Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)

Foster, Charles S. P.; Henwood, Murray J.; Ho, Simon Y. W.

doi:10.1016/j.ympev.2018.05.018

Cited by 25 publications

(25 citation statements)

References 64 publications

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“…In this study, inclusion of non-coding regions altered tree topology in the tribe Laureae, suggesting the existence of a conflicting signal between coding and non-coding regions. Non-coding regions are often discarded for being uninformative, or for being misleading due to saturation at deep time scales ( Foster, Henwood & Ho, 2018 ). In our study, tree topologies based on coding and non-coding regions were largely congruent, except for the relationships among the three subclades ( Figs.…”

Section: Discussionmentioning

confidence: 99%

“…Most relevant studies have focused on incongruent tree topologies among different genomic compartments ( Sun et al, 2015 ; Zhao et al, 2016 ; Walker et al, 2019 ) because these genes have evolved independently and their gene tree topologies have been influenced by biological processes. By contrast, relatively few studies have focused on tree conflicts among plastid genes (e.g., Foster, Henwood & Ho, 2018 ; Gonçalves et al, 2019 ; Walker et al, 2019 ; Zhang et al, 2020 ). Usually, plastomes are considered to be uniparentally inherited and to have evolved as a single unit, free from such biological sources of conflict ( Birky, 1995 ; Wicke et al, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

“…Heteroplasmy may, in rare cases, give rise to heteroplasmic recombination, which has been invoked to explain gene tree discordance ( Marshall, Newton & Ritland, 2001 ; Sullivan et al, 2017 ; Sancho et al, 2018 ). In addition to recombination events, the transfer of genes among plastid, mitochondrial and nuclear genomes; positive selection; tree length (a proxy for evolutionary rate); and GC content may also generate phylogenomic conflict (e.g., Stegemann et al, 2003 ; Smith, 2014 ; Wysocki et al, 2015 ; Piot et al, 2018 ; Saarela et al, 2018 ; Foster, Henwood & Ho, 2018 ). Aside from biological factors, non-biological factors (e.g., outlier genes, uninformative loci, and gaps) may cause conflict as well.…”

Section: Introductionmentioning

confidence: 99%

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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Xiao

Jin

et al. 2020

PeerJ

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Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)

Xiao

Jin

et al. 2020

PeerJ

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“…Chloroplast data are used at various time scales, and the accumulation of substitutions over long periods of evolutionary time increases the probability of encountering systematic error due to saturation (Rodríguez-Ezpeleta et al, 2007; Philippe et al, 2011). Conflict has been demonstrated among different functional groups of genes (Liu et al, 2012), among different regions of the plastome (Davis et al, 2013; Walker, Zanis & Emery, 2014), as well as among individual genes (e.g., Shepherd, Holland & Perrie, 2008; Foster, Henwood & Ho, 2018; Gonçalves et al, 2019). The rate of chloroplast evolution as a whole has been examined (and compared with the nuclear and mitochondrial genomes; Wolfe, Li & Sharp, 1987), and rate variation within the chloroplast—especially across the three major regions of the genome, i.e., the large single-copy (LSC) region, the small single-copy (SSC) region, and the inverted repeats (IRa, IRb)—has been explored to help determine the markers useful for phylogenetic inference at different time scales (e.g., Graham & Olmstead, 2000; Shaw et al, 2005; Shaw et al, 2007; Shaw et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Characterizing gene tree conflict in plastome-inferred phylogenies

Walker

Walker-Hale

Vargas

et al. 2019

PeerJ

101

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Evolutionary relationships among plants have been inferred primarily using chloroplast data. To date, no study has comprehensively examined the plastome for gene tree conflict. Using a broad sampling of angiosperm plastomes, we characterize gene tree conflict among plastid genes at various time scales and explore correlates to conflict (e.g., evolutionary rate, gene length, molecule type). We uncover notable gene tree conflict against a backdrop of largely uninformative genes. We find alignment length and tree length are strong predictors of concordance, and that nucleotides outperform amino acids. Of the most commonly used markers, matK, greatly outperforms rbcL; however, the rarely used gene rpoC2 is the top-performing gene in every analysis. We find that rpoC2 reconstructs angiosperm phylogeny as well as the entire concatenated set of protein-coding chloroplast genes. Our results suggest that longer genes are superior for phylogeny reconstruction. The alleviation of some conflict through the use of nucleotides suggests that stochastic and systematic error is likely the root of most of the observed conflict, but further research on biological conflict within plastome is warranted given documented cases of heteroplasmic recombination. We suggest that researchers should filter genes for topological concordance when performing downstream comparative analyses on phylogenetic data, even when using chloroplast genomes.

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“…Chloroplast data are used at various time scales, and the accumulation of substitutions over long periods of evolutionary time increases the probability of encountering systematic error due to saturation (Rodríguez-Ezpeleta et al, 2007; Philippe et al, 2011). Conflict has been demonstrated among different functional groups of genes (Liu et al, 2012), among different regions of the plastome (Walker et al, 2014), as well as among individual genes (e.g., Shepherd et al, 2008, Foster et al 2018). The rate of chloroplast evolution as a whole has been examined (and compared with the nuclear and mitochondrial genomes; Wolfe, 1987), and rate variation within the chloroplast—especially across the three major regions of the genome, i.e., the long single-copy (LSC) region, the short single-copy (SSC) region, and the inverted repeats (IRa, IRb)—has been explored to help determine the markers useful for phylogenetic inference at different time scales (e.g., Graham and Olmstead, 2000; Shaw et al, 2005, 2007, 2014).…”

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confidence: 99%