Abstract Detail

Genomics / Proteomics

Tiley, George [1], Burleigh, Gordon [2].

Evaluating evidence for ancient Whole Genome Duplications from Synonymous Substitution Rates.

The distribution of synonymous substitution rates between paralogous genes within a genome is often used to detect ancient whole genome duplication (WGD) events in plants. Recent studies suggest that distributions of synonymous substitution rates can fail to detect WGDs or falsely detect WGD in the presence of substitutional saturation; however, it is unclear if they can also mistake other gene duplication and loss processes for WGDs. Specifically, we examine if Gaussian mixture models may detect multiple peaks in distributions of synonymous substitution rates, suggesting WGDs due to heterogeneity in gene duplication and loss rates as well as estimator bias. We simulated gene families to evaluate evidence for the hypothesized ancestral angiosperm and seed plant whole genome duplications. Simulations are compared to the sequenced genome of Amborella trichopoda. The utility of distributions of synonymous substitution rates between paralogs should be critically assessed, as error in estimates of evolutionary distance increases with gene family age, especially when relying on empirical estimates of equilibrium codon frequencies. Distributions of synonymous substitution rates should reflect the patterns of gene duplication, driven by a proportion of gene families with relatively high duplication rates and low loss rates. It can be difficult to distinguish WGD events from patterns of non-WGD gene evolution, especially when gene loss rates immediately following whole genome duplications are high.

1 - University of Florida, Biology, Gainesville, FL, 32611, USA
2 - University Of Florida, P.O. Box 118526, Gainesville, FL, 32611, USA

Keywords:
gene family evolution
gene duplication
synonymous substitution rates
whole genome duplication.

Presentation Type: Oral Paper:Papers for Topics
Session: 48
Location: Salon 19/20/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 2:30 PM
Number: 48005
Abstract ID:615
Candidate for Awards:Margaret Menzel Award