Year: 2016
Type: preprint
Abstract: Muta on and selec on in Arabidopsis thalianaBecause coloniza ons and invasions are o en associated with gene c bo lenecks, they offer an opportunity to directly observe de novo muta ons and their subsequent fate.North America has recently been colonized by Arabidopsis thaliana , and many of the individuals found today belong to a single lineage, HPG1.To determine subs tu on rates under natural condi ons in this lineage, we have sequenced 100 HPG1 genomes from plants collected between 1863 and 2006.We infer that the last common HPG1 ancestor lived in the early 17th century, most likely the me when HPG1 began to colonize N. America.Demographic reconstruc ons infer substan al popula on size fluctua ons during the past four centuries.Even though changing demographics can undermine the effect of natural selec on, we observed that muta ons at coding sites were at lower frequency than muta ons at other sites, consistent with the effect of purifying selec on.Excep onally, some muta ons rose to high frequency and some had measurable effects in root development, consistent with posi ve selec on ac ng over muta ons with an adap ve value.Our work showcases how by applying genomics methods to a combina on of modern and historic samples we can learn about plant colonisa ons and invasions and observe "evolu on in ac on".Knowledge of muta on rates and efficacy of selec on, which together determine the subs tu ons that can be observed in a popula on, is essen al for understanding evolu on 1 .Muta on rates are required to es mate the effec ve diversity of popula ons 2 , to date historic popula on splits 3 , and to predict what opportuni es there are for rapid novel adapta ons, for instance, to drugs or pes cides 4,5 .Two extreme approaches to discover these parameters are either short-term muta on accumula on experiments in the laboratory 6 and pedigree-based es mates 7 , or interspecific phylogenomic comparisons over millions of years 8 .Since muta on rates are generally studied independently of natural selec on and popula on dynamics contexts, the two approaches o en yield es mates that do not coincide, which has generated a heated controversy 9,10 .An alterna ve not exploited so far is the analysis of naturally occurring "evolu onary experiments" such as colonizing or invasive popula ons associated with a recent and strong gene c bo leneck 11,12 .Both coloniza ons and invasions are increasingly common due to human movement 13,14 .The study of these natural experiments is especially powerful when me-stamped samples from historic specimens can be used as internal calibra on points 15,16 .Colonizing popula ons o en start with very few individuals and therefore have low gene c diversity.The N. American popula on of the self-fer lizing plant Arabidopsis thaliana is no excep on, with many individuals belonging to a gene cally very similar lineage, haplogroup-1 (HPG1), that spread over large geographic areas 17 .The study of the origin along with demographic and selec ve dynamics of muta ons in HPG1 can further help us solve the current paradox generated by two evolu onary conjectures: "Baker's law", inspired by the observa on that selfing species are more successfully colonizing new environments than outcrossing ones, and "Muller's ratchet", which posits that selfing popula ons are evolu onary dead ends, since low diversity and accumula on of more deleterious muta ons should hinder their ability to adapt to new environments [18][19][20][21] .To be er understand the evolu on of HPG1, we sequenced 27 herbarium specimens, from 1863-1993, and 76 live isolates of this lineage collected 1993-2006 (Fig. 1; Table S1).DNA retrieved from herbarium specimens showed biochemical features typical of ancient DNA 22 , which indicates that the DNA recovered from historic samples is authen c (Fig. S1, see Supplementary Online Material [SOM] for details).We mapped reads against an HPG1 pseudo-reference genome 23 , focusing on single nucleo de 2 .
Source: MPG.PuRe (Max Planck Society)
Institutions: Max Planck Institute for Developmental Biology, Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Austrian Academy of Sciences, University of Chicago, Chinese Academy of Sciences, Institute of Tibetan Plateau Research, University of Toronto, Max Planck Society, Max Planck Institute of Geoanthropology
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Funder: Max-Planck-Gesellschaft
OpenAlex ID: W2951466562