Statistical & Computational Biology

Publications

Upcoming

1. Link V, Kousathanas A, Veeramah K, Sell C, Scheu A & Wegmann D (2017) Atlas: analysis tools for low-depth and ancient samples. bioRxiv.
2. Hofmanová Z*, Reyna-Blanco C*, de C Becdelievre C, Schulz I, Bloecher J, Jovanovic J, Winkelbach L, Figarska S, Schulz A, Porcic M, Kvetina P, Tsoupas A, Currat M, Buzhilova A, Gerritsen F, Karul N, McGlynn G, Orschiedt J, Oezbal R, Peters J, Ridush B, Terberger T, Teschler-Nicola M, Zarina G, Zeeb-Lanz A, Stefanovic S, Burger J* & Wegmann D* (2022) Between fishing and farming: palaeogenomic analyses reveal cross-cultural interactions triggered by the arrival of the neolithic in the danube gorges. bioRxiv.
3. Tsoupas A, Reyna-Blanco C, Quilodrán C, Blöcher J, Brami M, Wegmann D, Burger J & Currat M (2024) Local increases in admixture with hunter-gatherers followed the initial expansion of neolithic farmers across continental europe. bioRxiv.

2024

1. Reyna-Blanco C, Caduff M, Galimberti M, Leuenberger C & Wegmann D (2024) Inference of locus-specific population mixtures from linked genome-wide allele frequencies. Mol.Biol.Evol. 41(7):msae137.
2. Caduff M, Eckel R, Leuenberger C & Wegmann D (2024) Accurate bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. Mol.Ecol.Resour. 24(3):e13913.

2023

1. Volery L, Vaz Fernandez M, Wegmann D & Bacher S (2023) A general framework to quantify and compare ecological impacts under temporal dynamics. Ecol.Lett. 26(10):1726-1739.
2. Wegmann D & Eckel R (2023) Human evolution: when admixture met selection. Curr.Biol. 33(7):R259-R261.
3. Singer L, Wietlisbach X, Hickisch R, Schoell E, Leuenberger C, Van den Broek A, Désalme M, Driesen K, Lyly M, Marucco F, Kutal M, Pagon N, Papp C, Milioni P, Uzdras R, Zihmanis I, Zimmermann F, Marsden K, Hackländer K, López-Bao J, Klenzendorf S & Wegmann D (2023) The spatial distribution and temporal trends of livestock damages caused by wolves in europe. Biol.Conserv. 282:110039.
4. Luqman H, Wegmann D, Fior S & Widmer A (2023) Climate-induced range shifts drive adaptive response via spatio-temporal sorting of alleles. Nat.Commun. 14(1).

2022

1. Probert A, Wegmann D, Volery L, Adriaens T, Bakiu R, Bertolino S, Essl F, Gervasini E, Groom Q, Latombe G, Marisavljevic D, Mumford J, Pergl J, Preda C, Roy H, Scalera R, Teixeira H, Tricarico E, Vanderhoeven S & Bacher S (2022) Identifying, reducing, and communicating uncertainty in community science: a focus on alien species. Biol.Invasions.
2. Silva N, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, Adaktylou F, Chondroyianni-Metoki A, Pappa M, Ziota C, Sampson A, Papathanasiou A, Vitelli K, Cullen T, Kyparissi-Apostolika N, Lanz A, Peters J, Rio J, Wegmann D, Burger J, Currat M & Papageorgopoulou C (2022) Ancient mitochondrial diversity reveals population homogeneity in neolithic greece and identifies population dynamics along the danubian expansion axis. Sci.rep. 12(1):1--15.
3. Marchi N*, Winkelbach L*, Schulz I*, Brami M*, Hofmanová Z, Blöcher J, Reyna-Blanco C, Diekmann Y, Thiéry A, Kapopoulou A, Link V, Piuz V, Kreutzer S, Figarska S, Ganiatsou E, Pukaj A, Struck T, Gutenkunst R, Karul N, Gerritsen F, Pechtl J, Peters J, Zeeb-Lanz A, Lenneis E, Teschler-Nicola M, Triantaphyllou S, Stefanović S, Papageorgopoulou C, Wegmann D*, Burger J* & Excoffier L* (2022) The genomic origins of the world’s first farmers. Cell 185(11):1842-1859.e18.

