Phylogenies in yeast species descriptions: In defense of neighbor‐joining

Abstract

The neighbor-joining (NJ) method of tree inference is examined, with special attention to its use in yeast species descriptions. How the often-vilified method works is often misunderstood. More importantly, given the right kind of data, its output is a phylogram that illustrates a hypothetical phylogeny that is just as credible as that obtained by any other method. And as with any other method, the result is greatly affected by sampling intensity, particularly the number of aligned positions used for analysis. I address various allegations, including the claim that the method is phenetic, and, therefore, not phylogenetic. I argue that NJ is the most suitable tree inference method to use in yeast species descriptions, primarily because it is best at visually preserving the extent of sequence divergence between close relatives, which continues to be the primary criterion for yeast species delineation. The relevance of bootstraps in the application of the phylogenetic species concept is discussed.

Spathaspora brunopereirae sp. nov. and Spathaspora domphillipsii sp. nov., two d-xylose-fermenting ascosporogenous yeasts from Amazonian Forest biomes

“…A neighbour-joining phylogram based on D1/D2 sequences was reconstructed with mega 6 from an alignment of 558 positions. The distance metric was the number of substitutions, calculated pairwise [22]. Bootstrap values were determined from 1000 pseudoreplications.…”

Teunomyces gombertii f.a., sp. nov., Teunomyces landelliae f.a., sp. nov., Teunomyces ledahaglerae f.a., sp. nov. and Teunomyces paulamoraisiae f.a., sp. nov., four yeast species isolated from mushrooms and drosophilids in a Brazilian Amazonian rainforest biome

“…The mention forma asexualis (f.a.) is added as a reminder that the sexual state is not known [31]. Isolates UFMG-CM-Y6355 and UFMG-CM-Y7245 presented identical ITS 5.8S and D1/D2 sequences and were phylogenetically related to T. aglyptinius .…”

Yueomyces silvicola sp. nov., a novel ascomycetous yeast species unable to utilize ammonium, glutamate, and glutamine as sole nitrogen sources

“…Sequences of closely related strains or species were retrieved from GenBank and were aligned using CLUSTAL_X version 1.81 (Thompson, 1997). Phylogenetic analyses were performed based on the evolutionary distance data calculated from Kimura's two‐parameter model (Kimura, 1980) using the neighbor‐joining algorithm executed in MEGA v.7 (Kumar et al, 2016; Lachance, 2022; Saitou & Nei, 1987). The confidence levels of the clades were estimated through bootstrap analysis with 1000 replicates (Felsenstein, 1985).…”

“…Phylogenetic analyses were performed based on the evolutionary distance data calculated from Kimura's two-parameter model (Kimura, 1980) using the neighbor-joining algorithm executed in MEGA v.7 (Kumar et al, 2016;Lachance, 2022;Saitou & Nei, 1987).…”