Publications

2024

Benjamin Teo, Paul Bastide and Cécile Ané (2024+). Leveraging graphical model techniques to study evolution on phylogenetic networks. arxiv. Code to reproduce analyses.
Julia package PhyloGaussianBeliefProp: code and documentation.

John A. Rhodes, Hector Baños, Jingcheng Xu and Cécile Ané (2024+). Identifying circular orders for blobs in phylogenetic networks. arXiv.

Cécile Ané, John Fogg, Elizabeth S. Allman, Hector Baños and John A. Rhodes (2024). Anomalous networks under the multispecies coalescent: theory and prevalence. Journal of Mathematical Biology 88:29. Free view-only. Code to reproduce simulations.
earlier version on bioRxiv (2023).

2023

Lauren Frankel and Cécile Ané (2023). Summary tests of introgression are highly sensitive to rate variation across lineages. Systematic Biology, 72(6):1357–1369. doi: 10.1093/sysbio/syad056.
code to reproduce analyses, earlier version on bioRxiv.
For this work, Lauren received the 2023 Margaret Menzel Award by the Genetics Section of the Botanical Society of America.

Duncan D. Smith, Mark A. Adams, Amanda M. Salvi, Christopher P. Krieg, Cécile Ané, Katherine A. McCulloh, Thomas J. Givnish (2023). Ecophysiological adaptations shape distributions of closely related trees along a climatic moisture gradient. Nature Communications 14, 7173.

John Fogg, Elizabeth S. Allman, and Cécile Ané (2023). PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow. Systematic Biology, 72(5):1171–1179. doi: 10.1093/sysbio/syad030.
earlier version on bioRxiv. Data on dryad to reproduce analyses.
Julia package PhyloCoalSimulations: code and documentation.

Prakash R Timilsena, Craig F Barrett, Alma P Nelson, Eric K Wafula, Saravanaraj Ayyampalayam, Joel R McNeal, Tomohisa Yukawa, Thomas J Givnish, Sean W Graham, J Chris Pires, Jerrold I Davis, Cécile Ané, Dennis W Stevenson, James Leebens-Mack, Esteban Martínez-Salas, Elena R Álvarez-Buylla, and Claude W dePamphilis (2023). Phylotranscriptomic analyses of mycoheterotrophic monocots show a continuum of evolutionary changes in expressed nuclear genes from three independent nonphotosynthetic lineages. Genome Biology and Evolution, 15(1):evac183.

Jingcheng Xu and Cécile Ané (2023). Identifiability of local and global features of phylogenetic networks from average distances. Journal of Mathematical Biology, 86(1):12. earlier on arXiv.

Benjamin Teo, Jeffrey P. Rose, Paul Bastide, Cécile Ané (2023). Accounting for within-species variation in continuous trait evolution on a phylogenetic network. Bulletin of the Society of Systematic Biologists, 2(3):1-29, doi: 10.18061/bssb.v2i3.8977.
part of the Reticulate Evolution Special Collection. earlier version on bioRxiv.

2022

Prakash R Timilsina, Eric K Wafula, Craig F Barrett, Saravanaraj Ayyampalayam, Joel R McNeal, Jeremy D Rentsch, Michael R. McKain, Karolina Heyduk, Alex Harkess, Matthieu Villegente, John G Conran, Nicola Illing, Bruno Fogliani, Cécile Ané, J Chris Pires, Jerrold I Davis, Wendy B Zomlefer, Dennis W Stevenson, Sean W Graham, Thomas J Givnish, James Leebens-Mack and Claude W dePamphilis (2022). Phylogenomic resolution of order- and family-level monocot relationships using 602 single copy nuclear genes and 1375 BUSCO genes. Frontiers in Plant Science, 13:876779.

Yen-Wen Wang and Cécile Ané (2022). KIMGENS: A novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure. Bioinformatics, 38(11):3044–3050.

Nisa Karimi, Samuel Saghafi, Ken Keefover-Ring, Sarah M. Venter, Cécile Ané, David A. Baum (2022). Evidence for hawkmoth pollination in the chiropterophilous African baobab (Adansonia digitata). Biotropica 54(1),113-124. doi: 10.1111/btp.13033. data availble on dryad.

2021

Qianshi Lin, Cécile Ané, Thomas Givnish and Sean Graham (2021). A new carnivorous plant lineage (Triantha) with a unique sticky-inflorescence trap. Proceedings of the National Academy of Sciences, 118(33):e2022724118.
Press coverage: news@UW, Science news, National Geographic, top 10 PNAS selected highlights of 2021.

Cécile Ané (2021) Dating with constraints. Peer Community in Evolutionary Biology, 100127. 10.24072/pci.evolbiol.100127

Ruoyi Cai and Cécile Ané (2021). Assessing the fit of the multi-species network coalescent to multi-locus data. Bioinformatics, 37(5):634–641. doi: 10.1093/bioinformatics/btaa863
Data and code available on the Open Science Framework.

