ArticleScientific reports2017
Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae).
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Plastome Phylogenomic and Biogeographical Study onBioMed research international · 2020Article
- The Origin and Evolution of Plastid Genome Downsizing in Southern Hemispheric Cypresses (Cupressaceae).Frontiers in plant science · 2020Article
- An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae.Applications in plant sciences · 2019Article
- A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae.Annals of botany · 2019Article
- Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae).BMC evolutionary biology · 2018Article
- Plastome characteristics of Cannabaceae.Plant diversity · 2018Article
- Practical considerations for plant phylogenomics.Applications in plant sciences · 2018Review
- Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae).Frontiers in plant science · 2018Article
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5 authors.
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Abstract
Long-branch attraction (LBA) is a major obstacle in phylogenetic reconstruction. The phylogenetic relationships among Juniperus (J), Cupressus (C) and the Hesperocyparis-Callitropsis-Xanthocyparis (HCX) subclades of Cupressoideae are controversial. Our initial analyses of plastid protein-coding gene matrix revealed both J and C with much longer stem branches than those of HCX, so their sister relationships may be attributed to LBA. We used multiple measures including data filtering and modifying, evolutionary model selection and coalescent phylogenetic reconstruction to alleviate the LBA artifact. Data filtering by strictly removing unreliable aligned regions and removing substitution saturation genes and rapidly evolving sites could significantly reduce branch lengths of subclades J and C and recovered a relationship of J (C, HCX). In addition, using coalescent phylogenetic reconstruction could elucidate the LBA artifact and recovered J (C, HCX). However, some valid methods for other taxa were inefficient in alleviating the LBA artifact in J-C-HCX. Different strategies should be carefully considered and justified to reduce LBA in phylogenetic reconstruction of different groups. Three subclades of J-C-HCX were estimated to have experienced ancient rapid divergence within a short period, which could be another major obstacle in resolving relationships. Furthermore, our plastid phylogenomic analyses fully resolved the intergeneric relationships of Cupressoideae.
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