Publications

For the most up to date list of publication please see google scholar. For published code please see our GitHub page. 

Lab members are in bold; * co-authorships; # authors for correspondence

• Blumer M, Burskaia V, Artiushin I, Saha J, Garcia JC, Elkin J, Fischer B, Zhou C, Gresham S, Malinsky M, Linderoth T, Sawasawa W, Bista I, Hickey A, Kucka M, Louzada S, Zatha R, Yang F, Rusuwa B,  Santos ME, Chan YF, Joyce DA, Böhne A, Miska EA, Ngochera M, Turner GF, Durbin R, Svardal H (2024) Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation. bioRxiv

• Almeida MV, Blumer M, Yuan CU, Sierra P, Price J, Quah FX, Friman A, Dallaire A, Vernaz G, Putman A, Smith A, Joyce D, Butter F, Haase A, Durbin R, Santos ME, Miska E (2024) Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. bioRxiv

• Quah FX, Almeida MV, Blumer M, Yuan CU, Fischer B, See K, Jackson B, Zatta R, Rusuwa B, Turner GF, Santos ME, Svardal H, Hemberg M, Durbin R, Miska E (2024) A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements. bioRxiv

• Badiane A, Viala S, Armisen D, Mignerey I, Forcet-Vauchel C, De Jesús Villanueva CN, Van Belleghem S, Crumière A, Santos ME, Francesconi M, Khila A (2024) A single giant cell at the origin of an evolutionary innovation. bioRxiv.

• Marconi A*#, Vernaz G*, Karunaratna A, Ngochera MJ, Durbin R, Santos ME# (2024) Genetic and developmental divergence in the neural crest programme between cichlid fish species. Molecular Biology and Evolution, msae217.

• Brown FD, Ishengoma E, Mayer G, Pabón-Mora NN, Santos ME, Sears KE, Oliveira IS (2024) Uncovering developmental diversity in the field. Development 151 (20), dev203084

• Sommer-Trembo C, Santos ME, Clark B, Werner W, Fages A, Matschiner M, Hornung S, Ronco F, Oliver C, Garcia C, Tschopp P, Malinsky M, Salzburger W (2024) The genetics of niche-specific behavioural tendencies in an adaptive radiation of cichlid fishes. Science 384:470-475 

• Clark B*, Hickey A*, Marconi A, Fischer B, Elkin J, Mateus R, Santos ME# (2024) Developmental plasticity and variability in the formation of egg-spots, a pigmentation ornament in the cichlid Astatotilapia calliptera. Evolution & Development, e12475.

• Edgley DE, Carruthers M, Gabagambi NP, Saxon D, Smith AM, Joyce DA, Vernaz G, Santos ME, Turner GF, Genner MJ (2024) Lateral line system diversification during the early stages of ecological speciation in cichlid fish. BMC Ecology and Evolution 24 (1), 24

• Clark B#, Kuwalekar B, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME#, Almeida  MV# (2023) Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open biology 13 (11), 230257

• Elkin J#, Martin A, Courtier-Orgogozo V, Santos ME# (2023) Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biological Reviews.

• Santos ME#, Lopes JF, Kratochwil CF# (2023) East African cichlid fishes. EvoDevo 14:1.

• Marconi A#, Yang C, McKay S, Santos ME# (2023) Morphological and temporal variation in early embryogenesis contributes to species divergence in Malawi cichlid fishes. Evolution & Development, 25(2):170-193.

• Armisén D, Viala S, Cordeiro IRS, Crumière AJJ, Hendaoui E, Le Bouquin A, Duchemin W, Santos ME, Toubiana W, Vargas-Lowman A, Floriano CFB, Polhemus DA, Wang Y, Rowe L, Moreira FFF, Khila A (2023) Transcriptome-based phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha) reveals patterns of lineage expansion in a series of new adaptive zones. Molecular Biology and Evolution, 10:3076-3080.

• Munby H, Linderoth T, Fisher B, Du M, Vernaz G, Tyers AM, Ngatunga BP, Shechonge A, Denise H, McCarthy SA, Bista I, Miska EA, Santos ME, Genner MJ, Turner GF, Durbin R (2021) Differential use of multiple genetic sex determination systems in divergent ecomorphs of an african crater lake cichlid. bioRxiv

• Vernaz G, Hudson AG, Santos ME, Fisher B, Carruthers M, Shechonge AH, Gabagambi NP, Tyers AM, Ngatunga BP, Malinsky M, Durbin R, Turner GF, Genner MJ, Miska EA (2021) Epigenetic divergence during early stages of speciation in african crater lake cichlid fish. Nature Ecology and Evolution, 1-12.

