Skip to main content

Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon.

Publication ,  Journal Article
Wessinger, CA; Freeman, CC; Mort, ME; Rausher, MD; Hileman, LC
Published in: American journal of botany
May 2016

Evolutionary radiations provide opportunities to examine large-scale patterns in diversification and character evolution, yet are often recalcitrant to phylogenetic resolution due to rapid speciation events. The plant genus Penstemon has been difficult to resolve using Sanger sequence-based markers, leading to the hypothesis that it represents a recent North American radiation. The current study demonstrates the utility of multiplexed shotgun genotyping (MSG), a style of restriction site-associated DNA sequencing (RADseq), to infer phylogenetic relationships within a subset of species in this genus and provide insight into evolutionary patterns.We sampled genomic DNA, primarily from herbarium material, and subjected it to MSG library preparation and Illumina sequencing. The resultant sequencing reads were clustered into homologous loci, aligned, and concatenated into data matrices that differed according to clustering similarity and amount of missing data. We performed phylogenetic analyses on these matrices using maximum likelihood (RAxML) and a species tree approach (SVDquartets).MSG data provide a highly resolved estimate of species relationships within Penstemon. While most species relationships were highly supported, the position of certain taxa remains ambiguous, suggesting that increased taxonomic sampling or additional methodologies may be required. The data confirm that evolutionary shifts from hymenopteran- to hummingbird-adapted flowers have occurred independently many times.This study demonstrates that phylogenomic approaches yielding thousands of variable sites can greatly improve species-level resolution of recent and rapid radiations. Similar to other studies, we found that less conservative similarity and missing data thresholds resulted in more highly supported topologies.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

American journal of botany

DOI

EISSN

1537-2197

ISSN

1537-2197

Publication Date

May 2016

Volume

103

Issue

5

Start / End Page

912 / 922

Related Subject Headings

  • Species Specificity
  • Pollination
  • Phylogeny
  • Penstemon
  • North America
  • Likelihood Functions
  • Genotyping Techniques
  • Flowers
  • Evolutionary Biology
  • 3108 Plant biology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Wessinger, C. A., Freeman, C. C., Mort, M. E., Rausher, M. D., & Hileman, L. C. (2016). Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon. American Journal of Botany, 103(5), 912–922. https://doi.org/10.3732/ajb.1500519
Wessinger, Carolyn A., Craig C. Freeman, Mark E. Mort, Mark D. Rausher, and Lena C. Hileman. “Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon.American Journal of Botany 103, no. 5 (May 2016): 912–22. https://doi.org/10.3732/ajb.1500519.
Wessinger CA, Freeman CC, Mort ME, Rausher MD, Hileman LC. Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon. American journal of botany. 2016 May;103(5):912–22.
Wessinger, Carolyn A., et al. “Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon.American Journal of Botany, vol. 103, no. 5, May 2016, pp. 912–22. Epmc, doi:10.3732/ajb.1500519.
Wessinger CA, Freeman CC, Mort ME, Rausher MD, Hileman LC. Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon. American journal of botany. 2016 May;103(5):912–922.

Published In

American journal of botany

DOI

EISSN

1537-2197

ISSN

1537-2197

Publication Date

May 2016

Volume

103

Issue

5

Start / End Page

912 / 922

Related Subject Headings

  • Species Specificity
  • Pollination
  • Phylogeny
  • Penstemon
  • North America
  • Likelihood Functions
  • Genotyping Techniques
  • Flowers
  • Evolutionary Biology
  • 3108 Plant biology