References
Acosta, M.C., Mathiasen, P., and Premoli, A.C. (2014). Retracing the evolutionary history of Nothofagus in its geo-climatic context: new developments in the emerging field of phylogeology. Geobiology12 , 497-510.
Agier, N., Delmas, S., Zhang, Q., Fleiss, A., Jaszczyszyn, Y., van Dijk, E., Thermes, C., Weigt, M., Cosentino-Lagomarsino, M., and Fischer, G. (2018). The evolution of the temporal program of genome replication. Nat Commun 9 , 2199.
Almeida, P., Barbosa, R., Zalar, P., Imanishi, Y., Shimizu, K., Turchetti, B., Legras, J.L., Serra, M., Dequin, S., Couloux, A., et al. (2015). A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol Ecol 24 , 5412-5427.
Almeida, P., Goncalves, C., Teixeira, S., Libkind, D., Bontrager, M., Masneuf-Pomarede, I., Albertin, W., Durrens, P., Sherman, D.J., Marullo, P., et al. (2014). A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun5 , 4044.
Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online at:http://wwwbioinformaticsbabrahamacuk/projects/fastqc(accessed December 5, 2019).
Banilas, G., Sgouros, G., and Nisiotou, A. (2016). Development of microsatellite markers for Lachancea thermotolerans typing and population structure of wine-associated isolates. Microbiol Res193 , 1-10.
Bansal, V., and Boucher, C. (2019). Sequencing Technologies and Analyses: Where Have We Been and Where Are We Going? iScience 18 , 37-41.
Bellut, K., Krogerus, K., and Arendt, E.K. (2020). Lachancea fermentati Strains Isolated From Kombucha: Fundamental Insights, and Practical Application in Low Alcohol Beer Brewing. Front Microbiol 11 , 764.
Bendixsen, D.P., Gettle, N., Gilchrist, C., Zhang, Z., and Stelkens, R. (2021). Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae. Genome Biol Evol 13 .
Bouckaert, R., Vaughan, T.G., Barido-Sottani, J., Duchene, S., Fourment, M., Gavryushkina, A., Heled, J., Jones, G., Kuhnert, D., De Maio, N., et al. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 15 , e1006650.
Bouckaert, R.R. (2010). DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 26 , 1372-1373.
Brickwedde, A., Brouwers, N., van den Broek, M., Gallego Murillo, J.S., Fraiture, J.L., Pronk, J.T., and Daran, J.G. (2018). Structural, Physiological and Regulatory Analysis of Maltose Transporter Genes in Saccharomyces eubayanus CBS 12357(T). Front Microbiol 9 , 1786.
Brion, C., Legrand, S., Peter, J., Caradec, C., Pflieger, D., Hou, J., Friedrich, A., Llorente, B., and Schacherer, J. (2017). Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts. PLoS Genet 13 , e1006917.
Browning, S.R., and Browning, B.L. (2007). Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81 , 1084-1097.
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N.A., and RoyChoudhury, A. (2012). Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29 , 1917-1932.
Cadez, N., Bellora, N., Ulloa, R., Hittinger, C.T., and Libkind, D. (2019). Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PLoS One 14 , e0210792.
Cadez, N., Bellora, N., Ulloa, R., Tome, M., Petkovic, H., Groenewald, M., Hittinger, C.T., and Libkind, D. (2021). Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments. Front Microbiol 12 , 679894.
Chen, J., Shen, W., Xu, H., Li, Y., and Luo, T. (2019). The Composition of Nitrogen-Fixing Microorganisms Correlates With Soil Nitrogen Content During Reforestation: A Comparison Between Legume and Non-legume Plantations. Front Microbiol 10 , 508.
Chen, S., Zhou, Y., Chen, Y., and Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34 , i884-i890.
Cubillos, F.A., Gibson, B., Grijalva-Vallejos, N., Krogerus, K., and Nikulin, J. (2019). Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast 36 , 383-398.
Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics (Oxford, England) 27 , 2156-2158.
Dashko, S., Zhou, N., Compagno, C., and Piskur, J. (2014). Why, when, and how did yeast evolve alcoholic fermentation? FEMS Yeast Res14 , 826-832.
