| Referências: |
Ahrens, C. W., P. D. Rymer, A. Stow, J. Bragg, S. Dillon, K. D. L. Umbers, and R. Y. Dudaniec. 2018. The
search for loci under selection: trends, biases and progress. Molecular Ecology 27:1342-1356.
Alvarado-Serrano, D.F. & Knowles, L.L. (2014) Ecological niche models in phylogeographic studies:
applications, advances and precautions. Molecular Ecology Resources, 14, 233-248.
Avise, J.C. (2009) Phylogeography: retrospect and prospect. Journal of Biogeography, 36, 3-15.
Barido-Sottani, J., V. Bošková, L. D. Plessis, D. Kühnert, C. Magnus, V. Mitov, N. F. Müller, J. PečErska, D.
A. Rasmussen, C. Zhang, A. J. Drummond, T. A. Heath, O. G. Pybus, T. G. Vaughan, and T. Stadler. 2017. Taming the BEAST—a community teaching material resource for BEAST 2. Systematic Biology, 67,170-174.
Beichman, A. C., E. Huerta-Sanchez, and K. R. Lohmueller. 2018. Using genomic data to infer historic
population dynamics of nonmodel organisms. Annual Review of Ecology, Evolution and Systematics 49:433-456.
Bouckaert, R.R., Heled, J., Kuhnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M.A., Rambaut, A. & Drummond, A.J. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLOS Computational Biology, 10, e1003537.
Bouckaert, R., T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kühnert, N. De Maio, M. Matschiner, F. K. Mendes, N. F. Müller, H. A. Ogilvie, L. du Plessis, A. Popinga, A. Rambaut, D. Rasmussen, I. Siveroni, M. A. Suchard, C.-H. Wu, D. Xie, C. Zhang, T. Stadler, and A. J. Drummond. 2019. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Computational Biology 15:e1006650.
Bouckaert, R. 2016. Phylogeography by diffusion on a sphere: whole world phylogeography. PeerJ 4:e2406.
Bravo, G. A., A. Antonelli, C. D. Bacon, K.
Bartoszek, M. Blom, S. Huynh, G. Jones, L. L. Knowles, S. Lamichhaney, T. Marcussen, H. Morlon, L. Nakhleh, B. Oxelman, B. Pfeil, A. Schliep, N. Wahlberg, F. Werneck, J. Wiedenhoeft, S. Willows-Munro, and S. V. Edwards. 2019. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 7:e6399. https://peerj.com/articles/6399/
Bromham, L., S. Duchêne, X. Hua, A. M. Ritchie, D. A. Duchêne, and S. Y. W. Ho. 2018. Bayesian molecular dating: opening up the black box. Biological Reviews 93:1165-1191.
Camargo, A., Morando, M., Avila, L.J. & Sites Jr., J.W. (2012) Species delimitation using ABC: accounting for speciation with gene flow in lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution, 66, 2834–2849.
Camargo, A., Avila, L.J., Morando, M. & Sites Jr., J.W. (2012) Accuracy and precision of species trees: effects of locus, individual, and base pair sampling on inference of species trees in lizards of the Liolaemus darwinii group (Squamata, Liolaemidae). Systematic Biology, 61, 272-288.
Carey, M. A., and J. A. Papin. 2018. Ten simple rules for biologists learning to program. PLoS Computational Biology 14:e1005871.
Carstens, B.C., Brennan, R.S., Chua, V., Duffie, C.V., Harvey, M.G., Koch, R.A., Mcmahan, C.D., Nelson,
B.J., Newman, C.R., Satler, J.D., Seeholzer, G., Posbic, K., Tank, D.C. & Sullivan, J. (2013) Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Molecular Ecology, 22, 4014-4028.
Carstens, B.C., Pelletier, T.A., Reid, N.M. & Satler, J.D. (2013) How to fail at species delimitation. Molecular Ecology, 22, 4369-4383.
Degnan, J.H. & Rosenberg, N.A. (2009) Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution, 24, 332-340.
Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 1-8.
Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969-1973.
