For links to my papers, please refer to my google profile.

Fitness costs

K Theys, AF Feder, M Gelbart, M Hartl, A Stern, PS Pennings
Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV. PLoS genetics 14 (6), e1007420 2018TheysPlosGenetics

Teaching related

A Kulkarni, I Yoon, PS Pennings, K Okada, C Domingo. Promoting diversity in computing. Proceedings of the 23rd Annual ACM Conference on Innovation and Technology …2018_Kulkarni_PINC_ACM_ITiCSE

Owens M.T., Trujillo, G., (…), Pennings, P.S., (…) Collectively Improving Our Teaching: Attempting Biology Department–wide Professional Development in Scientific Teaching. CBE-Life Sciences Education 17 (1), 2018. 2018OwensCollectivelyImprovingOurTeaching

Owens, M.T., Seidel, S.B., Wong, M., Bejines, T.E., Lietz, S., Perez, J.R., Sit, S., Subedar, Z.S., Acker, G.N., Akana, S.F. (…) Pennings, P.S., (…) and Balukjian, B., 2017. Classroom sound can be used to classify teaching practices in college science courses. Proceedings of the National Academy of Sciences, p.201618693. 2017Owens_PNAS


Alison F. Feder, Kline, C., Polacino, P., Cottrell, M., Kashuba, A.D., Keele, B.F., Hu, S.L., Petrov, D.A., Pennings, P.S. and Ambrose, Z., 2017. A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host. PLoS pathogens13(5), p.e1006358. 2017Feder_PlosPath.

Alison F. Feder, Soo-Yon Rhee, Robert W Shafer, Dmitri A Petrov, Pleuni S Pennings. 2015. More efficacious drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1. eLife. 2016. 2016Feder_eLife.
Winner of the Omenn prize! Video:

Stefany Moreno-Gamez, Alison L Hill, Daniel I.S. Rosenbloom, Dmitri A. Petrov, Martin A Nowak, Pleuni Pennings 2015. Imperfect drug penetration leads to spatial monotherapy and rapid evolution of multi-drug resistance. PNAS.
Blog post by myself about this paper at Haldane’s Sieve. Blog post on Microbe Post. Editorial in the Spotlights section of the July issue of Chemical Research in Toxicology. Video about the paper on Vimeo. 

Pennings, PS, Kryazhimskiy S, Wakeley J. 2014. PLoS Genetics. Loss and recovery of genetic diversity in adapting HIV populations. DOI: 10.1371/journal.pgen.1004000, 2014PennKryWakeleyPGeneticsWSupplMat
Using time series data, we find clear evidence for soft and hard selective sweeps in HIV. We find that recovery of diversity after a sweep is faster in non-synonymous than synonymous sites. Meredith Carpenter (Stanford) wrote a very nice blog post about the paper. The paper was also a runner-up for the Omenn prize, awarded by the International Society for Evolution, Medicine, and Public Health. 

PS Pennings, SP Holmes, RW Shafer. 2013. Editorial comment: HIV-1 Transmission Networks in a Small World, Journal of Infectious Diseases. doi: 10.1093/infdis/jit525
Recommended by F1000.

PS Pennings. 2013 HIV Drug resistance: Problems and Perspectives. Infectious Disease Reports. Vol 5, No 1S. Review. Infectious Disease Reports. 2013PenningsHIVReviewIDR.

Pennings, PS. 2012. Standing genetic variation and the evolution of drug resistance in HIV. PLoS Comp Biol. 8(6): e1002527. doi:10.1371/journal.pcbi.1002527. 2012PenningsPLoSCompBioWithSupplMat.
Using patient data and modeling approaches I quantified the role of pre-existing mutations for the evolution of drug resistance in HIV. A video abstract of this study can be found here: Article by The Scientist about this study:

Drug resistance in different organisms

Ben A. Wilson, Nandita R Garud, Alison F. Feder, Zoe J. Assaf, Pleuni S. Pennings. 2015. The population genetics of drug resistance evolution in natural populations of viral, bacterial, and eukaryotic pathogens, 2015Wilson_et_al-Molecular_Ecology (pdf) , link.

GG Perron, RF Inglis, PS Pennings, S Cobey. 2015. Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health. Evolutionary Applications 8 (3), 211-222.

Soft sweeps

Pleuni Pennings & Joachim Hermisson (picture taken in Luminy in 2012)

Pleuni Pennings & Joachim Hermisson (picture taken in Luminy in 2012)

Hermisson, J. and Pennings, P.S. 2017, Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods Ecol Evol, 8: 700–716. 2017Hermisson_Pennings_Methods_in_Ecology_and_Evolution. Video:

BA Wilson, PS Pennings, DA Petrov. Soft selective sweeps in evolutionary rescue. Genetics 205 (4), 1573-1586. 2017WilsonGenetics

Pennings, PS, Hermisson J. 2006. Soft sweeps III: The signature of positive selection from recurrent mutation, 2006. PLoS Genetics. 2(12):1998-2012. 2006bPenningsHermissonPlosGen
In this paper we described how a soft sweep due to recurrent mutation can be detected in sequence data.
Recommended by F1000.

