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Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus).

Publication ,  Journal Article
Crowl, AA; Manos, PS; McVay, JD; Lemmon, AR; Lemmon, EM; Hipp, AL
Published in: The New phytologist
May 2020

Botanists have long recognised interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterised and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci. Concatenation, species-tree and network analyses were carried out in an attempt to uncover the genomic signal of ancient introgression and infer the divergent phylogenetic topology for the white oak clade. Locus and site-level likelihood comparisons were then conducted to further explore the introgressed signal within our dataset. Historical, intersectional gene flow is suggested to have occurred between an ancestor of the Eurasian Roburoid lineage and Quercus pontica and North American Dumosae and Prinoideae lineages. Despite extensive time past, our approach proved successful in detecting the genomic signature of ancient introgression. Our results, however, highlight the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history.

Duke Scholars

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Published In

The New phytologist

DOI

EISSN

1469-8137

ISSN

0028-646X

Publication Date

May 2020

Volume

226

Issue

4

Start / End Page

1158 / 1170

Related Subject Headings

  • Quercus
  • Plant Biology & Botany
  • Phylogeny
  • Genomics
  • Gene Flow
  • Biological Evolution
  • 4102 Ecological applications
  • 4101 Climate change impacts and adaptation
  • 3108 Plant biology
  • 07 Agricultural and Veterinary Sciences
 

Citation

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Crowl, A. A., Manos, P. S., McVay, J. D., Lemmon, A. R., Lemmon, E. M., & Hipp, A. L. (2020). Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). The New Phytologist, 226(4), 1158–1170. https://doi.org/10.1111/nph.15842
Crowl, Andrew A., Paul S. Manos, John D. McVay, Alan R. Lemmon, Emily Moriarty Lemmon, and Andrew L. Hipp. “Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus).The New Phytologist 226, no. 4 (May 2020): 1158–70. https://doi.org/10.1111/nph.15842.
Crowl AA, Manos PS, McVay JD, Lemmon AR, Lemmon EM, Hipp AL. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). The New phytologist. 2020 May;226(4):1158–70.
Crowl, Andrew A., et al. “Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus).The New Phytologist, vol. 226, no. 4, May 2020, pp. 1158–70. Epmc, doi:10.1111/nph.15842.
Crowl AA, Manos PS, McVay JD, Lemmon AR, Lemmon EM, Hipp AL. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). The New phytologist. 2020 May;226(4):1158–1170.
Journal cover image

Published In

The New phytologist

DOI

EISSN

1469-8137

ISSN

0028-646X

Publication Date

May 2020

Volume

226

Issue

4

Start / End Page

1158 / 1170

Related Subject Headings

  • Quercus
  • Plant Biology & Botany
  • Phylogeny
  • Genomics
  • Gene Flow
  • Biological Evolution
  • 4102 Ecological applications
  • 4101 Climate change impacts and adaptation
  • 3108 Plant biology
  • 07 Agricultural and Veterinary Sciences