2021

1. Garcìa-Navas V, Tobias J, Schweizer M, Wegmann D, Schodde R, Norman J & Christidis L (2021) Trophic niche shifts and phenotypic trait evolution are largely decoupled in australasian parrots. BMCEcol.Evol. 21(1):212.
2. Luqman H, Widmer A, Fior S* & Wegmann D* (2021) Identifying loci under selection via explicit demographic models. Mol.Ecol.Resour. 21(8):2719-2737.
3. Louis M, Galimberti M, Archer F, Berrow S, Brownlow A, Fallon R, Nykänen M, O’Brien J, Roberston K, Rosel P, Simon-Bouhet B, Wegmann D, Fontaine M, Foote A & Gaggiotti O (2021) Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. Sci.Adv. 7(44):eabg1245.
4. Žegarac A, Winkelbach L, Blöcher J, Diekmann Y, Gavrilović M, Porčić M, Stojković B, Milašinović L, Schreiber M, Wegmann D, Veeramah K, Stefanović S & Burger J (2021) Ancient genomes provide insights into family structure and the heredity of social status in the early bronze age of southeastern europe. Sci.Rep. 11:10072.
5. Macháček J, Nedoma R, Dresler P, Schulz I, Lagonik E, Johnson S, Kaňáková L, Slámová A, Llamas B, Wegmann D* & Hofmanová Z* (2021) Runes from l\'any (czech republic) - the oldest inscription among slavs. A new standard for multidisciplinary analysis of runic bones. J.Archaeol.Sci. 127:105333.
6. Ait Kaci Azzou S, Singer L, Aebischer T, Caduff M, Wolf B & Wegmann D (2021) A sparse observation model to quantify species distributions and their overlap in space and time. Ecography 44(6):928--940.

2020

1. Dehasque M, Ávila-Arcos M, Díez-del-Molino D, Fumagalli M, Guschanski K, Lorenzen E, Malaspinas A, Marques-Bonet T, Martin M, Murray G, Papadopulos A, Therkildsen N, Wegmann D, Dalén L & Foote A (2020) Inference of natural selection from ancient dna. Evol.Lett. 4(2):94-108.
2. Bresadola L, Link V, Buerkle C, Lexer C & Wegmann D (2020) Estimating and accounting for genotyping errors in rad-seq experiments. Mol.Ecol.Resour. 20(4):856-870.
3. Galimberti M, Leuenberger C, Wolf B, Szilágyi S, Foll M & Wegmann D (2020) Detecting selection from linked sites using an f-model. Genetics 216(4):1205-1215.
4. Burger J*, Link V*, Blöcher J, Schulz A, Sell C, Pochon Z, Diekmann Y, Žegarac A, Hofmanová Z, Winkelbach L, Reyna-Blanco C, Bieker V, Orschiedt J, Brinker U, Scheu A, Leuenberger C, Bertino T, Bollongino R, Lidke G, Stefanović S, Jantzen D, Kaiser E, Terberger T, Thomas M, Veeramah K & Wegmann D (2020) Low prevalence of lactase persistence in bronze age europe indicates ongoing strong selection over the last 3,000 years. Curr.Biol. 30(21):4307--4315.
5. Aebischer T, Ibrahim T, Hickisch R, Furrer R, Leuenberger C & Wegmann D (2020) Apex predators decline after an influx of pastoralists in former central african republic hunting zones. Biol.Conserv. 241:108326.

2019

1. Wegmann D & Leuenberger C (2019) Statistical modeling and inference in genetics. Handbook of Statistical Genomics, edited by Balding D, Moltke I & Marioni J, pages 1--50.
2. Bresadola L, Caseys C, Castiglione S, Buerkle C*, Wegmann D* & Lexer C* (2019) Admixture mapping in interspecific populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. NewPhytol. 223(4):2076--2089.
3. Gros-Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S* & Khadari B* (2019) Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. PlantJ. 100(1):143--157.

