Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallic Me
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ORIGINAL PAPER
Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallic Metschnikowia species Marc-Andre´ Lachance
. Dong Kyung Lee . Tom Hsiang
Received: 1 August 2020 / Accepted: 2 October 2020 Ó Springer Nature Switzerland AG 2020
Abstract We determined pairwise average nucleotide identity (ANI) values for the genomes of 71 strains assigned to 36 Metschnikowia species, 28 of which were represented by multiple isolates selected to represent the range of genetic diversity of the species, and most of which were defined on the basis of reproductive isolation. Similar to what has been proposed for prokaryote species delineation, an ANI value of 95% emerged as a good guideline for the delineation of yeast species, although some overlap exists, whereby members of a reproductive community could have slightly lower values (e.g., 94.3% for M. kamakouana), and representatives of distinct sister species could give slightly higher values (e.g., 95.2% for the sister species M. drakensbergensis and M. proteae). Unlike what is observed in prokaryotes, a sizeable gap between intraspecific and interspecific ANI values was not encountered. Given the ease with which yeast draft genomes can now be obtained, ANI Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10482-020-01480-9) contains supplementary material, which is available to authorized users. M.-A. Lachance (&) D. K. Lee Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada e-mail: [email protected] T. Hsiang School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
values are poised to become the new standard upon which yeast species may be delineated on genetic distance. As borderline cases exist, however, the delineation of yeast species will continue to require careful evaluation of all available data. We also explore the often-neglected distinction between phylogenetic relatedness and sequence identity through the analysis of a tree constructed from ANI’ (100 - ANI) values. Keywords Yeast Species delineation Average nucleotide identity (ANI) Phylogenetic vs genetic distance Metschnikowia
Introduction Over a century before the advent of modern phylogenetics, Darwin (1859) anticipated that once in possession of the tree of life we would ‘‘at least be freed from the vain search for the undiscovered and undiscoverable essence of the term species’’. Quite exceptionally, this prophecy remains unfulfilled. In spite of the resounding success of molecular phylogenetics in the last two decades, a practical concept of species, at least as applied to yeasts, is not entirely resolved. Ideally, the pivotal unit of classification should describe populations that share a common, cohesive evolutionary history (i.e., evolutionary species, Mayden 1997).
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Antonie van Leeuwenhoek
Other species concepts are deemed operational, in that they use properties of in
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