2024
Evans BJ, Gvoždík V, Knytl M, Cauret CMS, Herrel A, Greenbaum E, Patel J, Premachandra T, Papenfuss T, Parente J, Horb ME, Measey J (2024) Rapid sex chromosome turnover in African clawed frogs (Xenopus) provides insights into the origins of new sex chromosomes. Submitted.
2023
Cauret CMS, Jordan DC, Kukoly LM, Burton SR, Anele EU, Kwiecien JM, Gansauge M-T, Senthillmohan S, Greenbaum E, Meyer M, Horb ME, Evans BJ (2023) Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis. Plos Genetics 19(10): e1010990 (27 pages)
Zhu J, Evans BJ (2023) Mitonuclear interactions and the origin of macaque societies. Genome Biology and Evolution 15(2):evad010 (15 pages)
Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Krylov V, Kubíčková S, Fokam EB, Badjedjea G, Evans BJ, Knytl M (2023) Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus Pipidae). European Journal of Wildlife Research: 69:81(12 pages).
McGuire JA, Huang X, Reilly SB, Iskandar D, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs A, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R (2023) Species delimitation, phylogenomics, and biogeography of Sulawesi flying lizards: A diversification history complicated by ancient hybridization, cryptic species, and arrested speciation. Systematic Biology: 72(4):885–911
Rong S, Neil CR, Maguire S, Meremikwu IC, Meyerson M, Evans BJ, Fairbrother, WG (2023) Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans. Proceedings of the National Academy of Science 120(21):e2218308120 (12 pages).
2022
Premachandra T, Cauret CMS, Conradie W, Measey J, Evans BJ (2022) Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa. Genes, Genomes, Genetics (G3) 13(2):jkac325 (13 pages)
Knytl M, Fornaini N, Bergelová B, Gvoždík V, Černohorská H, Kubíčková S,Fokam EB, Evans BJ*, Krylov V* (2022) Divergent subgenome evolution in the allotetraploid frog Xenopus calcaratus. Gene 851:146974 (12 pages)* joint last authors
Evans BJ, Mudd AB, Bredeson JV, Furman BLS, Wasonga DV, Lyons JB, Harland RM, Rokhsar DS (2022) New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog X. borealis. Journal of Evolutionary Biology 35(12):1777-1790
Hayashi S, Suda K, Fujimura F, Fujikawa M, Tamura K, Tsukamoto D, Evans BJ, Takamatsu N, Ito M (2022) Neofunctionalization of a noncoding portion of a DNA transposon in the coding region of the chimerical sex-determining gene dm-W in Xenopus frogs. Molecular Biology and Evolution 39(7):msac138 (12 pages)
Stevison L, Bailey NP, Szpiech ZA, Novak TE, Melnick DJ, Evans BJ, Wall JD (2022) Evolution of genes involved in the unusual genitals of the bear macaque, Macaca arctoides. Ecology and Evolution 12:e8897 (16 pages)
2021
Evans BJ, Peter BM, Melnick DJ, Andayani N, Supriatna J, Zhu J, Tosi AJ (2021) Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution. Proceedings of the Royal Society of London B 288:20211756 (11 pages)
Song X-Y, Furman BLS, Premachandra T, Knytl M, Cauret CMS, Wasonga DV, Measey J, Dworkin I, Evans BJ (2021) Sex chromosome degeneration, turnover, and sex-biased expression of sex-linked transcripts in African clawed frogs (Xenopus). Philosophical Transactions of the Royal Society of London B 376:20200095 (15 pages)