2018

1. Kousathanas A, Duchen P & Wegmann D (2018) A guide to general-purpose abc software. Handbook of Approximate Bayesian Computation, edited by Sisson S, Fan Y & Beaumont M, pages 369--413.
2. Veeramah K, Rott A*, Groß M*, Van Dorp L, López S, Kirsanow K, Sell C, Blöcher J, Wegmann D, Link V, Hofmanová Z, Peters J, Trautmann B, Gairhos A, Haberstroh J, Päffgen B, Hellenthal G, Haas-Gebhard B, Harbeck M* & Burger J* (2018) Population genomic analysis of elongated skulls reveals extensive female-biased immigration in early medieval bavaria. Proc.Natl.Acad.Sci.U.S.A. 115(13):3494--3499.
3. Scheib C, Li H, Desai T, Link V, Kendall C, Dewar G, Griffith P, Mörseburg A, Johnson J, Potter A, Kerr S, Endicott P, Lindo J, Haber M, Xue Y, Tyler-Smith C, Sandhu M, Lorenz J, Randall T, Faltyskova Z, Pagani L, Danecek P, O'Connell T, Martz P, Boraas A, Byrd B, Leventhal A, Cambra R, Williamson R, Lesage L, Holguin B, Soto E, Rosas J, Metspalu M, Stock J, Manica A, Scally A, Wegmann D, Malhi R & Kivisild T (2018) Ancient human parallel lineages within north america contributed to a coastal expansion. Science 360(6392):1024--1027.

2017

1. Aebischer T, Siguindo G, Rochat E, Arandjelovic M, Heilman A, Hickisch R, Vigilant L, Joost S, Wegmann D, Thierry A, Guy S, Estelle R, Mimi A, Amy H, Raffael H, Linda V, Stéphane J & Daniel W (2017) First quantitative survey delineates the distribution of chimpanzees in the eastern central african republic. Biol.Conserv. 213(November 2016):84--94.
2. Gros-Balthazard M, Galimberti M, Kousathanas A, Newton C, Ivorra S, Paradis L, Vigouroux Y, Carter R, Tengberg M, Battesti V, Santoni S, Falquet L, Pintaud J, Terral J, Wegmann D, Sylvain S, Falquet L, Pintaud J, Terral J* & Wegmann D* (2017) The discovery of wild date palms in oman reveals a complex domestication history involving centers in the middle east and africa. Curr.Biol. 27(14):2211--2218.
3. Fonseca Costa S, Wegmann D* & Ripperger J* (2017) Normalisation against circadian and age-related disturbances enables robust detection of gene expression changes in liver of aged mice. PlosOne 12(1):e0169615.
4. Duchen P, Leuenberger C, Szilágyi S, Harmon L, Eastman J, Schweizer M & Wegmann D (2017) Inference of evolutionary jumps in large phylogenies using l\'evy processes. Syst.Biol. 66(6):950--963.
5. Kousathanas A, Leuenberger C, Link V, Sell C, Burger J & Wegmann D (2017) Inferring heterozygosity from ancient and low coverage genomes. Genetics 205(1):317--332.

