MaBS

Rueffler C. (2012) Migration and the origin of species. in Messer M., Schroeder R. and Wodak R. (eds.) Migrations: Interdisciplinary Perspectives. Springer Vienna (preprint)
Rueffler C., Hermisson J., and Wagner, G. P. (2012) Evolution of Functional Specialization and Division of Labor. Proceedings of the National Academy of the Sciences U.S.A. (open access)
Rueffler C., Metz J. A. J., and Van Dooren T. J. M. (2012) What Life Cycle Graphs can Tell About the Evolution of Life Histories. Journal of Mathematical Biology (in press).
Servedio M., van Doorn S., Kopp M., Frame A. and Nosil P. (2012). Magic traits, pleiotropy, and effect sizes (Response to Haller et al.). Trends in Ecology and Evolution 27: 7-8. (doi).
Servedio M. and Kopp M. (2012). Sexual selection and magic traits in speciation with gene flow. Current Zoology (in press).
Bank C., Hermisson J. and Kirkpatrick, M. (2012): Can reinforcement complete speciation? Evolution 66: 229-239 (pdf).

2011

Hancock A.M., Brachi B., Faure N., Horton M.W., Sperone F.G., Jarymowycz L.B., Toomajian C., Roux F. and Bergelson J.B. (2011). Adaptation to climate across the Arabidopsis thaliana genome. Science 334: 83-86.
Lohmueller, K. E., A. Albrechtsen, Y. Li, S. Y. Kim, T. Kor- neliussen, N. Vinckenbosch, G. Tian, E. Huerta-Sanchez, A. F. Feder, N. Grarup, T. Jorgensen, T. Jiang, D. R. Witte, A. Sand-Baek, Hellmann, I. , T. Lauritzen, T. Hansen, O. Pedersen, J. Wang, and R. Nielsen (2011). Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genetics 7:e1002326.
Hancock A.M., Witonsky D.B., Alkorta-Aranburu G., Beall C., Gebremedhin A., Sukernik R., Utermann G., Pritchard J., Coop G. and Di Rienzo A. (2011). Adaptations to climate-mediated selective pressures in humans. PLoS Genetics 7: e1001375.
Hancock A.M., Clarc V.C., Qian Y. and Di Rienzo A. (2011). Population genetic analysis of the uncoupling proteins supports a role for UCP3 in cold resistance. Molecular Biology and Evolution 28: 601-614.
Johnson, P. L. F. and Hellmann, I. (2011). Mutation Rate Distribution In- ferred from Coincident SNPs and Coincident Substitutions. Genome Biology and Evolution 3: 842-850.
Mueller J.C., Hermisson J., Olano-Marin J., Hansson B. and Kempenaers B. (2010). Linking genetic mechanisms of heterozygosity-fitness correlations to footprints of selection at single loci. Evolutionary Ecology 25: 1-11. (doi)
Rettelbach, A., Hermisson, J., Dieckmann, U. and Kopp M. (2011). Effects of genetic architecture on the evolution of assortative mating under frequency-dependent disruptive selection. Theoretical Population Biology 79: 82-96. (doi)
Servedio M., van Doorn S., Kopp M., Frame A. and Nosil P. (2011). Magic traits in speciation: magic but not rare? Trends in Ecology and Evolution 26: 389-397. (doi).
Svardal H., Rueffler C., and Hermisson J. (2011). Comparing environmental and genetic variance as adaptive response to fluctuating selection. Evolution 65: 2492-2513. (pdf, if you are unable to access this reprint from the journal web site, request a pdf from the authors)
Uecker H. and Hermisson J. (2011). On the fixation process of a beneficial mutation in a variable environment. Genetics 188: 915-930.

2010

Ewing G. and Hermisson J. (2010). MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus. Bioinformatics 26: 2064-2065.
Hancock A.M., Witonsky D.B., Ehler E., Alkorta-Aranburu G., Beall C., Gebremedhin A., Sukernik R., Utermann G., Pritchard J., Coop G. and Di Rienzo A. (2010). Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proceedings of the National Academy of Sciences USA 107 (Suppl 2): 8924-8930.
Hancock A.M., Alkorta-Aranburu G., Witonsky D.B. and Di Rienzo A. (2010). Adaptations to new environments in humans: the role of subtle allele frequency shifts. Philosophical Transactions of the Royal Society, Biological Sciences Series B 365: 2459-2468.
Haß J., Matuszewski S., Cieslik, D. and Haase M. (2010). The role of swine as "mixing vessel" for interspecies transmission of the influenza A subtype H1N1: a simultaneous Bayesian inference of phylogeny and ancestral hosts. Infection, Genetics and Evolution (in press).
Kopp, M. (2010). Speciation and the neutral theory of biodiversity. BioEssays 32: 564-570. (pdf)
Pool J.E., Hellmann I., Jensen J.D., Nielsen R. (2010). Population genetic inference from genomic sequence variation. Genome Research 20: 291-300.
Svardal, H. (2010). Can epigenetics solve the "case of the midwife toad"? - A reply to Vargas. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. In press.