Drummond, A.J. & Bouckaert, R.R. (In Press) Bayesian evolutionary analysis with BEAST 2.0.
Eaton, D.A., 2014. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinf. 30,
1844–1849.
Eaton, D.A.R., Overcast, I., 2020. ipyrad: Interactive assembly and analysis of RADseq datasets Bioinfo,
btz966.Edwards, S.V. & Beerli, P. (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54, 1839-1854.
Flouri, T., Jiao, X., Rannala, B., Yang, Z. (2020). A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis. Molecular Biology and Evolution, 37, 1211-1223.
Forester, B. R., J. R. Lasky, H. H. Wagner, and D. L. Urban. 2018. Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations. Molecular Ecology 27:2215-2233.
Frichot, E., S. D. Schoville, G. Bouchard, and O. François. 2013. Testing for associations between loci and
environmental gradients using latent factor mixed models. Molecular Biology and Evolution 30:1687-1699.
Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G., & François, O. 2014. Fast and efficient estimation of individual ancestry coefficients. Genetics, 196, 973–983.
Frichot, E., and O. François. 2015. LEA: An R package for landscape and ecological association studies.
Methods in Ecology and Evolution 6:925-929.
Garrick, R.C., Bonatelli, I.A.S., Hyseni, C., Morales, A., Pelletier, T.A., Perez, M.F., Rice, E., Satler, J.D., Symula, R.E., Thomé, M.T.C. & Carstens, B. (2015) The evolution of phylogeographic data sets. Molecular Ecology, 24, 1164-1171.
Guillot, G., Renaud, S., Ledevin, R., Michaux, J. & Claude, J. (2012) A unifying model for the analysis of phenotypic, genetic, and geographic data. Systematic Biology, 61, 1-15.
Grummer, J.A., Bryson Jr., R.W. & Reeder, T.W. (2014) Species delimitation Using Bayes Factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Systematic Biology, 63, 119-133.
Heath, T.A. (2012) A hierarchical Bayesian model for calibrating estimates of species divergence times.
Systematic Biology, 61, 793-809.
Heled, J. & Drummond, A.J. (2012) Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Systematic Biology, 61, 138-149.
Heller, R., L. Chikhi, and H. R. Siegismund. 2013. The confounding effect of population structure on Bayesian Skyline Plot inferences of demographic history. PLoS One 8:e62992.
Hickerson, M.J., Carstens, B.C., Cavender-Bares, J., Crandall, K.A., Graham, C.H., Johnson, J.B., Rissler, L., Victoriano, P.F. & Yoder, A.D. (2011) Phylogeography’s past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics and Evolution, 54, 291-301.
Hickerson, M.J., Stahl, E.A. & Takebayashi, N. (2007) msBayes: pipeline for testing comparative
phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinformatics, 8, 268.
Ho, S. Y. W., and S. Duchêne. 2014. Molecular-clock methods for estimating evolutionary rates and
timescales. Molecular Ecology 23:5947-5965.
Huang, W., Takebayashi, N., Qi, Y. & Hickerson, M.J. (2011) MTML-msBayes: Approximate Bayesian
comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. BMC Bioinformatics, 12
Hudson, R.R. (2002) Generating samples under a Wright-Fisher neutral model of genetic variation.
Bioinformatics, 18, 337-338.
Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. von Haeseler, and L. S. Jermiin. 2017. ModelFinder: fast
model selection for accurate phylogenetic estimates. Nature Methods 14:587-589.
Knowles, L.L. & Maddison, W.P. (2002) Statistical phylogeography. Molecular Ecology, 11, 2623-2635.
Leaché, A.D., Fujita, M.K., Minin, V.N. & Bouckaert, R.R. (2014) Species delimitation using genome-wide SNP data. Systematic Biology, 63, 534-542.
Leigh, J. W., and D. Bryant. 2015. popart: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6:1110-1116.
Lemey, P., Rambaut, A., Drummond, A.J. & Suchard, M.A. (2009) Bayesian phylogeography finds its
roots. PLOS Computational Biology, 5, e1000520.
