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Abstract Detail



A synthesis of new paleontological and phylogenomic perspectives on gymnosperm evolution

Nagalingum, Nathalie [1].

Testing the effectiveness of RAD-seq in the cycads.

Cycads are the oldest living group of seed plants with the first fossils recovered from the Permian, and molecular estimates indicating that the living genera arose in the Mesozoic and early Cenozoic. Relationships among the 11 living genera have been difficult to infer with confidence, likely because of their ancient origins and the reliance on chloroplast markers. In the absence of a completed genome sequence or other genomic tools in cycads, RAD-seq (restriction site associated DNA sequencing) can provide numerous markers, especially from the nuclear region. However, for ancient divergence events RAD-seq often is thought to be ineffective because of “locus drop-out”, that is when taxa develop mutations in the restriction enzyme sites leading to the loss of homologous loci. In this study, RAD-seq was applied to the cycads to test if this approach can be used for deep-time phylogenetics. Using different assembly parameters, three matrices were generated, ranging from almost 90,000 bp and ~50% missing data to approximately 1,600 bp and ~25% missing data. The phylogenies inferred from these matrices were compared to previously inferred cycad relationships and were used to ascertain the utility of RAD-seq for resolving phylogenetic relationships across distantly related taxa.


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1 - California Academy of Sciences, 55 Music Concourse Dr, San Francisco, CA, 94118, USA

Keywords:
gymnosperm
Phylogenomics
Cycadales
RADseq
phylogeny.

Presentation Type: Colloquium Presentations
Session: C04, A synthesis of new paleontological and phylogenomic perspectives on gymnosperm evolution
Location: 102/Mayo Civic Center
Date: Monday, July 23rd, 2018
Time: 2:15 PM
Number: C04004
Abstract ID:658
Candidate for Awards:None


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