Pennings, PS, Hermisson J. 2006. Soft sweeps II-molecular population genetics of adaptation from recurrent mutation or migration, 2006. Molecular Biology and Evolution. 23(5):1076-1084. 2006aPenningsHermissonMBE
Recommended by F1000.

Hermisson, J, Pennings PS. 2005. Soft sweeps: Molecular population genetics of adaptation from standing genetic variation, 2005. Genetics. 169(4):2335-2352. 2005HermissonPenningsGenetics
In this paper we developed theory to determine under which circumstances standing genetic variation is important for adaptation to a suddenly changed environment. We introduced the term “soft sweep.”


Pleuni Pennings, Susanne Foitzik, Tobias Pamminger, Andreas Mödlmeier (West Virginia 2009)

Stefan Suette, Pleuni Pennings, Susanne Foitzik, Tobias Pamminger, Andreas Mödlmeier (West Virginia 2009)

Pamminger, T, Foitzik, S, Metzler, D, Pennings PS. Oh sister, where art thou? Indirect fitness benefit could maintain a host defense trait. 2014, Journal of Evolutionary Biology. DOI: 10.1111/jeb.12496 Watch video-abstract. Data and code on Figshare. 2014PammingerJEB.
Using detailed mapping and microsatellite data on 1800 ants, we discover small scale population structure in slaves and free-living ants.

Pamminger, T, Leingaertner A, Achenbach A, Pennings PS, Foitzik S. 2013 Geographic distribution of the anti-parasite trait “slave rebellion” and potential costs of the defense. Evolutionary Ecology. Published online before print. June 13, doi: 10.1007.  2012Pamminger_Evol_Ecol_Preprint

Steinmeyer, C, Pennings, PS, Foitzik, S. 2012. Multicolonial population structure and nestmate recognition in an extremely dense population of the European ant Lasius flavus. Insectes Sociaux. 59 (4):499-510. 2012SteinmeyerPenningsFoitzikINSO

Pamminger, T, Modlmeier A, Suette S, Pennings PS, Foitzik S. 2012 Raiders from the sky: slavemaker founding queens select for aggressive host colonies. Biology Letters. 8(5):748-750. 2012PammingerBioLettPreprint
We published a short video about this study, see

Pamminger, T, Scharf I, Pennings PS, Foitzik S. 2011. Increased host aggression as an induced defense against slave-making ants. Behavioral Ecology. 22(2):255-260. 2011PammingerScharfBE

Pennings, PS, Achenbach A, Foitzik S. 2011. Similar evolutionary potentials in an obligate ant parasite and its two host species. Journal of Evolutionary Biology. 24(4):871-886. 2011PenningsEtAlJEB

Foitzik, S, Bauer S, Laurent S, Pennings PS. 2009. Genetic diversity, population structure and sex-biased dispersal in three co-evolving species, 2009. Journal of Evolutionary Biology. 22(12):2470-2480. 2009FoitzikBauerLaurentPenningsJEB


Domingues, VS, Poh Y-P, Peterson BK, Pennings PS, Jensen JD, Hoekstra HE. 2012. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution. 66 (10):3209–3223.2012DominguesEtAlEvolution


Goering, LM, Hunt PK, Heighington C, Busick C, Pennings PS, Hermisson J, Kumar S, Gibson G. 2009. Association of orthodenticle with Natural Variation for Early Embryonic Patterning in Drosophila melanogaster, 2009. Journal of Experimental Zoology Part B-M. 2009GoeringGibson

Sympatric speciation

Pleuni Pennings, Joachim Hermisson, Michael Kopp, picture taken in Luminy in 2012.

Pleuni Pennings, Joachim Hermisson, Michael Kopp, picture taken in Luminy in 2012.

Pennings, PS, Kopp M, Meszena G, Dieckmann U, Hermisson J. 2008. An analytically tractable model for competitive speciation, 2008. American Naturalist. 171(1):E44-E71. 2008PenningsKoppAmNat.

This study of sympatric speciation unified several earlier results, that were thought to be contradicting.

Host-parasite interactions

Sicard, D, Pennings PS, Grandclement C, Acosta J, Kaltz O, Shykoff JA. 2007. Specialization and local adaptation of a fungal parasite on two host plant species as revealed by two fitness traits, 2007. Evolution. 61(1):27-41. 2007SicardPenningsEvolutionl

Collin, CL, Pennings PS, Rueffler C, Widmer A, Shykoff JA. 2002. Natural enemies and sex: how seed predators and pathogens contribute to sex-differential reproductive success in a gynodioecious plant, 2002. Oecologia. 131(1):94-102. 2002CollinPenningsetalOECO

Rigaud, T, Pennings PS, Juchault P. 2001. Wolbachia bacteria effects after experimental interspecific transfers in terrestrial isopods. Journal of Invertebrate Pathology. 77(4):251-257. 2001RigaudPennings


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