• Clark B*, Elkin J*, Marconi A, Turner GF, Smith AM, Joyce D, Miska EA, Juntti SA, Santos ME# (2022) oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera. Royal Society Open Science, 9:220077

• Vernaz G, Malinsky M, Svardal H, Du M, Tyers AM, Santos ME, Durbin R, Genner MJ, Turner GF, Miska EA (2021) Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes. Nature Communications, 12:5870

• Svardal H, Rusuwa B, Linderoth T, Kiran A, Charmantier A,  Lattorff HMG, Cagan A, Ommeh SC, Kamng’ona A, Katongo C, Santos ME, Durbin R, Kumwenda B,  Visscher PM, von der Heyden S, Participants of SMBE Malawi (2020) Evolutionary genomics at the human–environment interface in Africa. Molecular Biology and Evolution 37: 3076–3080

• Vargas-Lowman A, Armisen D, Floriano CFB, Silva Cordeiro IR, Viala S, Bouchet M, Bernard M, Le Bouquin A, Santos ME, Berlioz-Barbier A, SalvadorA, Moreira FFF, Bonneton F, Khila A (2019) Cooption of the pteridine biosynthesis pathway underlies the diversification of embryonic colors in water striders. PNAS 116:19046-19054.

• Souza da Motta F, Moreira FFF, Crumière AJJ, Santos ME, Khila A (2018) A new species of Rhagovelia Mayr, 1865 (Hemiptera: Heteroptera: Veliidae) from French Guiana, with new records of Gerromorpha from the the country. Zootaxa 4433:520-530

• Santos ME#, Le Bouquin A, Crumière AJJ, Khila A# (2017) Taxon-restricted genes at the origin of morphological novelty and ecological opportunity in water striders. Science 358:386-390

• Santos ME (2017) One gene, multiple alleles: insights into the microevolution of pigmentation patterns. Molecular Ecology 26:2605-2607

• Crumière AJJ, Santos ME, Sémon M, Armisén D, Moreira FFF, and Khila A (2016) Diversity in morphology and locomotory behavior is associated with niche expansion in the semi-aquatic bugs. Current Biology 26:3336-3342

• Santos ME#, Baldo L, Gu X, Boileau N, Musilova Z, Salzburger W# (2016) Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes. BMC Genomics 17: 712.

• Santos ME, Berger C, Refki P, Khila A# (2015) Integrating evo-devo with ecology for a better understanding of phenotypic evolution. Briefings in Functional Genomics, doi: 10.1093/bfgp/elv003

• Santos ME#, Braasch I, Boileau N, Meyer B, Boehne A, Affolter M, Salzburger W# (2014) The evolution of cichlid egg-spots are linked with a cis-regulatory change. Nature Communications, doi:10.1038/ncomms6149

• Colombo M, Diepeveen ET, Muschick M, Santos ME, Indermaur A, Boileau N, Barluenga M, Salzburger W (2013) The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes. Molecular Ecology, 22:670-684.

• Santos ME#, Salzburger W# (2012) How cichlids diversify. Science, 338:619-621.

• Baldo L, Santos ME, Salzburger W (2011) Comparative transcriptomics of Eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity. Genome Biology and Evolution, 3:443-55.

• Santos ME, Athanasiadis A, Leitão AB, Dupasquier L, Sucena E (2011) Alternative splicing and gene duplication in the evolution of the FoxP gene sub-family. Molecular Biology and Evolution, 28:237-47.

• Lopes PC, Sucena E, Santos ME, Magalhães S (2008) Rapid experimental evolution of pesticide resistance in C. elegans entails no costs and affects the mating system. PLoS ONE, 3(11): e3741.

Consortium publications

• Panfilio KA, Vargas Jentzsch IM, Benoit JB [ and 78 other, including Santos ME] (2018) Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biology, doi:10.1101/201731

• Armisen D, Rjakuma R, Friedrich M [ and 51 other, including Santos ME] (2018) The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to live on the water. BMC Genomics, doi:10.1101/242230

• Adelman Z, Reinhardt K, Dolan A, [ and 77 other, including Santos ME] (2016) Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nature Communications, doi:10.1038/ncomms10165.

• Brawand D, Wagner CE, Li YI, [ and 72 other, including Santos ME] (2014) The genomic substract for adaptive radiation in African cichlid fish. Nature, doi:10.1038/nature13726