2020

Claudia Solís-Lemus, Arrigo Coen and Cécile Ané (2020). On the identifiability of phylogenetic networks under a pseudolikelihood model. arxiv:2010.01758.

issue cover Nisa Karimi, Corrinne E Grover, Joseph P Gallagher, Jonathan F Wendel, Cécile Ané, David A Baum (2020). Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3):462-478. doi: 10.1093/sysbio/syz073.
data and code available on github.

Christopher Blair and Cécile Ané (2020). Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. Systematic Biology, 69(3):593–601. doi: 10.1093/sysbio/syz056.
This github gist has Julia code from this paper to calculate the D statistic (including locus bootstrapping).

2019

Justin L. Conover, Nisa Karimi, Noah Stenz, Cécile Ané, Corrinne E. Grover, C. Skema, Jennifer A. Tate, Kirsten Wolff, Samuel A. Logan, Jonathan F. Wendel and David A. Baum (2019). A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods? Journal of Integrative Plant Biology, 61(1):12-31.

2018

Thomas Givnish, Alejandro Zuluaga, Daniel Spalink, Marybel Soto Gomez, Vivienne Lam, Jeffrey Saarela, Chodon Sass, William Iles, Danilo Lima, James Leebens-Mack, J. Chris Pires, Wendy Zomlefer, Maria Gandolfo, Jerrold Davis, Dennis Stevenson, Claude dePamphilis, Chelsea Specht, Sean Graham, Craig Barrett and Cécile Ané (2018). Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. American Journal of Botany, 105(11):1888-1910. doi:10.1002/ajb2.1178.
Data and code available on the Open Science Framework.
Featured in Science News.

Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, K. William Sparks and Cécile Ané (2018). Phylogenetic comparative methods on phylogenetic networks with reticulations. Systematic Biology, 67(5):800–820. guest access. issue cover
SM on dryad: including tutorial code to calibrate phylogenetic networks and to conduct comparative analyses.
Part of the special issue on phylogenetic reticulation.
Accepted version on bioRχiv.
Julia package PhyloNetworks on GitHub, with documentation on continuous trait evolution.

Paul Bastide, Cécile Ané, Stéphane Robin and Mahendra Mariadassou (2018). Inference of Adaptive Shifts for Multivariate Correlated Traits. Systematic Biology, 67(4):662–680.
SM on dryad; guest access; earlier version on bioRχiv.
R package PhylogeneticEM on CRAN and on GitHub.

2017

Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). PhyloNetworks: a package for phylogenetic networks. PhyloNetworks logo Molecular Biology and Evolution, 34(12):3292–3298. abstract.
Software on GitHub: PhyloNetworks

Eric Goolsby, Jorn Bruggeman and Cécile Ané (2017). Rphylopars: Phylogenetic comparative methods for missing data and within-species variation. Methods in Ecology and Evolution, 8(1):22-27.
R package on GitHub (most current): Rphylopars and on CRAN.

Cécile Ané, Lam S.T. Ho and Sebastien Roch (2017). Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree. Journal of Mathematical Biology, 74:355-385. free view here. (earlier on arXiv).

2016

Bret Larget, Cécile Ané, Martin Bontrager, Steven J. Hunter, Noah Stenz and David A. Baum. Statistical evidence for common ancestry: New tests of universal ancestry. bioRχiv

Martin Bontrager, Bret Larget, Cécile Ané and David A. Baum. Statistical Evidence of Common Ancestry: Testing for Signal in Silent Sites. bioRχiv

David A. Baum, Cécile Ané, Bret Larget, Claudia Solís-Lemus, Lam Si Tung Ho, Peggy Boone, Chloe P. Drummond, Martin Bontrager, Steve Hunter and William Saucier (2016). Statistical evidence for common ancestry: Application to primates. Evolution, 70(6):1354–1363.

Claudia Solís-Lemus, Mengyao Yang and Cécile Ané. Inconsistency of species-tree methods under gene flow (2016). Systematic Biology, 65(5):843-851.

George Tiley, Cécile Ané and Gordon Burleigh (2016). Evaluating and characterizing ancient whole genome duplications in plants with gene count data. Genome Biology and Evolution, 8(4):1023-1037.

Claudia Solís-Lemus and Cécile Ané (2016). Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. PLoS Genetics, 12(3):e1005896. (earlier on arXiv 2015). SNaQ logo
Software on GitHub: SNaQ (Julia package).