2009

Abrams P.A. and Rueffler C. (2009). Coexistence and limiting similarity of consumer species competing for a linear array of resources. Ecology 90: 812-822. (pdf)
Alvarez-Castro J.-M., Kopp M. and Hermisson J. (2009). Effects of epistasis and the evolution of genetic architecture: exact results for a 2-locus model. Theoretical Population Biology 75: 109-122. (pdf)
Dannemann M., Lorenc A., Hellmann I., Khaitovich P., and Lachmann M. (2009). The effects of probe binding affinity differences on gene expression measurements and how to deal with them. Bioinformatics 25: 2772-2779.
Etheridge A., Pfaffelhuber P., and Wakolbiger A. (2009). How often does the ratchet click? Facts, heuristics, asymptotics. In: Blath J., Mörters P. and Scheutzow M. (eds.), Trends in Stochastic Analysis, Cambridge University Press.
Goering L.M., Hunt P.K., Heighington C., Busick C., Pennings P., Hermisson J., Kumar S. and Gibson G. (2009). Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster. J. Exp. Zool. (Mol. Dev. Evol.) 312B: 841-854. (pdf)
Greven A., Pfaffelhuber P., and Winter A. (2009). Convergence in distribution of random metric measure spaces: Lambda-coalescent measure trees. Prob. Theo. Rel. Fields 145: 285-322. ([ArXivmath.PR/0511743])
Hermisson J. (2009) Who believes in whole-genome scans for selection. Heredity 103: 283-284. (pdf)
Kopp M. and Hermisson J. (2009). The genetic basis of phenotypic adaptation I: Fixation of beneficial mutations in the moving optimum model. Genetics: 182: 233-249. (pdf)
Kopp M. and Hermisson J. (2009). The genetic basis of phenotypic adaptation II: The distribution of adaptive substitutions in the moving optimum model. Genetics 183: 1453-1476. (pdf)
Nielsen R., Hubisz M.J., Torgerson D., Andres A.M., Albrechtsen A., Gutenkunst R., Adams M., Cargill M., Boyko A., Indap A., Hellmann I. et al. (2009). Darwinian and demographic forces affecting human protein coding genes. Genome Research 19: 838-849.
Ptak S.E., Enard W., Wiebe V., Hellmann I., Krause J., Lachmann M. and Pääbo S. (2009). Linkage disequilibrium extends across putative selected sites in FOXP2. Molecular Biology and Evolution 26: 2181-2184.
Xia Q., Guo Y., Zhang Z., ..., Hellmann I., et al. (2009). Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326: 433-436.

2008

Abrams P.A., Rueffler C., and Dinnage R. (2008). Competition-similarity relationships and the nonlinearity of competitive effects in consumer-resource systems. American Naturalist 172: 463-474. (pdf, online appendix)
Abrams P.A., Rueffler C., and Kim G. (2008). Determinants of the strength of disruptive and/or divergent selection arising from resource competition. Evolution 62: 1571-1586. (pdf upon request)
Ewing G.B., Ebersberger I., Schmidt H.A., and von Haeseler A. (2008). Rooted triple consensus and anomalous gene trees. BMC Evolutionary Biololgy 8: 118.
Hancock A.M., Witonsky D.B., Gordon A.S., Eshel G., Pritchard J.K., Coop G.C. and Di Rienzo A. (2008). Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genetics 4: e32.
Hancock A.M. and Di Rienzo A. (2008). Detecting the signature of natural selection in human populations. Annual Review of Anthropology 37: 197-217.
Hellmann I., Mang Y., Gu Z., Li P., de la Vega F.M., Clark A.G. and Nielsen R. (2008). Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Research 18: 1020-1029.
Hermisson J. and McGregor, A.P. (2008). Pleiotropic scaling and QTL data. Nature 456: E3-E4.
Hermisson J. and Pfaffelhuber P. (2008). The pattern of genetic hitchhiking under recurrent mutation. Electronic Journal of Probability 13: 2069-2106. (pdf)
Kopp M. and Hermisson J. (2008). Competitive speciation and costs of choosiness. Journal of Evolutionary Biology 21: 1005-1023. (pdf)
Pennings P.S., Kopp M., Meszena G., Dieckmann U., and Hermisson J. (2008). An analytically tractable model for competitive speciation. American Naturalist 171: E44-E71. (pdf)
Wang J., Wang W., Li R., Li Y., Tian G., Goodman L., Fan W., Zhang J., Li J., Zhang J., Hellmann I. et al. (2008). The diploid genome sequence of an Asian individual. Nature 456: 60-65.