Lemey, P., Rambaut, A., Welch, J.J. & Suchard, M.A. (2010) Phylogeography takes a relaxed random walk in continuous space and time. Molecular Biology and Evolution, 27, 1877-1885.
Liu, X., and Y.-X. Fu. 2015. Exploring population size changes using SNP frequency spectra. Nature Genetics 47:555-559.
Maddison, W.P. (1997) Gene trees in species tree. Systematic Biology, 46, 523-536.
Maddison, W.P. & Knowles, L.L. (2006) Inferring phylogeny despite incomplete lineage sorting. Systematic Biology, 55, 21-30.
Marchi, N., F. Schlichta, and L. Excoffier. 2021. Demographic inference. Current Biology 31:R276-R279.
Marske, K.A., Rahbek, C. & Nogués-Bravo, D. (2013) Phylogeography: spanning the ecology-evolution continuum. Ecography, 36, 001-013.
Nylinder, S., Lemey, P., de Bruyn, M., Suchard, M.A., Pfeil, B.E., Walsh, N. & Anderberg, A.A. (2014) On the biogeography of Centipeda: a species-tree diffusion approach. Systematic Biology, 63, 178-191.
Olave, M., Sola, E. & Knowles, L.L. (2014) Upstream analyses create problems with DNA-based species delimitation. Systematic Biology, 63, 263-271.
Papadopoulou, A. & Knowles, L.L. (2016) Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proceedings of the National Academy of Sciences of the United States of America, 113, 8018-8024.
Paradis, E., T. Gosselin, J. Goudet, T. Jombart, and K. Schliep. 2017. Linking genomics and population genetics with R. Molecular Ecology Resources 17:54-66.
Paradis, E. 2018. Analysis of haplotype networks: The randomized minimum spanning tree method. Methods in Ecology and Evolution 9:1308-1317.
Petkova, D., Novembre, J., & Stephens, M. (2016). Visualizing spatial population structure with estimated effective migration surfaces. Nature Genetics, 48(1), 94–100. https ://doi.org/10.1038/ng.3464
Porras-Hurtado, L., Ruiz, Y., Santos, C., Phillips, C., Carracedo, A. & Lareu, M.V. (2013) An overview of STRUCTURE: applications, parameter settings, and supporting software. Frontiers in Genetics, 4, 1-13
Rambaut, A., Suchard, M.A. & Drummond, A.J. (2014) Tracer v1.6, Available from http://beast.bio.ed.ac.uk/Tracer.
Rannala, B. & Yang, Z. (2013) Improved reversible jump algorithms for Bayesian species delimitation. Genetics, 194, 245-253.
Rellstab, C., F. Gugerli, A. J. Eckert, A. M. Hancock, and R. Holderegger. 2015. A practical guide to environmental association analysis in landscape genomics. Molecular Ecology 24:4348-4370.
Rosenberg, N.A. & Nordborg, M. (2002) Genealogical trees, coalescent theory and the analysis of
genetic polymorphisms. Nature Reviews Genetics, 3, 380-390.
Savolainen, O., M. Lascoux, and J. Merila. 2013.Ecological genomics of local adaptation. Nature Reviews
Genetics 14:807-820.
Schraiber, J. G., and J. M. Akey. 2015. Methods and models for unravelling human evolutionary history.
Nature Reviews Genetics 16:727-740.
Sousa, V., and J. Hey. 2013. Understanding the origin of species with genome-scale data: modelling gene flow. Nature Reviews Genetics 14:404-414.
Sukumaran, J. & Knowles, L.L. (2017) Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America, 14, 1607–1612.
Tsai, Y.-H.E. & Carstens, B. (2013) Assessing model fit in phylogeographical investigations: an example from the North American sandbar willow Salix melanopsis. Journal of Biogeography, 40
Yang, Z. & Rannala, B. (2010) Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences of the United States of America, 107, 9264-9269.
Yang, Z. (2015) The BPP program for species tree estimation and species delimitation. Current Zoology, 61, 854-865. |
