Publications

2024

Mackintosh A, Vila R, Martin SH, Setter D, & Lohse K
Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies.
Molecular Ecology In Press https://doi.org/10.1111/mec.17146

2023

Laetsch DR, Bisschop G, Martin SH, Aeschbacher, S, Setter D, & Lohse K
Demographically explicit scans for barriers to gene flow using gIMble
PLOS Genetics, 19(10), e1010999 https://doi.org/10.1371/journal.pgen.1010999

Rougemont Q, Huber B, Martin SH, Whibley A, Estrada C, Solano D, Orpet R, McMillan WO, Frérot, B & Joron M
Subtle Introgression Footprints at the End of the Speciation Continuum in a Clade of Heliconius Butterflies
Molecular Biology and Evolution, 40, msad166 https://doi.org/10.1093/molbev/msad166

Baird RB, Urban JM, Mongue AJ, Jaron KS, Hodson CN, Grewoldt M, Martin SH, & Ross L
Recent Evolution of a Maternally Acting Sex-Determining Supergene in a Fly with Single-Sex Broods
Molecular Biology and Evolution, 40, msad148 https://doi.org/10.1093/molbev/msad148

Lovell RSL, Collins S, Martin SH, Pigot AL & Phillimore AB
Space-for-time substitutions in climate change ecology and evolution
Biological Reviews, 98 (6), 2243-2270 https://doi.org/10.1111/brv.13004

Malmberg J, Martin SH, Gordon IJ, Sihvonen P & Duplouy A
Morphological changes in female reproductive organs in the African monarch butterfly, host to a male-killing Spiroplasma
PeerJ, 11, e15853 https://doi.org/10.7717/peerj.15853

Mongue AJ, Martin SH, Manweiler REV, Scullion H, Koehn JL, de Roode JC & Walters JR
Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: Cryptic diversity and response to host-sequestered plant chemicals
BMC Genomics, 24(1), 278 https://doi.org/10.1186/s12864-023-09350-0

Mackintosh A, Vila R, Laetsch DR, Hayward A, Martin SH*, Lohse K*
Chromosome fissions and fusions act as barriers to gene flow between Brenthis fritillary butterflies
Molecular Biology and Evolution 40 (3), msad043 https://doi.org/10.1093/molbev/msad043

Rutagarama VP, Ireri PM, Sibomana C, Omufwoko KS, Martin SH, ffrench-Constant RH, Eckardt W, Kaplin BK, Smith DAS & Gordon I
African Queens find mates when males are rare
Ecology and Evolution, 13(4), e9956. https://doi.org/10.1002/ece3.9956

2022

Kim KW, De-Kayne R, Gordon IJ, Omufwoko KS, Martins DJ, Martin SH
Stepwise evolution of a butterfly supergene via duplication and inversion
Philosophical Transactions of the Royal Society B 377 (1856), 20210207 https://doi.org/10.1098/rstb.2021.0207

Liu W, Smith DA, Raina G, Stanforth R, Ng’Iru I, Ireri P, Martins DJ, Gordon IJ, Martin SH
Global biogeography of warning coloration in the butterfly Danaus chrysippus
Biology Letters 18(6) p.20210639 https://doi.org/10.1098/rsbl.2021.0639

Singh KS, De-Kayne R, Omufwoko KS, Martins DJ, Bass C, Ffrench-Constant R, Martin SH
Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus
G3, 12(3), p.jkab449 https://doi.org/10.1093/g3journal/jkab449

Montejo-Kovacevich G, Meier JI, Bacquet CN, Warren IA, Chan YF, Kucka M, Salazar C, Rueda-MN, Montgomery SH, McMillan WO, Kozak, KM, Nadeau NJ, Martin SH, Jiggins CD
Repeated genetic adaptation to altitude in two tropical butterflies
Nature Communications, 13(1) pp.1-16 https://doi.org/10.1038/s41467-022-32316-x

Nouhaud P, Martin SH, Portinha B, Sousa VC, Kulmuni J
Rapid and predictable genome evolution across three hybrid ant populations
Plos Biology 20 (12), e3001914 https://doi.org/10.1371/journal.pbio.3001914

Ndatimana G, Kayitete L, Martin SH, Smith DA, Hagenimana T, Nkundimana A, Muhayimana S, Antony J, Sibomana C, Uwizelimana JDD, Omufwoko KS, Nyirakanani C, Gordon IJ
Morph frequencies, sex ratios and infections in Danaus chrysippus populations in Rwanda
African Journal of Ecology 60(3) 633-640 https://doi.org/10.1111/aje.13014