Stock M, Kratochvil L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y (2021) A brief review of vertebrate sex evolution with a pledge for integrative research – towards ‘sexomics’. Philosophical Transactions of the Royal Society of London B 376:20200426 (23 pages)
2020
Furman BLS, Cauret CMS, Knytl M, Song X-Y, Premachandra T, Ofori-Boateng, C, Jordan DC, Horb ME, Evans BJ (2020) A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome. Plos Genetics 16(11):e1009121(27 pages)
Evans BJ, Gansauge M-T, Tocheri MW, Schillaci MA, Sutikna T, Jatmiko, Saptomo EW, Klegarth A, Tosi AJ, Melnick DJ, Meyer M (2020) Mitogenomics of macaques (Macaca) across Wallace’s Line in the context of modern human dispersals. Journal of Human Evolution 146:102852 (14 pages)
Cauret CMS, Gansauge M-T, Tupper AS, Furman BLS, Knytl M, Song X, Greenbaum E, Meyer M, Evans BJ (2020) Developmental systems drift and the drivers of sex chromosome evolution. Molecular Biology and Evolution 37(3):799–810
Kelley DB, Ballagh IH, Barkan CL, Bendesky A, Elliot TM, Evans BJ, Hall IC, Kwon YM, Kwong-Brown U, Leininger EC, Perez EC, Rhodes HJ, Villain A, Yamaguchi A, Zornik E (2020) Generation, coordination, and evolution of neural circuits for vocal communication. The Journal of Neuroscience 40(1):22-36
2019
Evans BJ, Gansauge M-T, Stanley EL, Furman BLS, Cauret CMS, Ofori-Boateng C, Gvoždík V, Streicher JW, Greenbaum E, Tinsley RC, Meyer M, Blackburn DC (2019) Xenopus fraseri: Mr. Fraser, where did your frog come from? PLoS One 14(9): e0220892 (14 pages)
Ackermann RR, Arnold ML Baiz MD. Cahill JA,Cortés-Ortiz L, Evans BJ, Grant BR, Grant PR, Hallgrimsson B, Humphreys RA, Jolly CJ, Malukiewicz J, Percival CJ, Ritzman TB, Roos C, Roseman CC, Schroeder L, Smith FH, Warren KA, Wayne RK, and Zinner Z. (2019) Hybridization in human evolution: insights from other organisms. Evolutionary Anthropology 28(4):189-209
2018
Furman BLS, Dang UJ, Evans BJ, Golding GB (2018) Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus). Journal of Evolutionary Biology 31:1945–1958
Furman BLS, Evans BJ (2018) Divergent evolutionary trajectories of two young, homomorphic, and closely related sex chromosome systems. Genome Biology and Evolution 3(1):742–755
Frantz L, Rudzinski A, Mansyursyah Surya Nugraha A, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease E, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas M, Johansson F, Mustari A, Williams J, Mohamad K, Damayanti C, Wiryadi I, Obbles D, Day H, Yasin M, Meker S, McGuire J, Evans BJ, von Rintelen T, Ho S, Searle J, Kitchener A, Macdonald A, Shaw D, Hall R, Galbusera P, Larson G (2018) Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events. Proceedings of the Royal Society of London B 285:20172566 (8 pages)
2017
Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ (2017) Speciation over the edge: Gene flow among non-human primate species across a formidable biogeographic barrier. Royal Society Open Science 4:170351 (12 pages)
Evans BJ, Upham NS, Golding GB, Ojeda RA, Ojeda AA (2017) Evolution of the largest mammalian genome. Genome Biology and Evolution 9(6):1711–1724.