Davies, B.J., Darvill, C.M., Lovell, H., Bendle, J.M., Dowdeswell, J.A., Fabel, D., Garcia, J.L., Geiger, A., Glasser, N.F., Gheorghiu, D.M., et al. (2020). The evolution of the Patagonian Ice Sheet from 35 ka to the present day (PATICE). Earth-Sci Rev 204 .
DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., Philippakis, A.A., del Angel, G., Rivas, M.A., Hanna, M., et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet43 , 491-498.
Dujon, B.A., and Louis, E.J. (2017). Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina). Genetics 206 , 717-750.
Esteve-Zarzoso, B., Peris-Toran, M.J., Garcia-Maiquez, E., Uruburu, F., and Querol, A. (2001). Yeast population dynamics during the fermentation and biological aging of sherry wines. Appl Environ Microbiol 67 , 2056-2061.
Evanno, G., Regnaut, S., and Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14 , 2611-2620.
Fay, J.C., and Benavides, J.A. (2005). Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet 1 , 66-71.
Ford, C.B., Funt, J.M., Abbey, D., Issi, L., Guiducci, C., Martinez, D.A., Delorey, T., Li, B.Y., White, T.C., Cuomo, C., et al.(2015). The evolution of drug resistance in clinical isolates of Candida albicans. Elife 4 , e00662.
Fournier, T., Gounot, J.S., Freel, K., Cruaud, C., Lemainque, A., Aury, J.M., Wincker, P., Schacherer, J., and Friedrich, A. (2017). High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing. G3 (Bethesda) 7 , 3243-3250.
Friedrich, A., Jung, P., Reisser, C., Fischer, G., and Schacherer, J. (2015). Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast. Mol Biol Evol 32 , 184-192.
Friedrich, A., Jung, P.P., Hou, J., Neuveglise, C., and Schacherer, J. (2012). Comparative mitochondrial genomics within and among yeast species of the Lachancea genus. PLoS One 7 , e47834.
Fujita, S.I., Senda, Y., Nakaguchi, S., and Hashimoto, T. (2001). Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains. J Clin Microbiol39 , 3617-3622.
Gabaldon, T., and Fairhead, C. (2019). Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal. Curr Genet65 , 93-98.
Gallone, B., Steensels, J., Prahl, T., Soriaga, L., Saels, V., Herrera-Malaver, B., Merlevede, A., Roncoroni, M., Voordeckers, K., Miraglia, L., et al. (2016). Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell 166 , 1397-1410 e1316.
García-Alcalde, F., Okonechnikov, K., Carbonell, J., Cruz, L.M., Götz, S., Tarazona, S., Dopazo, J., Meyer, T.F., and Conesa, A. (2012). Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28 , 2678-2679.
Gerstein, A.C., Cleathero, L.A., Mandegar, M.A., and Otto, S.P. (2011). Haploids adapt faster than diploids across a range of environments. J Evol Biol 24 , 531-540.
Gerstein, A.C., and Otto, S.P. (2009). Ploidy and the causes of genomic evolution. J Hered 100 , 571-581.
Goncalves, M., Pontes, A., Almeida, P., Barbosa, R., Serra, M., Libkind, D., Hutzler, M., Goncalves, P., and Sampaio, J.P. (2016). Distinct Domestication Trajectories in Top-Fermenting Beer Yeasts and Wine Yeasts. Curr Biol 26 , 2750-2761.
Gonzalez, S.S., Barrio, E., and Querol, A. (2007). Molecular identification and characterization of wine yeasts isolated from Tenerife (Canary Island, Spain). J Appl Microbiol 102 , 1018-1025.
Gounot, J.S., Neuveglise, C., Freel, K.C., Devillers, H., Piskur, J., Friedrich, A., and Schacherer, J. (2020). High Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population. Genome Biol Evol 12 , 795-807.
Guaragnella, N., Chiara, M., Capece, A., Romano, P., Pietrafesa, R., Siesto, G., Manzari, C., and Pesole, G. (2019). Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential. Front Microbiol10 , 3133.
Hagman, A., Sall, T., and Piskur, J. (2014). Analysis of the yeast short-term Crabtree effect and its origin. FEBS J 281 , 4805-4814.
Hall, B.G., Acar, H., Nandipati, A., and Barlow, M. (2014). Growth rates made easy. Mol Biol Evol 31 , 232-238.
Hewitt, G. (2000). The genetic legacy of the Quaternary ice ages. Nature405 , 907-913.
