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Abstract Detail

Recent Topics Posters

Liu, Tongjian [1], Yan, Haifei [2], Hao, Gang [1], Ge, Xuejun [3].

Phylogenomic Analysis reveal conflicting evolutionary histories of nuclear and chloroplast in a recent radiation group Primula L. (Primulaceae).

Despite Information-rich datasets from genomic level sequences are common used in recent phylogenetic and evolutionary studies, the species relationships inferred from hundreds or thousands of genes are still a challenge with underlying phylogenetic signal conflicts. Especially, it is unclear that the extent of these conflicts within or between two genomic regions, nuclear and chloroplast, from rapid diversification plants. We examined Primula, considered as a rapid radiation plant group in Himalaya-Hengduan mountains, which contains 24 sections ca. 300 species in this area, as a typical example for species tree reconstruction and unveiling gene conflicts behind phylogenomic inference. 81 transcriptomes (74 newly sequencing in this study) and 12 chloroplast genomes were used to generate two datasets. The first one only includes nuclear transcripts, and second compose of chloroplast transcripts and genomic sequences, both were analyzed by concatenation and coalescent-based phylogenetic methods. We also analyzed gene tree supporting and conflicting patterns for each node on the species tree and estimated paired RF-distance to explore the distribution of gene trees in tree space. Furthermore, divergence time estimate was performed on filtered clocklike genes based on each topology hypothesis. We found all phylogenomic analyses using nuclear genes obtained well-support topologies but exhibit extensive conflicts among gene trees. The chloroplast phylogenies basically agreed with the previous studies from limited chloroplast barcode markers, and it is significantly different from phylogenies inferred by nuclear dataset. However, there is a remarkable shift that Omphalogramma vinciflorum was placed in Primula in all nuclear phylogenies, with a stronger gene conflict than other backbone nodes. We demonstrate this shift not only supported by the majority of nuclear genes, also supported by part of chloroplast genes, while the “right” phylogeny (sister to Primula) is driven by the rest of genes. Finally, divergence time inferred from two alternative phylogenetic hypotheses with filtered clocklike genes may prove to be a practical way for large dataset and the MCRA nodes were very close to each other. Our result of phylotranscriptomic analyses in Primula provides an evidence for 1) significant incongruence between nuclear and chloroplast phylogenies; 2) extensive underlying gene conflicts found behind the well-support phylogeny; 3) gene tree supporting pattern could determine the bias dominated by a small subset of genes with distinctive and strong conflict signals; And 4) “gene shopping” could be a better solution for dating analysis and returns reasonable ages on a large phylogenomic dataset.

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1 - South China Agricultural University, College of Life Sciences, Guangzhou, Guangdong, 510642, China
2 - Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, China
3 - South China Botanical Garden, Chinese Academy Of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou, 510650, China

gene tree conflict
clock-like gene
orthology inference

Presentation Type: Recent Topics Poster
Session: P, Recent Topics Posters
Location: Grand Ballroom - Exhibit Hall/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 5:30 PM
Number: PRT022
Abstract ID:1315
Candidate for Awards:None

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