2007

Kopp M. and Hermisson J. (2007). Adaptation of a quantitative trait to a moving optimum. Genetics 176: 715-719. (pdf)
Nielsen R., Hellmann I., Hubisz M., Bustamante C., and Clark A.G. (2007). Recent and ongoing selection in the human genome. Nature Reviews Genetics 8: 857-868.
Rodrigo A.G., Ewing G.B., and Drummond A.J. (2007). The evolutionary analysis of measurably evolving populations using serially sampled gene sequences. In: Mathematics of Evolution and Phylogenetics (eds. O. Gascuel and M. A. Steel), Oxford University Press.
Rueffler C., Van Dooren T.J.M., and Metz J.A.J. (2007). The interplay between behavior and morphology in the evolutionary dynamics of resource specialization. American Naturalist 169: E34-E52. (pdf)
Weber M., Hellmann I., Stadler M.B., Ramos L., Pääbo S., Rebhan M., and Schübeler D. (2007). Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics 39: 457-466.

2006

Ewing, G.B. and Rodrigo, A.G. (2006). Coalescent-based estimation of population parameters when the number of demes changes over time. Molecular Biology and Evolution 33: 951-958.
Ewing, G.B. and Rodrigo, A.G. (2006). Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden. Evolutionary Bioinformatics Online 2: 239-247.
Hansen T.F., Alvarez-Castro J.-M., Carter A.J.R., Hermisson J., and Wager G.P. (2006). Evolution of genetic architecture under directional selection. Evolution 60: 1523-1536. (pdf)
Khaitovich P., Tang K., Franz H., Kelso J., Hellmann I., Enard W., Lachmann M., and Pääbo S. (2006). Positive selection on gene expression in the human brain. Current Biology 16: R356-358.
Kopp M. and Hermisson J. (2006), The evolution of genetic architecture under frequency-dependent disruptive selection. Evolution 60: 1537-1550. (pdf)
Pennings P.S. and Hermisson J. (2006). Soft sweeps III - The signature of positive selection from recurrent mutation. PLoS Genetics 2: e186. (pdf)
Pennings P.S. and Hermisson J. (2006). Soft sweeps II - Molecular population genetics of adaptation from recurrent mutation or migration. Mol. Biol. Evol. 23: 1076-1084. (pdf)
Rueffler C., Egas M., and Metz J.A.J. (2006). Evolutionary predictions should be based on individual-level traits. American Naturalist 168: E148-E162. (pdf)
Rueffler C., Van Dooren T.J.M., Leimar O., and Abrams, P.A. (2006). Disruptive selection and then what? Trends in Ecology and Evolution 21: 238-245. (pdf)
Rueffler C., Van Dooren T.J.M., and Metz J.A.J. (2006). The evolution of resource specialization through frequency-dependent and frequency-independent mechanisms. American Naturalist 167: 81-93. (pdf)

2005

Carter A.J.R., Hermisson J., and Hansen T.F. (2005). The role of epistatic gene interactions in the response to selection and the evolution of evolvability. Theor. Pop. Biol. 68, 179-196. (pdf)
Hellmann I., Prüfer K., Ji H., Zody M.C. Pääbo, S. and Ptak S.E. (2005). Why do human diversity levels vary at a megabase scale? Genome Research 15: 1222-1231.
Hermisson J. and Pennings P.S. (2005). Soft Sweeps - Molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352. (pdf)
Hermisson J. and Wagner G.P. (2005). Evolution of phenotypic robustness. Book chapter appeared in: Robust Design: A Repertoire from Biology, Ecology, and Engineering, E. Jen (ed.), Oxford University Press, Oxford, pp 47-70. (pdf)
Khaitovich P., Hellmann I., Enard W., Nowick K., Leinweber M., Franz H., Weiss G., Lachmann M., and Pääbo S. (2005). Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850-1854.
Mikkelsen T.S., Hillier L.W., Eichler E.E., Zody M.C., Jaffe, D.B., Yang, S.P., Enard W., Hellmann, I., et al. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
Stoletzki N., Welch J., Hermisson J., and Eyre-Walker A. (2005). A dissection of volatility in yeast. Mol. Biol. Evol. 22, 2022-2026. (pdf)