Hill, R.S. (1992). Nothofagus: Evolution from a southern perspective. Trends Ecol Evol 7 , 190-194.
Hinojosa, L.F., Gaxiola, A., Perez, M.F., Carvajal, F., Campano, M.F., Quattrocchio, M., Nishida, H., Uemura, K., Yabe, A., Bustamante, R., et al. (2016). Non-congruent fossil and phylogenetic evidence on the evolution of climatic niche in the Gondwana genus Nothofagus. Journal of Biogeography 43 , 555-567.
Hinojosa, L.F.V., C. (1997). Historia de los bosques del sur de Sudamérica, I: antecedentes paleobotánicos, geológicos y climáticos del Terciario del cono sur de América. Rev Chil Hist Nat 70 , 225-239.
Hirakawa, M.P., Martinez, D.A., Sakthikumar, S., Anderson, M.Z., Berlin, A., Gujja, S., Zeng, Q., Zisson, E., Wang, J.M., Greenberg, J.M., et al. (2015). Genetic and phenotypic intra-species variation in Candida albicans. Genome Res 25 , 413-425.
Hoang, D.T., Chernomor, O., von Haeseler, A., Minh, B.Q., and Vinh, L.S. (2018). UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 35 , 518-522.
Hranilovic, A., Bely, M., Masneuf-Pomarede, I., Jiranek, V., and Albertin, W. (2017). The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems. PLoS One 12 , e0184652.
Hranilovic, A., Gambetta, J.M., Schmidtke, L., Boss, P.K., Grbin, P.R., Masneuf-Pomarede, I., Bely, M., Albertin, W., and Jiranek, V. (2018). Oenological traits of Lachancea thermotolerans show signs of domestication and allopatric differentiation. Sci Rep 8 , 14812.
Kessi-Perez, E.I., Araos, S., Garcia, V., Salinas, F., Abarca, V., Larrondo, L.F., Martinez, C., and Cubillos, F.A. (2016). RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Res 16 .
Kodama, K., and Kyono, T. (1974). Ascosporogenous yeasts isolated from tree exudates in Japan. v. 52 .
Kopelman, N.M., Mayzel, J., Jakobsson, M., Rosenberg, N.A., and Mayrose, I. (2015). Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour15 , 1179-1191.
Kurtzman, C. (2003). Phylogenetic circumscription of , and other members of the Saccharomycetaceae, and the proposal of the new genera , , , and. FEMS Yeast Research 4 , 233-245.
Lachance, M.-A., and Kurtzman, C.P. (2011). Lachancea. In The Yeasts, pp. 511-519.
Langdon, Q.K., Peris, D., Eizaguirre, J.I., Opulente, D.A., Buh, K.V., Sylvester, K., Jarzyna, M., Rodriguez, M.E., Lopes, C.A., Libkind, D., et al. (2020). Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids. PLoS Genet 16 , e1008680.
Lawson, D.J., Hellenthal, G., Myers, S., and Falush, D. (2012). Inference of population structure using dense haplotype data. PLoS Genet8 , e1002453.
Leache, A.D., Fujita, M.K., Minin, V.N., and Bouckaert, R.R. (2014). Species delimitation using genome-wide SNP data. Syst Biol 63 , 534-542.
Lee, C.F., Yao, C.H., Liu, Y.R., Hsieh, C.W., and Young, S.S. (2009). Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan. Int J Syst Evol Microbiol 59 , 1818-1822.
Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 1303 .
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 , 2078-2079.
Li, Y.L., and Liu, J.X. (2018). StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Mol Ecol Resour 18 , 176-177.
Libkind, D., Hittinger, C.T., Valerio, E., Goncalves, C., Dover, J., Johnston, M., Goncalves, P., and Sampaio, J.P. (2011). Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci U S A 108 , 14539-14544.
Lindenbaum, P., and Redon, R. (2018). bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. Bioinformatics 34 , 1224-1225.
Liti, G., Carter, D.M., Moses, A.M., Warringer, J., Parts, L., James, S.A., Davey, R.P., Roberts, I.N., Burt, A., Koufopanou, V., et al. (2009). Population genomics of domestic and wild yeasts. Nature458 , 337-341.
