A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae1

  title={A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae1},
  author={Jennifer R. Mandel and Rebecca B. Dikow and Vicki A. Funk and Rishi R. Masalia and S. Evan Staton and Alexander Kozik and Richard W. Michelmore and Loren H. Rieseberg and John M. Burke},
  journal={Applications in Plant Sciences},
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous… 

Using phylogenomics to resolve mega‐families: An example from Compositae

Target capture of low copy sequences followed by next‐generation sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae) provides a solid foundation for future work aimed at understanding gene family evolution in the compositae as well as providing a model for phylogenomic analyses in other plant mega‐families.

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This study inferred a Br Jurassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes.

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The selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well‐supported clades, but nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids.



Universal markers for comparative mapping and phylogenetic analysis in the Asteraceae (Compositae)

The results indicate that these loci are phylogenetically informative, and hence can be used to resolve evolutionary relationships between taxa within the family as well as within species.

The value of sampling anomalous taxa in phylogenetic studies: major clades of the Asteraceae revealed.

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It is suggested that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies.

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This work reveals for the first time a highly resolved gene tree for Helianthus and suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids.

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A method to multiplex the analysis of up to eight samples was developed and sequence data showed that multiplexed capture was reproducible among 24 haploid samples, and can be applied for high-throughput analysis of targeted genes in large populations.

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A revised generic-level classification is presented that divides the approximately 350 species of the subtribe among 21 genera, andalyses of the two molecular datasets provided conflicting evidence on relationships among some groups, supporting the hypothesis that hybridization has played a significant role in the divergence of thesubribe.