2004

Ewing G.B., Nicholls G., and Rodrigo A. (2004). Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics 168: 2407 - 2420.
Hermisson J. and Wagner G.P. (2004). The population genetic theory of hidden variation and genetic robustness. Genetics 168:2271-2284. (pdf) Featured in Nature Reviews Genetics Vol. 6 Feb 2005 (pdf)
Khaitovich P., Muetzel B., She X., Lachmann M., Hellmann I., Dietzsch J., Steigele S., Do H.H., Weiss G., Enard W., et al. (2004). Regional patterns of gene expression in human and chimpanzee brains. Genome Research 14: 1462-1473.
Khaitovich P., Weiss G., Lachmann M., Hellmann I., Enard W., Muetzel B., Wirkner U., Ansorge W., and Pääbo S. (2004). A neutral model of transcriptome evolution. PLoS Biology 2: E132.
Rueffler C., Van Dooren T.J.M., and Metz J.A.J. (2004). Adaptive walks on changing landscapes: Levins' approach extended. Theoretical Population Biology 65: 165-178. (pdf)
Shpak M., Stadler P.F., Wagner G.P., and Hermisson J. (2004). Aggregation of variables and system decomposition: application to fitness landscape analysis. Theory in Biosciences 123(1):33-68.
Watanabe H., Fujiyama A., Hattori M., Taylor T.D., Toyoda A., Kuroki Y., Noguchi H., BenKahla A., Lehrach H., Sudbrak R., Hellmann I. et al. (2004). DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature 429: 382-388.

2003

Bagheri-Chaichian H., Hermisson J., Vaisnys J.R., and Wagner G.P. (2003). Effects of epistasis on phenotypic robustness in metabolic pathways. Mathematical Biosciences 184:27-51.
Hellmann I., Zollner S., Enard W., Ebersberger I., Nickel B., and Pääbo S. (2003). Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Research 13: 831-837.
Ross H.A., Lento G.M., Dalebout M.L., Goode M., Ewing G.B., McLaren P., Rodrigo A.G., Lavery S., and Baker C.S. (2003). DNA Surveillance: Web-based molecular identification of whales, dolphins and porpoises. Journal of Heredity 94: 111-114.
Hellmann I. . Ebersberger I., Ptak S.E., Pääbo S., and Przeworski M. (2003). A neutral explanation for the correlation of diversity with recombination rates in humans. American Journal of Human Genetics 72: 1527-1535.
Hermisson J., Hansen T.F., and Wagner G.P. (2003). Epistasis in polygenic traits and the evolution of genetic architecture under stabilizing selection. American Naturalist 161:708-734. (pdf)
Sakaki Y., Watanabe H., Taylor T., Hattori M., Fujiyama A., Toyoda A., Kuroki Y., Itoh T., Saitou N., Oota S., Hellmann I. et al. (2003). Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication. Cold Spring Harbor Symposia on Quantitative Biology 68: 455-460.
Thiel M., Zander A., Valdivia N., Baeza J.A. and Rueffler C. (2003). Host fidelity of a symbiotic porcellanid crab: the importance of host characteristics. Journal of Zoology 261: 353-362.
de Visser J.A.G.M., Hermisson J. et. al.(2003). Perspective: Evolution and detection of genetic robustness. Evolution 57:1959-1972. (pdf)

2002

Collin C.L., Pennings P.S., Rueffler C., Widmer, A. and Shykoff, J.A. (2002). Natural enemies and sex: how seed predators and pathogens contribute to sex-differential reproductive success in a gynodioecious plant. Oecologia 131: 94-102.
Hermisson J., Redner O., Wagner H., and Baake E. (2002). Mutation-selection balance: ancestry, load, and maximum principle. Theor. Pop. Biol. 62: 9-46. (pdf)

2001

Hermisson J., Wagner H., and Baake M. (2001). Four-state quantum chain as a model for sequence evolution. J. Stat. Phys. 102: 315-343. (pdf)

Non peer-reviewed

Hermisson J. (2009). Modern evolutionary research in Vienna: Developments and challenges (in German). (pdf)