Liu, W., Luo, Z., Wang, Y., Pham, N.T., Tuck, L., Pérez-Pi, I., Liu, L., Shen, Y., French, C., Auer, M., et al. (2018). Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nature Communications 9 , 1936.
Lynch, M., Sung, W., Morris, K., Coffey, N., Landry, C.R., Dopman, E.B., Dickinson, W.J., Okamoto, K., Kulkarni, S., Hartl, D.L., et al.(2008). A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci U S A 105 , 9272-9277.
Magalhães, K.T., de Melo Pereira, G.V., Campos, C.R., Dragone, G., and Schwan, R.F. (2011). Brazilian kefir: structure, microbial communities and chemical composition. Braz J Microbiol 42 , 693-702.
Marsh, A.J., O’Sullivan, O., Hill, C., Ross, R.P., and Cotter, P.D. (2014). Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiol 38 , 171-178.
Mesquita, V.A., Magalhães-Guedes, K., Silva, C., and Schwan, R. (2013). The molecular phylogenetic diversity of bacteria and fungi associated with the cerrado soil from different regions of Minas Gerais, Brazil. Int J Microbiol Res 4 , 119-131.
Mirza, B.S., Potisap, C., Nusslein, K., Bohannan, B.J., and Rodrigues, J.L. (2014). Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest. Appl Environ Microbiol80 , 281-288.
Morata, A., Loira, I., Tesfaye, W., Bañuelos, M., González, C., and Suárez Lepe, J. (2018). Lachancea thermotolerans Applications in Wine Technology. Fermentation 4 .
Nespolo, R.F., Solano-Iguaran, J.J., Paleo-Lopez, R., Quintero-Galvis, J.F., Cubillos, F.A., and Bozinovic, F. (2020a). Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts. Ecol Evol 10 , 5240-5250.
Nespolo, R.F., Villarroel, C.A., Oporto, C.I., Tapia, S.M., Vega-Macaya, F., Urbina, K., De Chiara, M., Mozzachiodi, S., Mikhalev, E., Thompson, D., et al. (2020b). An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages. PLoS Genet 16 , e1008777.
Nguyen, L.T., Schmidt, H.A., von Haeseler, A., and Minh, B.Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32 , 268-274.
Nova, M.X.V., Schuler, A.R.P., Brasileiro, B.T.R.V., and Morais, M.A. (2009). Yeast species involved in artisanal cachaça fermentation in three stills with different technological levels in Pernambuco, Brazil. Food Microbiology 26 , 460-466.
Ortiz., E.M. (2019). vcf2phylip v2.0: convert a VCF matrix into several matrix formats for phylogenetic analysis. (Zenodo.https://doi.org/10.5281/zenodo.2540861).
Parts, L., Batte, A., Lopes, M., Yuen, M.W., Laver, M., San Luis, B.J., Yue, J.X., Pons, C., Eray, E., Aloy, P., et al. (2021). Natural variants suppress mutations in hundreds of essential genes. Mol Syst Biol 17 , e10138.
Passer, A.R., Coelho, M.A., Billmyre, R.B., Nowrousian, M., Mittelbach, M., Yurkov, A.M., Averette, A.F., Cuomo, C.A., Sun, S., and Heitman, J. (2019). Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens. mBio 10 .
Patterson, N., Price, A.L., and Reich, D. (2006). Population structure and eigenanalysis. PLoS Genet 2 , e190.
Peakall, R., and Smouse, P.E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research–an update. Bioinformatics 28 , 2537-2539.
Pembleton, L.W., Cogan, N.O., and Forster, J.W. (2013). StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations. Mol Ecol Resour 13 , 946-952.
Pereira, L.F., Costa, C.R.L., Brasileiro, B., and de Morais, M.A. (2011). Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaca fermentation process. Int J Syst Evol Microbiol61 , 989-992.
Peter, J., De Chiara, M., Friedrich, A., Yue, J.X., Pflieger, D., Bergstrom, A., Sigwalt, A., Barre, B., Freel, K., Llored, A., et al. (2018). Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature 556 , 339-344.
Peter, J., and Schacherer, J. (2016). Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale. Yeast33 , 73-81.
Pfeifer, B., Wittelsburger, U., Ramos-Onsins, S.E., and Lercher, M.J. (2014). PopGenome: an efficient Swiss army knife for population genomic analyses in R. Mol Biol Evol 31 , 1929-1936.