Mohammad Khabbazian, Ricardo Kriebel, Karl Rohe and Cécile Ané (2016). Fast and accurate detection of evolutionary shifts in Ornstein-Uhlenbeck models. Methods in Ecology and Evolution, 7(7):811–824.
Software on GitHub: ℓ1ou

2015

Noah W. M. Stenz, Bret Larget, David A. Baum, and Cécile Ané (2015). Exploring tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Systematic Biology, 64(5):809-823.
Software, including TICR, available on GitHub, and data available from the Dryad digital repository.

Claudia Solís-Lemus, L. Lacey Knowles and Cécile Ané (2015). Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution, 69(2):492-507.
Software iBPP on GitHub, scripts available on Dryad, and lizard data available on Dryad as well.
Featured in the Molecular Ecologist blog here and here.

2014

Lam Ho and Cécile Ané (2014). Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models. Methods in Ecology and Evolution, 5(11):1133-1146. Tools available in the R package phylolm v2.2 (and on github).

Lam Ho and Cécile Ané (2014). A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic Biology, 63(3):397-408.
received the Publisher's award for Excellence in Systematic Research.
R package: phylolm is on CRAN.

Charles-Elie Rabier, Tram Ta and Cécile Ané (2014). Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. Molecular Biology and Evolution, 31(3):750-762, doi.
R package: WGDgc

2013

Yujin Chung, Nicole T. Perna and Cécile Ané (2013). Computing the joint distribution of tree shape and tree distance for gene tree inference and recombination detection. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(5):1263-1274. preprint and pdf

Aaron W. Kolb, Cécile Ané and Curtis R. Brandt (2013). Using HSV-1 genome phylogenetics to track past human migrations. PLoS ONE, 8(10):e76267. Press release from University News and NBCNews.

Richard J. Wang, Cécile Ané and Bret A. Payseur (2013). The Evolution of hybrid incompatibilities along a phylogeny. Evolution, 67(10):2905-2922.

Lam Ho and Cécile Ané (2013). Asymptotic theory with hierarchical autocorrelation: Ornstein-Uhlenbeck tree models. Annals of Statistics, 41(2):957-981, pdf.

2012

Tom D. Mand, D. Döpfer, B. Ingham, C. Ané, C.W. Kaspar (2012). Growth and survival parameter estimates and relation to RpoS levels in serotype O157:H7 and non-O157 Shiga toxin-producing Escherichia coli. Journal of Applied Microbiology. 114(1):242-255.

B. Marazzi, C. Ané, M.F. Simon, A. Delgado-Salinas, M. Luckow, M.J. Sanderson (2012). Locating evolutionary precursors on a phylogenetic tree Evolution, 66(12):3918-3930.

K.W. Broman, S. Kim, S. Sen, C. Ané, B.A. Payseur (2012). Mapping quantitative trait loci onto a phylogenetic tree. Genetics, 192:267-279 (issue highlights)

D. Cai, F. Rodríguez, Y. Teng, C. Ané, M. Bonierbale, L.A. Mueller, D. Spooner. Single copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota) (2012). BMC Evolutionary Biology, 12:70 (highly accessed), ScienceOpen.

2011

Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kuback A, Narro M, Hopkins N, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim S, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston K, Soltis P, Soltis D, O'Meara B, Ané C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Kvilekval K, Manjunath B, Vision TJ, Enquist BJ, Boyle B, Lowenthal D, Akoglu A, Micklos D, Andrews G, Ram S, Ware D, Stein L and Stanzione D (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Genetics and Genomics. 2:34

S.C. Ingham, Y. Hu and C. Ané (2011). Comparison of bulk-tank standard plate count and somatic cell count for Wisconsin dairy farms in three size categories. Journal of Dairy Science, 94(8):4237-4241.

C. Ané (2011). Detecting phylogenetics breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biology and Evolution, 3:246-258.
Program download: tarball

Y. Chung, C. Ané (2011). Comparing two Bayesian methods for gene tree / species tree reconstruction: A simulation with incomplete lineage sorting and horizontal gene transfer. Systematic Biology. 60(3): 261-275 abstract, pdf.

2010

B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010). BUCKy: Gene tree / species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26(22): 2910-2911.
Program available here: BUCKy

C. Ané (2010). Reconstructing concordance trees and testing the coalescent model from genome-wide data sets. Chapter 3, p.35-52 in "Estimating species trees: Practical and theoretical aspects", L. Knowles and L. Kubatko, eds. Wiley-Blackwell.

S.C. Ingham, D.L. Borneman, C. Ané and B.H. Ingham (2010). Predicting growth-no growth of Listeria monocytogenes on vacuum-packaged ready-to-eat meats. Journal of Food Protection 73(4):708-714.

2009

M.A. White, C. Ané, C.N. Dewey, B.R. Larget, B.A. Payseur (2009). Fine scale phylogenetic discordance across the house mouse genome. PloS Genetics. 5(11):e1000729.

