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Abstract Detail

Comparative Genomics/Transcriptomics

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

Simulating Haploid-Diploid Evolution: the (real) SLiM3 shadie.

All sexually reproducing plants have both haploid (gametophyte) and diploid (sporophyte) lifestages, but most evolutionary models assume organisms are either haploid or diploid for their entire lifespan. The gametophyte stage in angiosperms is generally reduced and short-lived. By contrast, pteridophytes (ferns and lycophytes) have a free-living gametophyte lifestage upon which the sporophyte is nutritionally dependent for a time and bryophytes (mosses, hornworts, and liverworts) have a gametophyte-dominant life cycle with an ephemeral sporophyte. Plants with a long-lived, free-living gametophyte lifestage have the potential to be subjected to different selective pressures than a diploid organism. Selection acting on the gametophyte has the potential to influence evolutionary outcomes e.g. rates of adaptation and expression of genetic conflicts. Lineages with free-living gametophyte lifestages offer a unique and underutilized resource for understanding the differing effects of selection between major plant groups. Simulation approaches that model these varied biphasic plant life histories have the potential to contextualize the outcomes of gametophyte selection studies. Here, we introduce a new Python program, `shadie`. ` shadie ` is a Python API wrapper around the forward-in-time evolution simulation software, SLiM3. `shadie` also utilizes coalescent methods developed in `pyslim` and `msprime` to speed up simulation time by overlaying neutral mutations using backwards-in-time coalescence after a SLiM simulation is completed. Evolutionary simulations can be useful for generating expectations and evaluating the outcome of empirical studies. They can also be used to generate null hypotheses for virtually endless evolutionary questions, and aid in study design. Although `shadie` can be used by researchers to address any number of evolutionary questions in many different systems, we have specifically designed `shadie` to be able to address questions in plant systems by implementing alternation of haploid and diploid generations that reflect the life cycles of major plant lineages. As an example, we use `shadie` to investigate the question of whether purifying selection acts more efficiently on plants with a free-living gametophyte life-stage (e.g., ferns and bryophytes) compared to those with a short-lived and reduced gametophyte (e.g., angiosperms).

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Related Links:
SHaDiE Github Repository

1 - Columbia University, Ecology, Evolution, and Environmental Biology, 1200 Amesterdam Avenue, Schermerhorn Ext. 1007, New York, New York, 10027, United States
2 - The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458, United States
3 - Columbia University, Ecology, Evolution, And Environmental Biology, 1200 Amsterdam Ave. , Schermerhorn Ext. Office 1007, New York, NY, 10027, United States

evolutionary simulation
alternation of generations
modeling lifecycles.

Presentation Type: Poster
Session: P1, Comparative Genomics/Transcriptomics Posters
Location: Virtual/Virtual
Date: Monday, July 19th, 2021
Time: 5:00 PM(EDT)
Number: P1GT001
Abstract ID:463
Candidate for Awards:None

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