Furman BLS, Cauret MS, Colby GA, Measey J, Evans BJ (2017) Limited genomic consequences of hybridization between two African clawed frogs, Xenopus gilli and X. laevis (Anura: Pipidae). Scientific Reports 7:1091 (11 pages)
Kelley DB, Elliott TM, Evans BJ, Hall IC, Leininger EC, Rhodes HJ, Yamaguchi A, Zornik E (2017) Probing forebrain to hindbrain circuit functions in Xenopus. Genesis: The Journal of Genetics and Development 55(1–2):e22999 (8 pages)
Knytl M, Smolík O, Kubíčková S, Tlapáková S, Evans BJ, Krylov V (2017) Chromosome divergence during evolution of the tetraploid clawed frogs, Xenopus mellotropicalis and Xenopus epitropicalis as revealed by Zoo-FISH. PLoS One 12(5): e0177087 (16 pages)
2016
Furman BLS, Evans BJ (2016) Sequential turnovers of sex chromosomes in African clawed frogs (Xenopus) suggests some genomic regions are good at sex determination. Genes, Genomes, Genetics 6:3625–3633
Ghenu H, Bolker BM, Melnick DJ, Evans BJ (2016) Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 17:157 (17 pages)
Hoffman Russell JN, Marsh AK, Willer DO, Ambagala APM, Dzamba M, Chan JK, Pilon R, Fournier J, Brudno M, Antony JM, Sandstrom P, Evans BJ, MacDonald KS (2016) A novel strain of cynomolgus macaque cytomegalovirus: Implications for host-virus co-evolution. BMC Genomics 17:277 (17 pages)
2015
Evans BJ, Carter TF, Greenbaum E, Gvoždík V, Kelley DB, McLaughlin PJ, Pauwels OSG, Portik DM, Stanley EL, Tinsley RC, Tobias ML, Blackburn DC (2015) Genetics, morphology, advertisement calls, and historical records distinguish six new polyploid species of African clawed frog (Xenopus, Pipidae) from West and Central Africa. PLoS ONE 10(12):e0142823 (51 pages).
Evans BJ, Kwon T (2015) Molecular polymorphism and divergence of duplicated genes in tetraploid African clawed frogs (Xenopus). Cytogenetic and Genome Research 145:243–253. Special edition on “Xenopus Genomics;” Evans BJ, Schmid M, Eds.
Schmid M, Evans BJ, Bogart JP (2015) Polyploidy in Amphibia. Cytogenetic and Genome Research 145:315–330. Special edition on “Xenopus Genomics;” Evans BJ, Schmid M, Eds.
Furman BLS, Bewick AJ, Harrison TL, Greenbaum E, Gvoždík V, Kusamba C, Evans BJ (2015) Pan-African phylogeography of a model organism, the African clawed frog ‘Xenopus laevis‘. Molecular Ecology 24:909–925
2014
Evans BJ, Zeng K, Esselstyn JA, Charlesworth B, Melnick DJ (2014) Reduced representation genome sequencing suggests low diversity on the sex chromosomes of Tonkean macaque monkeys. Molecular Biology and Evolution 31(9):2425–2440
Iskandar DT, Evans BJ, McGuire JA. (2014) A novel reproductive mode in frogs: A new species of fanged frog with internal fertilization and birth of tadpoles. PLOS One 9(12):e115884 (14 pages)
2013
Esselstyn JA, Maharadatunkamsi, Achmadi AS, Siler C, Evans BJ (2013) Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia. Molecular Ecology 22:4972–4987
Evans BJ, Charlesworth B (2013) The effect of non-independent mate pairing on the effective population size. Genetics 193: 545–556
Linkem CW, Brown RM, Siler CD, Evans BJ, Austin CC, Iskandar DT, Diesmos AC, Supriatna J, Andayani N, McGuire JA (2013) Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific Island lizards (Squamata: Scincidae: Lamprolepis smaragdina). Journal of Biogeography 40:507–520
Shen JJ, Dushoff J, Bewick AJ, Chain FJJ, Evans BJ (2013) Genomic dynamics of transposable elements in the Western Clawed Frog (Silurana tropicalis). Genome Biology and Evolution 5(5):998–1009
Bewick AJ, Chain FJJ, Zimmerman LB, Sesay A, Gilchrist MJ, Owens NDL, Seifertova E, Krylov V, Macha J, Tiapakova T, Kubickova S, Cernohorska H, Zarsky V, Evans BJ (2013) A large pseudoautosomal region on the sex chromosomes of the frog Silurana tropicalis. Genome Biology and Evolution 5(6):1087–1098
