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When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships.

ABSTRACT: DNA barcoding is based on the premise that the barcode sequences can distinguish individuals (strains) of different species because their sequence variation between species exceeds that within species. The primary barcodes used in fungal and yeast taxonomy are the ITS segments and the LSU (large subunit) D1/D2 domain of the homogenized multicopy rDNA repeats. The secondary barcodes are conserved segments of protein-encoding genes, which usually have single copies in haploid genomes. This study shows that the analysis of barcode sequences fails to reconstruct accurate species trees and differentiate species when the organisms have chimeric genomes composed of admixed mosaics of different origins. It is shown that the type strains of 10 species of the pulcherrima clade of the ascomycetous yeast genus Metschnikowia cannot be differentiated with standard barcodes because their intragenomic diversity is comparable to or even higher than the interstrain diversity. The analysis of a large group of genes of the sequenced genomes of the clade and the viability and segregation of the hybrids of ex-type strains indicate that the high intragenomic barcode differences can be attributed to admixed genome structures. Because of the mosaic structures of the genomes, the rDNA repeats do not form continuous arrays and thus cannot be homogenized. Since the highly diverse ITS and D1/D2 sequences of the type strains form a continuous pool including pseudogenes, the evolution of their rDNA appears to involve reticulation. The secondary barcode sequences and the nonbarcode genes included in the analysis show incongruent phylogenetic relationships among the type strains, which can also be attributed to differences in the phylogenetic histories of the genes.

SUBMITTER: Sipiczki M

PROVIDER: S-EPMC9303175 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:We aim to assess the influence of phylogenetic scale on the relationships of taxonomic and phylogenetic turnovers with environment for angiosperms in China. Specifically, we quantify the effects of contemporary climate on β-diversity at different phylogenetic scales representing different evolutionary depths of angiosperms. We sampled a latitudinal gradient and a longitudinal gradient of angiosperm assemblages across China (each ≥3400 km). Species composition in each assemblage was documented. Three metrics of β-diversity (βsim.tax measuring taxonomic β-diversity; βsim.phy and Dpw measuring tip- and basal-weighted phylogenetic β-diversity, respectively) were quantified among assemblages at sequential depths in the evolutionary history of angiosperms from the tips to deeper branches. This was done by slicing the angiosperm phylogenetic tree at six evolutionary depths (0, 15, 30, 45, 60, and 75 million years ago). β-diversity at each evolutionary depth was related to geographic and climatic distances between assemblages. In general, the relationship between β-diversity and climatic distance decreased from shallow to deep evolutionary time slice for all the three metrics. The slopes of the decreasing trends for βsim.tax and βsim.phy were much steeper for the latitudinal gradient than for the longitudinal gradient. The decreasing trend of the strength of the relationship was monotonic in all cases except for Dpw across the longitudinal gradient. Geographic distance between assemblages explained little variation in β-diversity that was not explained by climatic distance. Our study shows that the strength of the relationship between β-diversity and climatic distance decreases conspicuously from shallow to deep evolutionary depth for the latitudinal gradient, but this decreasing trend is less steep for the longitudinal gradient than for the latitudinal gradient, which likely reflects the influence of historical processes (e.g., the collision of the Indian plate with the Eurasian plate) on β-diversity.

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When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships.

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