2021

Cicconardi F, Lewis JJ, Martin SH, Reed RD, Danko CG, Montgomery SH
The effects of chromosome fusions on genetic diversity and evolutionary turnover of functional loci consistently depends on chromosome size
Molecular Biology and Evolution https://doi.org/10.1101/2021.01.06.425547

Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH
The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies
Genome Biology and Evolution https://doi.org/10.1093/gbe/evab128

Smith DA, Bennie JJ, Gordon IJ, Martin SH, Ireri P, Omufwoko KS, Ffrench-Constant RH
Hybrid effects in field populations of the African monarch butterfly, Danaus chrysippus (L.)(Lepidoptera: Nymphalidae)
Biological Journal of the Linnean Society 133: 671-684 https://doi.org/10.1093/biolinnean/blab036

Martin SH and Amos W
Signatures of introgression across the allele frequency spectrum
Molecular Biology and Evolution 38(2): 716-726 https://doi.org/10.1093/molbev/msaa239

2020

Satokangas I, Martin SH, Helanterä H, Saramäki J and Kulmuni J
Multi-locus interactions and the build-up of reproductive isolation
Philosophical Transactions of the Royal Society B 375: 20190543 https://doi.org/10.1098/rstb.2019.0543

Martin SH, Singh KS, Gordon IJ, Omufwoko KS, Collins S, Warren IA, Munby H, Brattström O, Traut W, Martins DJ, Smith DAS, Jiggins CD, Bass C, ffrench-Constant RH
Whole-chromosome hitchhiking driven by a male-killing endosymbiont
PLOS Biology 18 (2), e3000610 https://doi.org/10.1371/journal.pbio.3000610

Dierickx E, Sin S, van Veelen P, Brooke M de L, Liu Y, Edwards S, Martin SH
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark
Proceedings of the Royal Society B 287(1922) https://doi.org/10.1098/rspb.2019.2613

Montejo-Kovacevich G, Martin SH, Meier JI, Bacquet CN, Monllor M, Jiggins CD, Nadeau NJ.
Microclimate buffering and thermal tolerance across elevations in a tropical butterfly
Journal of Experimental Biology 223(8):jeb220426.

Lawal RA, Martin SH, Vanmechelen K, Vereijken, A, Silva P, Al-Atiyat RM, Aljumaah RS, Mwacharo JM, Wu DD, Zhang YP, Hocking PM, Smith J, Wragg D, Hanotte O
The wild species genome ancestry of domestic chickens
BMC Biology 18: 13 https://doi.org/10.1186/s12915-020-0738-1

Moest M, Van Belleghem SM, James JE, Salazar C, Martin SH, Barker SL, Moreira GRP, Mérot C, Joron M, Nadeau NJ, Steiner FM, Jiggins CD
Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation
PLOS Biology 18 (2), e3000597 https://doi.org/10.1371/journal.pbio.3000597

Yan Z, Martin SH, Gotzek D, Arsenault SV, Duchen P, Helleu Q, Riba-Grognuz O, Hunt BG, Salamin N, Shoemaker D, Ross KG, Keller L
Evolution of a supergene that regulates a trans-species social polymorphism
Nature Ecology & Evolution, 4(2): 240–249 https://doi.org/10.1038/s41559-019-1081-1

Morris J, Hanly JJ, Martin SH, Van Belleghem SM, Salazar C, Jiggins CD, Dasmahapatra KK
Deep convergence, shared ancestry, and evolutionary novelty in the genetic architecture of Heliconius mimicry
Genetics, 216(3):765-80. https://doi.org/10.1534/genetics.120.303611

Arias M, Davey JW, Martin SH, Jiggins C, Nadeau N, Joron M, Llaurens V
How do predators generalize warning signals in simple and complex prey communities? Insights from a videogame
Proc. R. Soc. B 287 https://doi.org/10.1098/rspb.2020.0014

2019

Marburger S, Monnahan P, Seear PJ, Martin SH, Koch J, Paajanen P, Bohutínská M, Higgins JD, Schmickl R and Yant L
Interspecific introgression mediates adaptation to whole genome duplication
Nature Communications (10) 5218 https://doi.org/10.1038/s41467-019-13159-5

