open Research 8: 129. [Link]
Boyes, D., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).’ Wellcome Open Research 8: 45 [Link]
Boyes, D., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).’ Wellcome Open Research 8: 66 [Link]
Boyes, D., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766)’ Wellcome Open Research 8: 63 [Link]
Falk, S., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome sequence of the lesser worm flesh fly, Sarcophaga (Sarcophaga) subvicina (Baranov, 1937)’ Wellcome Open Research 8: 65 [Link]
Falk, S., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome of Roselle’s flesh fly Sarcophaga (Helicophagella) rosellei (Böttcher, 1912).’ Wellcome Open Research 8: 43 [Link]
Falk, S., Mulley, J.F., Darwin Tree of Life Consortium (2023) ‘The genome sequence of the bluish flesh fly, Sarcophaga (Robineauella) caerulescens (Zetterstedt, 1838).’ Wellcome Open Research 8: 17 [Link]
Major, T., Bracegirdle, R., Gandini, A., Russell, G.L., Pozzi, A.V., Morgan, R., Mulley, J.F., Wüster, W. (2023) ‘Mate today, gone tomorrow: male on female cannibalism in Zamenis longissimus (Laurenti, 1768) in North Wales.’ Herpetology Notes 16: 51-54 [Link]
2022
Crowley, L.M., Mulley, J.F., Darwin Tree of Life Consortium (2022) ‘The genome sequence of the hawthorn shieldbug, Acanthosoma haemorrhoidale (Linnaeus, 1758).’ Wellcome Open Research 7: 178 [Link]
Mulley, JF. (2022) ‘Regulation of posterior Hox genes by sex steroids explains vertebral variation in inbred mouse strains.’ Journal of Anatomy 240 (4): 735-745. doi: 10.1111/joa.13580 [Link]
2020
Pracana, R., Hargreaves, AD., Mulley, JF., Holland, PWH. (2020) ‘Runaway GC evolution in gerbil genomes.’ Molecular Biology and Evolution 37 (8): 2197-2210 [Link]
2019
Mulley, JF (2019) ‘Greater loss of female embryos during human pregnancy: A novel mechanism.’ BioEssays 41, 1900063 [Link] [Preprint]
Brekke, TD., Supriya, S., Denver, MG., Thom, A., Mulley JF. (2019) ‘A high-density genetic map and molecular sex-typing assay for gerbils’ Mammalian Genome 30 (3-4): 63-70 [Link] [Preprint]
Zancolli, G., Calvete, JJ., Cardwell, MD., Greene, HW., Hayes, WK., Hegarty, MJ., Herrmann, HW., Holycross, AT., Lannutti, DI., Mulley, JF., Sanz, L., Travis, ZD., Whorley, JR., Wüster, CE., Wüster, W. (2019) ‘When one phenotype is not enough-divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species’ Proceedings of the Royal Society B 286: 20182735 [Link] [Preprint]
2018
Brekke, TD., Steele, KS., and Mulley, JF. (2018) ‘Inbred or Outbred? Genetic diversity in laboratory rodent colonies’ G3: Genes, Genomes, Genetics 8: 679-686 [PubMed] [Link] [Preprint]
2017
Hargreaves, AD, Zhou, L., Christensen, J., Marletaz, F., Liu, S., Jansen, PD., Spiga, E., Hansen, MT., Pedersen, SVH., Biswas, S., Serikawa, K., Fox, BA., Taylor, WR., Mulley, JF., Zhang, G., Heller, RS., Holland, PWH. (2017) ‘Genome sequence of a diabetes-prone desert rodent reveals a mutation hotspot around the ParaHox gene cluster’ PNAS 114 (29): 7677–7682 [PubMed] [Link] Pdf
2016
Braasch, I, Gehrke, AR, Smith, JJ, Kawasaki, K, Manousaki, T, Pasquier, J, Amores, A, Desvignes, T, Batzel, P, Catchen, J, Berlin, AM, Campbell, MS, Barrell, D, Martin, KJ, Mulley, JF, Ravi, V, Lee, AP, Nakamura, T, Chalopin, D, Fan, S, Wcisel, D, Cañestro, C, Sydes, J, Beaudry, FEG, Sun, Y, Hertel, J, Beam, MJ, Fasold, M, Ishiyama, M, Johnson, J, Kehr, S, Lara, M, Letaw, JH, Litman, W, Litman, RT, Mikami, M, Ota, T, Saha, NR, Williams, L, Stadler, PF, Wang, H, Taylor, JS, Fontenot, Q, Ferrara, A, Searle, SMJ, Aken, B, Yandell, M, Schneider, I, Yoder, JA, Volff, J-N, Meyer, A, Amemiya, CT, Venkatesh, B, Holland, PWH, Guiguen, Y, Bobe, J, Shubin, NH, Di Palma, F, Alföldi, J, Lindblad-Toh, K, Postlethwait, JH (2016) ‘The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons’ Nature Genetics 48: 427-437 [PubMed] [Link] Pdf
