首页|Phylotranscriptomic discordance is best explained by incomplete lineage sorting within Allium subgenus Cyathophora and thus hemiplasy accounts for interspecific trait transition

Phylotranscriptomic discordance is best explained by incomplete lineage sorting within Allium subgenus Cyathophora and thus hemiplasy accounts for interspecific trait transition

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The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification.Much can be learned about this process from phylogeny-based trait evolution.However,such inference is often plagued by genome-wide gene-tree discordance(GTD),mostly due to incomplete lineage sorting(ILS)and/or introgressive hybridization,especially when the genes underlying the traits appear discordant.Here,by collecting transcriptomes,whole chloroplast genomes(cpDNA),and population genetic datasets,we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent"phylogenetic discordance"between different morphological traits and probable species phy-logeny in the Allium subg.Cyathophora.Both concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes(SCGs),as supported by the Ks distribution.However,GTD was high across the genomes of subg.Cyathophora:-27％-38.9％of the SCG trees were in conflict with the species tree.Plasmid and nuclear incongruence was also present.Our coalescent simulations indicated that such GTD was mainly a product of ILS.Our hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the subg.Cyathophora phylogeny may have caused the character transition,as well as the anomalous cpDNA tree.Our study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.

HemiplasyMultispecies coalescenceLineage sortingGene tree discordancePhylotranscriptomicsAllium subg.Cyathophora

Zengzhu Zhang、Gang Liu、Minjie Li

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State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems,College of Ecology,Lanzhou University,Lanzhou 730000,Gansu,PR China

Key Science and Technology Project of Gansu Province国家重点研发计划Supercomputing Center of Lanzhou University

22ZD6NA0072021YFD2200202

2024

10.1016/j.pld.2023.07.004

植物多样性(英文)
中国科学院昆明植物研究所，中国植物学会

植物多样性(英文)

CSTPCD
影响因子：0.617
ISSN：2096-2703
年,卷(期)：2024.46(1)
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