Martin SH, Davey JW, Salazar C, Jiggins CD
Recombination rate variation shapes barriers to introgression across butterfly genomes
PloS Biology 17(2): e2006288 https://doi.org/10.1371/journal.pbio.2006288

Merrill RM, Rastas P, Martin SH, Melo MC, Barker S, Davey J, McMillan WO, Jiggins CD
Genetic dissection of assortative mating behavior
PloS Biology 17(2): e2005902 https://doi.org/10.1371/journal.pbio.2005902

Pinharanda A, Rousselle M, Martin SH, Hanly JJ, Davey JW, Kumar S, Galtier N, Jiggins CD
Sexually dimorphic gene expression and transcriptome evolution provides mixed evidence for a fast-Z effect in Heliconius
Journal of Evolutionary Biology 32(3): 194-204 https://doi.org/10.1111/jeb.13410

2018

Van Belleghem SM, Baquero M, Papa R, Salazar C, McMillan WO, Counterman BA, Jiggins CD, Martin SH
Patterns of Z chromosome divergence among Heliconius species highlight the importance of historical demography
Molecular Ecology 27:3852–3872 http://doi.wiley.com/10.1111/mec.14560

2017

Martin SH, Jiggins CD
Interpreting the genomic landscape of introgression
Current Opinion in Genetics & Development 47:69-74 https://doi.org/10.1016/j.gde.2017.08.007

Enciso-Romero J, Pardo-Díaz C, Martin SH, Arias C, Linares M, McMillan WO, Jiggins CD, Salazar C
Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies
Molecular Ecology 26: 5160-5172 https://doi.org/10.1111/mec.14277

Jiggins CD, Martin SH
Glittering gold and the quest for Isla de Muerta
Journal of Evolutionary Biology 30:1509–1511 http://doi.wiley.com/10.1111/jeb.13110

Davey JW, Barker SL, Rastas PM, Pinharanda A, Martin SH, Durbin R, Merrill RM, Jiggins CD
No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions
Evolution Letters 1:138–154 http://doi.wiley.com/10.1002/evl3.12

Martin SH, Van Belleghem SM
Exploring evolutionary relationships across the genome using topology weighting
Genetics 206:429–428: https://doi.org/10.1534/genetics.116.194720

Van Belleghem SM, Rastas P, Papanicolaou A, Martin SH, Arias CF, Supple MA, Hanly JJ, Mallet J, Lewis JJ, Hines HM, Ruiz M, Salazar C, Linares M, Moreira GRP, Jiggins CD, Counterman BA, McMillan WO, Papa R
Complex modular architecture around a simple toolkit of wing pattern genes
Nature Ecology and Evolution 1:52 https://doi.org/10.1038/s41559-016-0052

Pinharanda A, Martin SH, Barker SL, Davey JW, Jiggins CD
The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno
Heredity 118:78–87 https://doi.org/10.1038/hdy.2016.107

2016

Martin SH, Moest M, Palmer WJ, Salazar C, McMillan WO, Jiggins FM, Jiggins CD
Natural selection and genetic diversity in the butterfly Heliconius melpomene
Genetics 203:525–541 https://doi.org/10.1534/genetics.115.183285

Lohse K, Chmelik M, Martin SH, Barton NH
Efficient strategies for calculating blockwise likelihoods under the coalescent
Genetics 202:775–86 https://doi.org/10.1534/genetics.115.183814

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
Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling
PLoS Biology 14:e1002353 https://doi.org/10.1371/journal.pbio.1002353

2015

Merrill RM, Dasmahapatra KK, Davey JW, Dell’Aglio DD, Hanly JJ, Huber B, Jiggins CD, Joron M, Kozak KM, Llaurens V, Martin SH, Montgomery SH, Morris J, Nadeau NJ, Pinharanda a L, Rosser N, Thompson MJ, Vanjari S, Wallbank RWR, Yu Q
The diversification of Heliconius butterflies: What have we learned in 150 years?
Journal of Evolutionary Biology 28:1417–38 http://doi.wiley.com/10.1111/jeb.12672

Martin SH, Davey JW, Jiggins CD
Evaluating the Use of ABBA-BABA Statistics to Locate Introgressed Loci
Molecular Biology and Evolution 32:244–57 https://doi.org/10.1093/molbev/msu269