S.D. Smith, C. Ané, D.A. Baum (2009). Macroevolutionary tests of pollination syndromes: A reply to Fenster et al. Evolution. 63(10):2763-2767.

F. Rodriguez, F. Wu, C. Ané, S. Tanksley, D.M. Spooner (2009). Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evolutionary Biology 9:191.

D.L. Borneman, S.C. Ingham, C. Ané (2009). Mathematical approaches to estimating lag-phase duration and growth rate for predicting growth of Salmonella serovars, Escherichia coli O157:H7, and Staphylococcus aureus in raw beef, bratwurst, and poultry. Journal of Food Protection 72(6):1190-1200.

D.L. Borneman, S.C. Ingham, C. Ané (2009). Predicting growth-no growth of Staphylococcus aureus on vacuum-packaged ready-to-eat meats. Journal of Food Protection 72(3):539-548.

C. Ané, O. Eulenstein, R. Piaggio-Talice and M.J. Sanderson (2009). Groves of phylogenetic trees. Annals of Combinatorics 13(2):139-167. Technical report available here (2006).

2008

C. Ané (2008). Analysis of comparative data with hierarchical autocorrelation. Annals of Applied Statistics 2(3):1078-1102. arXiv

S. Martin, E.L. Epperson,J. Rose,C. Kurtz, C. Ané, H. Carey (2008). Proteomic analysis of the winter-protected phenotype of hibernating ground squirrel intestine. AJP- Regulatory, Integrative and Comparative Physiology, 295:316-328. cover

J.P. Huelsenbeck, C. Ané, B. Larget and F. Ronquist (2008). A Bayesian perspective on a non-parsimonious parsimony model. Systematic Biology, 57(3):406-419.

S.D. Smith, C. Ané and D.A. Baum (2008). The role of pollinator shifts in the floral diversification of Iochroma (Solanaceae). Evolution 62(4):793-806.

E.S. Allman, C. Ané, J.A. Rhodes (2008). Identifiability of a Markovian model of molecular evolution with Gamma-distributed rates. Advances in Applied Probability 40(1), 229-249. Abstract or preprint.

≤ 2007

M.J. Sanderson, C. Ané, O. Eulenstein, D. Fernández-Baca, J. Kim, M.M. McMahon, R. Piaggio-Talice (2007). Fragmentation of large data sets in phylogenetic analyses. Chapter 7 (p. 199-216) in Reconstructing Evolution: New Mathematical and Computational Advances. Olivier Gascuel and Mike Steel, editors. Oxford University Press.

C. Ané, B. Larget, D.A. Baum, S.D. Smith, A. Rokas (2007). Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution 24(2), 412-426. Abstract and Erratum. Software available here.

B.C. O'Meara, C. Ané, M.J. Sanderson, P.C. Wainwright (2006). Testing for different rates of continuous trait evolution using likelihood. Evolution 60(5), 922-933.

C. Ané, J.G. Burleigh, M.M. McMahon, M.J. Sanderson (2005). Covarion structure in plastid genome evolution: A new statistical test. Molecular Biology and Evolution 22(4), 914-924. Abstract, full text and supplemental data.

C. Ané and M.J. Sanderson (2005). Missing the forest for the trees: phylogenetic compression and its implication for inferring complex evolutionary histories. Systematic Biology, 54(1), 146-157. and supplemental data

C. Ané, O. Eulenstein, and R. Piaggio-Talice (2005). Phylogenetic compression and model selection: an improved encoding scheme. Technical report here.

A.C. Driskell, C. Ané, J.G. Burleigh, M.M. McMahon, B.C. O'Meara, M.J. Sanderson (2004). Prospects for building the tree of life from large sequence databases. Science, 306(5699), 1172-1174.

D. Concordet, F. Léger, C. Ané (2004). Population PK/PD Analysis. In Encyclopedia of Biopharmaceutical Statistics, 2nd Ed.; S. Chow, Ed.; Marcel Dekker, Inc.: New York.

C. Ané and D. Concordet (2003). Population pharmacokinetics - pharmacodynamics relationships of an anticancer drug. Statistics in Medicine 22(6), 833-846.

C. Ané and D. Chafai (2000). Entropy inequalities in information theory (in french). Chapter 10 of the book Sur les ingalités de Sobolev logarithmiques, Panoramas et Syntheses no 10, SMF. Mathematical Review report. More here.

C. Ané (2001). Clark-Ocone formulas and Poincaré inequalities on the discrete cube. Annales de l'Institut Henri Poincaré, Probab. Statist. 37(1), 101-137.

C. Ané and M. Ledoux (2000). On logarithmic Sobolev inequalities for continuous time random walks on graphs Probability Theory and Related Fields, 116(4), 573-602.

C. Ané (1997). Large deviations in small time for a Markov process with countable state space (in french). C. R. Acad. Sc. Paris, I 325, 1025-1028.