2018
DOI: 10.1016/j.ympev.2018.07.020
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Abstract: Many cases of rapid evolutionary radiations in plant and animal lineages are known; however phylogenetic relationships among these lineages have been difficult to resolve by systematists. Increasing amounts of genomic data have been sequentially applied in an attempt to resolve these radiations, dissecting their evolutionary patterns into a series of bifurcating events. Here we explore one such rapid radiation in the tropical plant order Zingiberales (the bananas and relatives) which includes eight families, a… Show more

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Cited by 57 publications
(53 citation statements)
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References 74 publications
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“…HybPhyloMaker generates contigs by mapping to the reference sequence using BLAT (Kent, ) and calling a consensus sequence for each locus using Kindel v. 0.1.4 (Constantinides and Robertson, ). A 70% majority rule consensus was applied for positions with >4× coverage (Carlsen et al., ). The sequences for each sample after mapping to the three different references were processed to obtain the maximum numbers of loci per sample.…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…HybPhyloMaker generates contigs by mapping to the reference sequence using BLAT (Kent, ) and calling a consensus sequence for each locus using Kindel v. 0.1.4 (Constantinides and Robertson, ). A 70% majority rule consensus was applied for positions with >4× coverage (Carlsen et al., ). The sequences for each sample after mapping to the three different references were processed to obtain the maximum numbers of loci per sample.…”
Section: Methodsmentioning
confidence: 99%
“…[Heyduk et al., ]). Such a lineage‐specific design may also work at higher taxonomic levels (e.g., families Annonaceae [Couvreur et al., ], Arecaceae [de La Harpe et al., ], and Fabaceae [Vatanparast et al., ] and order Zingiberales [Carlsen et al., ]) and even at lower taxonomic levels (e.g., at the population‐level in Euphorbia balsamifera Aiton using a genus‐level probe set for Euphorbia L. [Villaverde et al., ]). In contrast to lineage‐specific probe sets, a universal angiosperm‐wide set for anchored hybrid enrichment of ~400 loci has been developed (Buddenhagen et al., ) that has been successfully applied to a number of studies, for example for Aristolochia L. (Wanke et al., ) and Protea L. (Mitchell et al., ).…”
Section: Aimsmentioning
confidence: 99%
“…The filtered 27 alignments were concatenated and analyzed with BEAST v.2.6.1 (Bouckaert et al 2014) with independent GTR+G models for each gene partition. As a prior, we used a chronogram with relationships fixed based on a Zingiberales phylo-transcriptomic analysis (Carlsen et al 2018) and our concatenated tree. Branch lengths for the prior tree were calculated with IQ-Tree and later parameterized with TreePL (Smith and O'Meara 2012).…”
Section: Phylogenetic Analysismentioning
confidence: 99%
“…Target enrichment is a cost-effective strategy to obtain markers for phylogenetic analysis at multiple taxonomic levels, including a set of markers for the entire flowering plants (angiosperms) (Budenhagen et al, 2016; Johnson et al, 2018). This approach has been successfully applied in several plant families (Carlsen et al, 2018; Comer et al, 2016; Herrando-Morairaa et al, 2018; Mandel et al, 2015, 2014; Moore et al, 2018) and it has proved useful to reconstruct relationships among closely related genera, within the same genus (Bogarin et al, 2018; Fragoso-Martíneza et al, 2017; Heyduk et al, 2016; Mitchell et al, 2017; Schmickl et al, 2016) and at species level (Nicholls et al, 2015; Villaverde et al, 2018). Within Leguminosae, this approach has been applied on lineages of the Papilionoideae and Caesalpinoideae (De Sousa et al, 2014; Nicholls et al, 2015; Ogutcen et al, 2018; Vatanparast et al, 2018) and our study is the first to use target enrichment outside these subfamilies using a complete sampling representing the entire extant diversity of the target group.…”
Section: Discussionmentioning
confidence: 99%