2016

1. Broushaki F, Thomas M, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy L, Díez-del-Molino D, Kousathanas A, Sell C, Robson H, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davoudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig O, Bradley D, Shennan S, Veeramah K, Mashkour M, Wegmann D*, Hellenthal G* & Burger J* (2016) Early neolithic genomes from the eastern fertile crescent. Science 353(6298):499--503.
2. Ferrer-Admetlla A, Leuenberger C, Jensen J & Wegmann D (2016) An approximate markov model for the wright\textendashfisher diffusion and its application to time series data. Genetics 203(2):831--846.
3. Liu Y, Hu J, Li S, Duchen P, Wegmann D & Schweizer M (2016) Sino-himalayan mountains act as cradles of diversity and immigration centres in the diversification of parrotbills (paradoxornithidae). J.Biogeogr. 43:1488--1501.
4. Christe C, Stölting K, Bresadola L, Fussi B, Heinze B, Wegmann D & Lexer C (2016) Selection against recombinant hybrids maintains reproductive isolation in hybridizing \textitpopulus species despite f\textsubscript1 fertility and recurrent gene flow. Mol.Ecol..
5. Kousathanas A, Leuenberger C, Wegmann D, Helfer J, Quinodoz M, Foll M & Wegmann D (2016) Likelihood-free inference in high-dimensional models. Genetics 203(2):893--904.
6. Hofmanová Z*, Kreutzer S*, Hellenthal G, Sell C, Diekmann Y, Díez-Del-Molino D, van Dorp L, López S, Kousathanas A, Link V, Kirsanow K, Cassidy L, Martiniano R, Strobel M, Scheu A, Kotsakis K, Halstead P, Triantaphyllou S, Kyparissi-Apostolika N, Urem-Kotsou D, Ziota C, Adaktylou F, Gopalan S, Bobo D, Winkelbach L, Blöcher J, Unterländer M, Leuenberger C, Çilingiroğlu Ç, Horejs B, Gerritsen F, Shennan S, Bradley D, Currat M, Veeramah K, Wegmann D, Thomas M, Papageorgopoulou C & Burger J (2016) Early farmers from across europe directly descended from neolithic aegeans. Proc.Natl.Acad.Sci.U.S.A. 113(25):6886--6891.

2015

1. Bruford M, Ginja C, Hoffmann I, Joost S, Wengel P, Alberto F, Amaral A, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferencakovic M, Fischer D, Fitak R, Groeneveld L, Hall S, Hanotte O, Hassan F, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra J, Ajmone-Marsan P, Masembe C, Megens H, Miele M, Neuditschko M, Nicolazzi E, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Da Gama L, Tixier-Boichard M, Wegmann D & Zhan X (2015) Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front.Genet. 6(OCT):1--11.

2014

1. Dussex N, Wegmann D & Robertson B (2014) Postglacial expansion and not human influence best explains the population structure in the endangered kea \textitnestor notabilis. Mol.Ecol. 23(9):2193--2209.
2. Gray M, Wegmann D, Haasl R, a M White M, Gabriel S, Searle J, Cuthbert R, Ryan P & a B Payseur B (2014) Demographic history of a recent invasion of house mice on the isolated island of gough.. Mol.ecol. 23(8):1923--1939.
3. Zawistowski M*, Reppell M*, Wegmann D, St Jean P, Ehm M, Nelson M, Novembre J & Zöllner S (2014) Analysis of rare variant population structure in europeans explains differential stratification of gene-based tests.. Eur.j.hum.genet..
4. Wegmann D & Currat M (2014) Recipient of the 2013 molecular ecology prize: laurent excoffier.. Mol.ecol. 23(1):16--9.
5. Foll M*, Poh Y*, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas A, Ewing G, Liu P, Wegmann D, Caffrey D, Zeldovich K, Bolon D, Wang J, Kowalik T, a C Schiffer C, Finberg R & Jensen J (2014) Influenza virus drug resistance: a time-sampled population genetics perspective.. PLoSgenet. 10(2):e1004185.
6. Adrion J*, Kousathanas A*, Pascual M, Burrack H, Haddad N, Bergland A, Machado H, Sackton T, a T Schlenke T, Watada M, Wegmann D* & Singh N* (2014) Drosophila suzukii: the genetic footprint of a recent, worldwide invasion. Mol.biol.evol..

2013

1. Chu J*, Wegmann D*, Yeh C, Lin R, Yang X, Lei F, Yao C, Zou F & Li S (2013) Inferring the geographic mode of speciation by contrasting autosomal and sex-linked genetic diversity. Mol.Biol.Evol. 30(11):2519-2530.
2. Schaibley V, Zawistowski M, Wegmann D, Ehm M, Nelson M, St Jean P, Abecasis G, Novembre J, Zöllner S & Li J (2013) The influence of genomic context on mutation patterns in the human genome inferred from rare variants.. Genomeres. 23(12):1974--84.