2015
Hargreaves AD and Mulley JF (2015) ‘Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing’ PeerJ 3:e1441; DOI 10.7717/peerj.1441 [PubMed] [Link] Pdf
Hargreaves, AD, Tucker, A, Mulley JF (2015) ‘A Critique of the Toxicoferan Hypothesis’ Evolution of Venomous Animals and Their Toxins (Part of the series Toxinology, Eds: P. Gopalakrishnakone, Anita Malhotra) ISBN: 978-94-007-6727-0 (Online) pp 1-15 [Link] Pdf
Mulley JF (2015) ‘Developmental biology teaching – the importance of a practical approach’ F1000Research 4: 216 [Link] Pdf
2014
Mulley JF, Hargreaves AD, Hegarty MJ, Heller RS, Swain MT (2014) ‘Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function’ BMC Genomics 15: 1074 [PubMed] [Link] Pdf Preprint
Associated data on the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.s1f22
Hargreaves AD, Swain MT, Logan DW and Mulley JF (2014) ‘Testing the Toxicofera: comparative reptile transcriptomics casts doubt on the single, early evolution of the reptile venom system’ Toxicon 92: 140-156 [PubMed] Pdf Preprint
Hargreaves AD & Mulley JF (2014) ‘A plea for standardized nomenclature of snake venom toxins’ Toxicon 90: 351-353 [PubMed] Pdf
Hargreaves AD, Swain MT, Hegarty MJ, Logan DW and Mulley JF (2014) ‘Restriction and recruitment – gene duplication and the origin and evolution of snake venom toxins’ Genome Biology and Evolution 6(8): 2088-2095 [PubMed] Pdf Preprint
Mulley, JF & Holland, PWH (2014) “Genomic organisation of the seven ParaHox genes of coelacanths.” Journal of Experimental Zoology B: Molecular and Developmental Evolution (Coelacanth genome companion issue) 322B: 352-358 [PubMed] Pdf
2010 or earlier
Mulley, JF & Holland, PWH (2010) “Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths.” Molecular Biology and Evolution 27: 2386 [PubMed] Pdf
Mulley, JF, Zhong, Y-F. & Holland, PWH (2009) “Comparative genomics of Chondrichthyan hoxa clusters.” BMC Evolutionary Biology 9: 218 [PubMed] Pdf
Furlong, RF & Mulley, JF (2008) “ParaHox Cluster Evolution – Hagfish and Beyond.” Zoological Science 25: 955 [PubMed] Pdf
Mulley, JF, Chiu, C-H & Holland, PWH (2006) “Break-up of a homeobox gene cluster after genome duplication in teleosts.” PNAS 103: 10369 [PubMed] Pdf
Mulley, J & Holland P (2004) “Small genome, big insights.” Nature 431: 916 [PubMed] Pdf
Daly, D, Waltham, K, Mulley, J, Watts, P, Rosin, A, Kemp, S & Saccheri, I (2004) “Trinucleotide microsatellite loci for the peppered moth (Biston betularia)” Molecular Ecology Notes 4: 179-181 Pdf
Miscellaneous
Hawkins P, McBride A, Paiba G, Rose R, Prescott M, Mulley J, Izzard S, Ridley D, Melotti L, Kappel S and Hubrecht R (2018). “Report of the 2017 RSPCA/UFAW Rodent and Rabbit Welfare Group meeting.” Animal Technology and Welfare 17(2), 75-84.
Martin, KJ, Mulley, JF & Holland, PWH (2009) “The hox gene complement of a basal teleost, Pantodon bucholzi (Osteoglossomorpha)” Mechanisms of Development 126 (Supplement): S261 Pdf
Longbottom, A, Mulley, J & Forey, PL (2010) “Bony Fishes” In: Lord, A. R. & Davis, P. G. (eds) ‘Fossils from the Lower Lias of the Dorset Coast’ Palaeontological Association Field Guide to Fossils Number 13.
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