Mechkarska M, Prajeep M, Leprince J, Vaudry H, Meetani MA, Evans BJ, Conlon JM (2013) A comparison of host-defense peptides in skin secretions of female Xenopus laevis x Xenopus borealis and X. borealis x X. laevis F1 hybrids. Peptides 45:1–8
2012
Evans BJ, Pyron RA, Wiens JJ (2012) Polyploidy and sex chromosome evolution in amphibians. Pp 385 – 410 in “Polyploidy and Genome Evolution” (Soltis PS and Soltis DE, Eds). Springer
Bewick AJ, Chain FJJ, Heled J, Evans BJ (2012) The pipid root. Systematic Biology 61(5):913–926
Evans BJ (2012) Coalescent-based analysis of demography: applications to biogeography on Sulawesi. Pp 270 – 289 in “Biotic evolution and environmental change in Southeast Asia” (Gower DJ, Johnson KG, Richardson JE, Rosen BR, Rüber L, Williams ST, Eds). Cambridge University Press, UK
Esselstyn JA, Evans BJ, Sedlock JL, Khan FAA, Heaney LR (2012) Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats. Proceedings of the Royal Society B 279:3678–3686
2011
Chain FJJ, Dushoff J, Evans BJ (2011) The odds of duplicate gene persistence after polyploidization. BMC Genomics 12:599 (7 pages)
Evans BJ, Bliss SM, Mendel SA, Tinsley RC (2011) The Rift Valley is a major barrier to dispersal of African clawed frogs (Xenopus) in Ethiopia. Molecular Ecology 20:4216–4230
Sun S, Evans BJ, Golding GB (2011) “Patchy-tachy” leads to false positives for recombination. Molecular Biology and Evolution 28(9):2549–2559
Setiadi MI, McGuire JA, Brown RM, Zubairi M, Iskandar DT, Andayani N, Supriatna J, Evans BJ (2011) Adaptive radiation and ecological opportunity in Sulawesi and Philippine fanged frog (Limnonectes) communities. American Naturalist 178(2):221–240
Bewick AJ, Anderson DW, Evans BJ. (2011) Evolution of the closely related, sex-related genes DM-W and DMRT1 in African clawed frogs. Evolution 65(3):698–712
Tobias ML, Evans BJ, Kelley DB (2011) Evolution of advertisement calls in African clawed frogs. Behaviour 148:519–549
Evans BJ, Greenbaum E, Kusamba C, Carter TF, Tobias ML, Mendel SA, Kelley DB. (2011) Description of a new octoploid frog species (Anura: Pipidae: Xenopus) from the Democratic Republic of the Congo with discussion of the biogeography of African clawed frogs in the Albertine Rift. Journal of Zoology, London 283:276–290
2010
Evans BJ, Pin L, Melnick DJ, Wright SI (2010) Sex-linked inheritance in macaque monkeys: Implications for effective population size and dispersal. Genetics 185:927–937 (featured on cover)
Setiadi MI, Hamidy A, Abidin Z, Susanto D, Brown RM, Peterson AT, Li X, Evans BJ (2010) Genetic structure of herpetofauna on Halmahera Island, Indonesia: Implications for Aketajawe-Lolobata National Park. Conservation Biology 24(2):553–562
Blackburn DC, Evans BJ, Pessier AP, Vredenburg VT (2010) An enigmatic mortality event in the only population of the critically endangered Cameroonian frog Xenopus longipes. African Journal of Herpetology:1–12 (featured on cover)
Brown RM, Linken CW, Siler CD, Sukumaran J, Esselstyn JA, Diesmos AC, Iskandar DT, Bickford D, Evans BJ, McGuire JA, Grismer L, Supriatna J, Andayani N. (2010) Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: Evidence for recent human-mediated range expansion? Molecular Phylogenetics and Evolution 57:598–610
2009
Anderson D, Evans BJ (2009) Regulatory evolution of a duplicated heterodimer across species and tissues of allopolyploid clawed frogs (Xenopus). Journal of Molecular Evolution 68:236–247
2008
Chain FJJ, Ilieva D, Evans BJ (2008) Single-species microarrays and comparative transcriptomics. PLoS One 3(9):e3279 (10 pages)