2012

1. Rubio J, Topp S*, Warren L*, St Jean P, Wegmann D, Kessner D, Novembre J, Shen J, Fraser D, Aponte J, Nangle K, Cardon L, Ehm M, Chissoe S, Whittaker J, Nelson M & Mooser V (2012) Deep sequencing of the lrrk2 gene in 14,002 individuals reveals evidence of purifying selection and independent origin of the p.arg1628pro mutation in europe.. Hum.mutat. 33(7):1087--98.
2. Nelson M*, Wegmann D*, Ehm M, Kessner D, St. Jean P, Verzilli C, Shen J, Tang Z, Bacanu S, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall M, Nangle K, Wang J, Abecasis G, Cardon L, Zöllner S, Whittaker J, Chissoe S, Novembre J* & Mooser V* (2012) An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337(6090):100--104.
3. Stahl E, Wegmann D, Trynka G, Gutierrez-Achury J, Do R, Voight B, Kraft P, Chen R, Kallberg H, Kurreeman F, Kathiresan S, Wijmenga C, Gregersen P, Alfredsson L, Siminovitch K, Worthington J, De Bakker P, Raychaudhuri S & Plenge R (2012) Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat.Genet. 44(5):483--489.

2011

1. Slater G, Harmon L, Wegmann D, Joyce P, Revell L & Alfaro M (2011) Fitting mmdels of continuous trait evolution to incompletely sampled comparative data using approximate bayesian computation. Evolution.
2. Veeramah K*, Tönjes A*, Kovacs P, Gross A, Wegmann D, Geary P, Gasperikova D, Klimes I, Scholz M, Novembre J & Stumvoll M (2011) Genetic variation in the sorbs of eastern germany in the context of broader european genetic diversity.. Eur.j.hum.genet. 19(9):995--1001.
3. Thalmann O*, Wegmann D*, Spitzner M, Arandjelovic M, Guschanski K, Leuenberger C, Bergl R & Vigilant L (2011) Historical sampling reveals dramatic demographic changes in western gorilla populations.. BMCevol.biol. 11(1):85.
4. Veeramah K, Wegmann D, Woerner A, Mendez F, Watkins J, Destro-Bisol G, Soodyall H, Louie L & Hammer M (2011) An early divergence of khoesan ancestors from those of other modern humans is supported by an abc-based analysis of autosomal re-sequencing data. Mol.Biol.Evol. 29(2):617--630.
5. Wegmann D, Kessner D, Veeramah K, Mathias R, Nicolae D, Yanek L, Sun Y, Torgerson D, Rafaels N, Mosley T, Becker L, Ruczinski I, Beaty T, Kardia S, Meyers D, Barnes K, Becker D, Freimer N & Novembre J (2011) Recombination rates in admixed individuals identified by ancestry-based inference. Nat.Genet. 43(9):847--853.

2010

1. Wegmann D, Leuenberger C, Neuenschwander S & Excoffier L (2010) Abctoolbox: a versatile toolkit for approximate bayesian computations.. BMCbioinform. 11:116.
2. Wegmann D & Excoffier L (2010) Bayesian inference of the demographic history of chimpanzees.. Mol.biol.evol. 27(6):1425--35.
3. Peter B, Wegmann D & Excoffier L (2010) Distinguishing between population bottleneck and population subdivision by a bayesian model choice procedure.. Mol.ecol. 19(21):4648--60.
4. Ray N, Wegmann D, Fagundes N, Wang S, Ruiz-Linares A & Excoffier L (2010) A statistical evaluation of models for the initial settlement of the american continent emphasizes the importance of gene flow with asia.. Mol.biol.evol. 27(2):337--345.
5. Leuenberger C & Wegmann D (2010) Bayesian computation and model selection without likelihoods.. Genetics 184(1):243--52.

2009

1. Wegmann D, Leuenberger C & Excoffier L (2009) Efficient approximate bayesian computation coupled with markov chain monte carlo without likelihood.. Genetics 182(4):1207--18.
2. Hofer T, Ray N, Wegmann D & Excoffier L (2009) Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection.. Ann.hum.genet. 73(1):95--108.

2008

1. Wegmann D, Dupanloup I & Excoffier L (2008) Width of gene expression profile drives alternative splicing.. PloSone 3(10):e3587.

2006

1. Wegmann D, Currat M & Excoffier L (2006) Molecular diversity after a range expansion in heterogeneous environments.. Genetics 174(4):2009--20.