Abstract Detail

Reproductive Processes

Sorojsrisom, Elissa Suphapun [1], Haller, Benjamin [2], Ambrose, Barbara [3], Eaton, Deren [4].

Gametophytes cloning and living free: exploring evolutionary consequences of plant life cycles with (SLiM) shadie.

All land plants have a life cycle that alternates generations between multicellular haploid gametophyte and diploid sporophyte life stages. The degree to which the gametophyte is dependent on the sporophyte, or vice versa, is a key trait that distinguishes the major lineages of land plants from one another, however the evolutionary consequences of this variation among plant lineages is poorly understood. We developed a simple Python program, shadie (Simulating Haploid-Diploid Evolution) for designing, implementing, and analyzing simulations with alternation-of-generations using SLiM 3 as a simulation back-end. shadie supports six models based on realistic plant life cycles and three variations of Wright-Fisher models. These models incorporate the spectrum of gametophyte- vs. sporophyte- dependence and sexual systems across land plants.
To test the significance of plant life cycle variation on genome evolution, we implement evolutionary simulations under a Wright-Fisher model and three realistic plant lifecycle models supported in shadie using both standardized and biologically realistic parameter settings. We found that the fixation dynamics of a single beneficial mutation does not vary drastically between models, but resulting spatial patterns of genome diversity under repeated mutations does differ significantly. In particular, the rate of linkage disequilibrium decay away from selected sites varied depending on model parameters such as cloning and selfing rates, likely through their impact on effective population sizes. These simulations demonstrate that differences in life history and parameter settings affect both genetic diversity and linkage disequilibrium.
Evolutionary simulations are an exciting, underutilized approach in evolutionary research and education. shadie can aid plant researchers in developing null hypotheses, examining theory, and designing empirical studies, in order to investigate the role of the gametophyte life stage, and the effects of variation in plant life cycles, on plant genome evolution.

Related Links:
shadie on GitHub
shadie Docs

1 - Columbia University, Ecology, Evolution, and Environmental Biology, 1200 Amsterdam Ave, Schermerhorn Ext., New York, NY, 10027, USA
2 - Cornell, Department of Computational Biology, Ithaca, NY, 4853, USA
3 - The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458, United States
4 - Columbia University, Ecology, Evolution, And Environmental Biology, 1200 Amsterdam Ave. , Schermerhorn Ext. Office 1007, New York, NY, 10027, United States

Keywords:
gametophyte
alternation of generations
simulation
life history
haploid selection.

Presentation Type: Oral Paper
Number: RP1001
Abstract ID:843
Candidate for Awards:None