Evans BJ (2008) Genome evolution and speciation genetics of clawed frogs (Xenopus and Silurana). Frontiers in Bioscience 13: 4687–4706
Evans BJ, McGuire JA, Brown RM, Andayani N, Supriatna J (2008) A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads. Biology Letters 4:430–433
Evans BJ, Carter TF, Tobias ML, Kelley DB, Hanner R, Tinsley RC (2008) A new species of clawed frog (genus Xenopus) from the Itombwe Massif, Democratic Republic of the Congo: implications for DNA barcodes and biodiversity conservation. Zootaxa 1780:55–68
Chain FJJ, Ilieva D, Evans BJ (2008) Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization. BMC Evolutionary Biology 8:43 (16 pages)
Bickford D, Supriatna J, Andayani N, Iskandar D, Evans BJ, Brown RM, Townsend T, Umilaela, Azhari D, McGuire J. (2008) Indonesia’s protected areas need more protection: suggestions from island examples. Pp 53–78 in “Biodiversity and human livelihoods in protected areas: case studies from the Malay Archipelago” (NS Sodhi, G Acciaioli, M Erb, and AK Tan, Eds.) Cambridge University Press, Cambridge UK
2007
Evans BJ (2007) Ancestry influences the fate of duplicated genes millions of years after polyploidization of clawed frogs (Xenopus). Genetics 176:1119–1130
2006
Chain FJJ, Evans BJ (2006) Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis. PLoS Genetics 2(4):e56 (13 pages)
2005
Evans BJ, Kelley DB, Melnick DJ and Cannatella DC (2005) Evolution of RAG-1 in polyploid clawed frogs. Molecular Biology and Evolution 22(5):1193–1207
2004
Evans BJ, Cannatella DC, and Melnick DJ (2004) Understanding the origins of areas of endemism in phylogeographic analyses: a reply to Bridle et al. Evolution 58:1397–1400
Evans BJ, Kelley DB, Tinsley RC, Melnick DJ, and Cannatella DC (2004) A mitochondrial DNA phylogeny of clawed frogs: phylogeography on sub-Saharan Africa and implications for polyploid evolution. Molecular Phylogenetics and Evolution 33:197–213
2003
Evans BJ , Brown RM, McGuire JA, Supriatna J, Andayani N, Diesmos A, Iskandar D, Melnick DJ, Cannatella DC (2003) Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the Asian and Australian faunal zones. Systematic Biology 52(6):794–819
Evans BJ , Supriatna J, Andayani N, Melnick DJ (2003) Diversification of Sulawesi macaque monkeys: decoupled evolution of mitochondrial and autosomal DNA. Evolution 57(8):1931–1946
Evans BJ , Supriatna J, Andayani N, Setiadi MI, Cannatella D, Melnick DJ (2003) Monkeys and toads define areas of endemism on the island of Sulawesi. Evolution 57(6):1436–1443
before 2002
Evans, BJ , Supriatna, J, Melnick, DJ (2001) Hybridization and population genetics of two macaque species in Sulawesi, Indonesia. Evolution 55(8):1686–1702
Fernando P, Evans BJ, Morales JC, and Melnick DJ (2001) Electrophoresis artefacts – A previously unrecognized cause of error in microsatellite analysis. Molecular Ecology Notes 1(4):325–32
Evans BJ , Morales JC, Supriatna J, Melnick DJ (1999) Origin of the Sulawesi macaques (Cercopithecidae: Macaca ) as suggested by mitochondrial DNA phylogeny. Biological Journal of the Linnean Society 66:539–560
Evans BJ , Morales JC, Picker MD, Melnick DJ, Kelley DB (1998) Absence of extensive introgression between Xenopus gilli and Xenopus laevis laevis (Anura: Pipidae), in southwestern Cape Province, South Africa. Copeia (2):504–509
Evans BJ , Morales JC, Picker MD, Kelley DB, Melnick DJ (1997) Comparative molecular phylogeography of two Xenopus species, X. gilli and X. laevis, in the southwestern Cape Province, South Africa. Molecular Ecology 6(4):333–343
The Laboratory of Ben Evans 