2014

De Vos L, Steenkamp ET, Martin SH, Santana QC, Fourie G, van der Merwe N a., Wingfield MJ, Wingfield BD
Genome-Wide Macrosynteny among Fusarium Species in the Gibberella fujikuroi Complex Revealed by Amplified Fragment Length Polymorphisms
PLoS One 9(12):e114682 https://doi.org/10.1371/journal.pone.0114682

Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe P a, Peichel CL, Saetre G-P, Bank C, Brännström A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques D a, Martin SH, Matthews B, Meier JI, Möst M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A.
Genomics and the origin of species
Nature Reviews Genetics 15:176–92 https://doi.org/10.1038/nrg3644

2013

Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD
Genome-wide evidence for speciation with gene flow in Heliconius butterflies
Genome Research 23:1817–28 https://doi.org/10.1101/gr.159426.113

Briscoe AD, Macias-Muñoz A, Kozak KM, Walters JR, Yuan F, Jamie G a., Martin SH, Dasmahapatra KK, Ferguson LC, Mallet J, Jacquin-Joly E, Jiggins CD
Female Behaviour Drives Expression and Evolution of Gustatory Receptors in Butterflies
PLoS Genetics 9(7):e1003620 https://doi.org/10.1371/journal.pgen.1003620

Nadeau NJ, Martin SH, Kozak KM, Salazar C, Dasmahapatra KK, Davey JW, Baxter SW, Blaxter ML, Mallet J, Jiggins CD
Genome-wide patterns of divergence and gene flow across a butterfly radiation
Molecular Ecology 22:814–26 https://doi.org/10.1111/j.1365-294X.2012.05730.x

Martin SH, Steenkamp ET, Wingfield MJ, Wingfield BD
Mate-recognition and species boundaries in the ascomycetes
Fungal Diversity 58:1–12 https://doi.org/10.1007/s13225-012-0217-2

2012

Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, Nadeau NJ, Zimin A V, Hughes DST, Ferguson LC, Martin SH, Salazar C, Lewis JJ, Adler S, Ahn S-J, Baker DA, Baxter SW, Chamberlain NL, Chauhan R, Counterman BA, Dalmay T, Gilbert LE, Gordon K, Heckel DG, Hines HM, Hoff KJ, Holland PWH, Jacquin-Joly E, Jiggins FM, Jones RT, Kapan DD, Kersey P, Lamas G, Lawson D, Mapleson D, Maroja LS, Martin A, Moxon S, Palmer WJ, Papa R, Papanicolaou A, Pauchet Y, Ray DA, Rosser N, Salzberg SL, Supple MA, Surridge A, Tenger-Trolander A, Vogel H, Wilkinson PA, Wilson D, Yorke JA, Yuan F, Balmuth AL, Eland C, Gharbi K, Thomson M, Gibbs RA, Han Y, Jayaseelan JC, Kovar C, Mathew T, Muzny DM, Ongeri F, Pu L-L, Qu J, Thornton RL, Worley KC, Wu Y-Q, Linares M, Blaxter ML, Ffrench-Constant RH, Joron M, Kronforst MR, Mullen SP, Reed RD, Scherer SE, Richards S, Mallet J, Owen McMillan W, Jiggins CD
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
Nature 487:94–98 https://doi.org/10.1038/nature11041

Wingfield BD, Steenkamp ET, Santana QC, Coetzee MPA, Bam S, Barnes I, Beukes CW, Chan WY, De Vos L, Fourie G, Friend M, Gordon TR, Herron DA, Holt C, Korf I, Kvas M, Martin SH, Mlonyeni XO, Naidoo K, Phasha MM, Postma A, Reva O, Roos H, Simpson M, Slinski S, Slippers B, Sutherland R, Van der Merwe NA, Van der Nest MA, Venter SN, Wilken PM, Yandell M, Zipfel R, Wingfield MJ
First fungal genome sequence from Africa: A preliminary analysis
South African Journal of Science 108 https://doi.org/10.4102/sajs.v108i1/2.537

2011

Martin SH, Wingfield BD, Wingfield MJ, Steenkamp ET
Structure and evolution of the Fusarium mating type locus: new insights from the Gibberella fujikuroi complex
Fungal Genetics and Biology 48:731–40 https://doi.org/10.1016/j.fgb.2011.03.005

Martin SH, Wingfield BD, Wingfield MJ, Steenkamp ET
Causes and consequences of variability in peptide mating pheromones of ascomycete fungi
Molecular Biology and Evolution 28:1987–2003 https://doi.org/10.1093/molbev/msr022