Published papers

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.

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]

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 Research8 (169), 169. [Link]

D Boyes, JF Mulley, Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Common Pug, Eupithecia vulgata (Haworth, 1809).’ Wellcome Open Research, 8 (129), 129. [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]

D Boyes, JF Mulley, Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Riband Wave, Idaea aversata (Linnaeus, 1758).’ Wellcome Open Research 8 (45), 45 [Link]

D Boyes, JF Mulley, Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).’ Wellcome Open Research 8 (66), 66 [Link]

D Boyes, JF Mulley, Darwin Tree of Life Consortium (2023) ‘The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766)’ Wellcome Open Research 8 (63), 63 [Link]

S Falk, JF Mulley, 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), 65 [Link]

S Falk, JF Mulley, Darwin Tree of Life Consortium (2023) ‘The genome of Roselle’s flesh fly Sarcophaga (Helicophagella) rosellei (Böttcher, 1912).’ Wellcome Open Research 8 (43), 43 [Link]

S Falk, JF Mulley, Darwin Tree of Life Consortium (2023) ‘The genome sequence of the bluish flesh fly, Sarcophaga (Robineauella) caerulescens (Zetterstedt, 1838).’ Wellcome Open Research 8 (17), 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]

LM Crowley, J Mulley, Darwin Tree of Life Consortium (2022) ‘The genome sequence of the hawthorn shieldbug, Acanthosoma haemorrhoidale (Linnaeus, 1758).’ Wellcome Open Research 7 (178), 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]

Pracana, R., Hargreaves, AD., Mulley, JF., Holland, PWH. (2020) ‘Runaway GC evolution in gerbil genomes.’ Molecular Biology and Evolution 37 (8): 2197-2210 [Link]

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]

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]

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[LinkPdf

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

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] [LinkPdf

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 [LinkPdf

Mulley JF (2015) ‘Developmental biology teaching – the importance of a practical approach’ F1000Research 4: 216 [LinkPdf

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] [LinkPdf Preprint
Associated data on the Dryad Digital Repository:

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 [PubMedPdf Preprint

Hargreaves AD & Mulley JF (2014) ‘A plea for standardized nomenclature of snake venom toxins’ Toxicon 90: 351-353 [PubMedPdf

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

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


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.


Brekke, TD, Shier, L, Hegarty, MJ, Mulley, JF (2019) ‘Shed skin as a source of DNA for genotyping-by-sequencing (GBS) in reptiles’ bioRxiv doi: [Preprint]

Mulley, JF and Kuncheva, LI (2017) ‘Intrauterine position probabilities in mice, rats and gerbils’. bioRxiv doi: [Preprint]