Pfliegler, W.P., Horvath, E., Kallai, Z., and Sipiczki, M. (2014). Diversity of Candida zemplinina isolates inferred from RAPD, micro/minisatellite and physiological analysis. Microbiol Res169 , 402-410.
Phaff, H.J., Miller, M.W., and Shifrine, M. (1956). The taxonomy of yeasts isolated from Drosophila in the Yosemite region of California. Antonie Van Leeuwenhoek 22 , 145-161.
Piskur, J., Rozpedowska, E., Polakova, S., Merico, A., and Compagno, C. (2006). How did Saccharomyces evolve to become a good brewer? Trends Genet 22 , 183-186.
Ponce JF, and M., F. (2014). Climatic and Environmental History of Isla de los Estados, Argentina.
Porter, T.J., Divol, B., and Setati, M.E. (2019a). Investigating the biochemical and fermentation attributes of Lachancea species and strains: Deciphering the potential contribution to wine chemical composition. Int J Food Microbiol 290 , 273-287.
Porter, T.J., Divol, B., and Setati, M.E. (2019b). Lachancea yeast species: Origin, biochemical characteristics and oenological significance. Food Res Int 119 , 378-389.
Ramasamy, R.K., Ramasamy, S., Bindroo, B.B., and Naik, V.G. (2014). STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. SpringerPlus 3 , 431.
Rambaut, A., Drummond, A.J., Xie, D., Baele, G., and Suchard, M.A. (2018). Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol 67 , 901-904.
Romano, P., and Suzzi, G. (1993a). Higher alcohol and acetoin production by Zygosaccharomyces wine yeasts. Journal of Applied Bacteriology75 , 541-545.
Romano, P., and Suzzi, G. (1993b). Potential use for Zygosaccharomyces species in winemaking. Journal of Wine Research 4 , 87-94.
Ruderfer, D.M., Pratt, S.C., Seidel, H.S., and Kruglyak, L. (2006). Population genomic analysis of outcrossing and recombination in yeast. Nat Genet 38 , 1077-1081.
Sampaio, J.P., and Goncalves, P. (2008). Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus. Appl Environ Microbiol 74 , 2144-2152.
Team, R.D.C. (2008). R: A Lenguage and Environment for Statisctical Computing. R Foundation for Statistical Computing.
Tzanetakis, N., Hatzikamari, M., and Litopoulou-Tzanetaki, E. (1998). Yeasts of the surface microflora of Feta cheese.
Vakirlis, N., Hebert, A.S., Opulente, D.A., Achaz, G., Hittinger, C.T., Fischer, G., Coon, J.J., and Lafontaine, I. (2018). A Molecular Portrait of De Novo Genes in Yeasts. Mol Biol Evol 35 , 631-645.
Vakirlis, N., Sarilar, V., Drillon, G., Fleiss, A., Agier, N., Meyniel, J.P., Blanpain, L., Carbone, A., Devillers, H., Dubois, K., et al. (2016). Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res 26 , 918-932.
Van der Auwera, G.A., Carneiro, M.O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013a). From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Current protocols in bioinformatics 43 , 11.10.11-33.
Van der Auwera, G.A., Carneiro, M.O., Hartl, C., Poplin, R., Del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013b). From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 43 , 11.10.11-11.10.33.
Varela, C., Sundstrom, J., Cuijvers, K., Jiranek, V., and Borneman, A. (2020). Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii. Sci Rep 10 , 14716.
Villarreal, P., Quintrel, P.A., Olivares-Muñoz, S., Ruiz, J.I., Nespolo, R.F., and Cubillos, F.A. (2021). Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia. Yeast.
Weir, B.S., and Cockerham, C.C. (1984). Estimating F-Statistics for the Analysis of Population Structure. Evolution 38 , 1358-1370.
Wojtatowicz, M., Chrzanowska, J., Juszczyk, P., Skiba, A., and Gdula, A. (2001). Identification and biochemical characteristics of yeast microflora of Rokpol cheese. International Journal of Food Microbiology69 , 135-140.
Woodward, F.I., Lomas, M.R., and Kelly, C.K. (2004). Global climate and the distribution of plant biomes. Philos Trans R Soc Lond Ser B-Biol Sci359 , 1465-1476.