Inference of transitions to self-fertilization using haplotype genomic variation

Mating systems play an essential role in the evolution of natural populations. The reproductive mode of a population affects the evolutionary forces and recombination. Shifts in mating systems change major evolutionary traits of natural populations and affect the life-history cycle on many different levels. Among all transitions of mating schemes, a shift from outcrossing to selfing is one of the major shifts in plants. Such shifts have repeatedly occurred on the phylogenetic level. Despite their importance, there were no published tools to estimate such transitions in natural populations using genetic data on a genome- wide level. Existing estimates rely on estimating the loss-of-function mutations of causal loci. However, such estimates rely on the knowledge of the underlying genetic mechanism to induce the shift from outcrossing to selfing. Thus, such estimates are restricted to be conducted on very few species. In this study, we investigated the genetic consequences of shifts from outcrossing to selfing (Chapter 1). We used extensive simulations of the forward- in-time Wright-Fisher model and the backward-in-time coalescent model. We found the previously described theoretical work on implementing partial selfing in the coalescent to suffice in simulating transitions to selfing. We developed an Approximate Bayesian Computation approach (tsABC) to identify and estimate the date of transitions from outcrossing to selfing using a pairwise comparison of genomes (Chapter2). Finally, in collaboration with Thibaut Sellinger, we introduced the modified PSMC’ (teSMC) to estimate piecewise-constant selfing rates through time jointly with piecewise-constant population sizes for single- population demographies and analyzed its accuracy (Chapter 3). Taken together, we provide not only an approximate Bayesian but also a maximum likelihood approach to identify and estimate transitions to selfing for single populations. We found tsABC to be a versatile tool to identify and estimate transitions to selfing. Under carefully made assumptions for the proposed models, transitions to selfing can be detected under a broad range of scenarios. Moreover, the assumed model in the teSMC method improved the estimates of demography and detected transitions to selfing at least as powerful as the tsABC. The automized parametrization of teSMC allows users with little expertise in scripting to use it. We used both methods to estimate the transition from outcrossing to selfing for three genetic clusters of Arabidopsis thaliana. Our results were consistent with each other and existing estimates from the literature. With our study, we not only contributed to the understanding of evolutionary processes that formed the genetic diversity of natural populations but also provided two powerful tools to investigate the demographic history of natural populations in the context of transitions to selfing. Recombination provides a molecular clock on a separate time scale compared to mutation that interacts with all the four evolutionary forces at various levels. Eventually, that will contribute to understanding the functions of genes and their relationship and interaction with the bearing individual, the population, and the environment. Taken together, selfing as a breeding scheme or reproductive strategy is a crucial trait that interferes and connects evolutionary forces, adaptive potential, and life- history traits of natural populations

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species

Joint inference of evolutionary transitions to self-fertilization and demographic history using whole-genome sequences

International audienceThe evolution from outcrossing to selfing is a transition that occurred recurrently throughout the eukaryote tree of life, in plants, animals, fungi and algae. Despite some short-term advantages, selfing is supposed to be an evolutionary dead-end reproductive strategy on the long-term and its tippy distribution on phylogenies suggests that most selfing species are of recent origin. However, dating such transitions is challenging while it is central for this hypothesis. We build on previous theories to explicit the differential effect of past changes in selfing rate or in population size on the probability of recombination events along the genome. This allows us to develop two methods making use of full genome polymorphism data to 1) test if a transition from outcrossing to selfing occurred, and 2) infer its age. The sequentially Markov coalescent based (teSMC) and the Approximate Bayesian Computation (tsABC) methods use a common framework based on a transition matrix summarizing the distribution of times to the most recent common ancestor along the genome, allowing to estimate changes in the ratio of population recombination and mutation rates in time. We first demonstrate that our methods can disentangle between past change in selfing rate from past changes in demographic history. Second, we assess the accuracy of our methods and show that transitions to selfing as old as approximatively 2.5N(e) generations can be identified from polymorphism data. Third, our estimates are robust to the presence of linked negative selection on coding sequences. Finally, as a proof of principle, we apply both methods to three populations from Arabidopsis thaliana, recovering a transition to selfing which occurred approximately 600,000 years ago. Our methods pave the way to study recent transitions to predominant self-fertilization in selfing organisms and to better account for variation in mating systems in demographic inferences

Structures of KlenTaq DNA Polymerase caught while incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates

The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2′-deoxynucleoside-5′-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications

Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns.

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species

Primers used for developing ILs.

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.</div

The <i>SPL9</i> QTL cluster as a driver of local adaptation in the Azores.

(A) Signatures of selection at the SPL9 QTL cluster. The upper panel shows a Manhattan plot with the pcadapt results for 753 C. hirsuta strains (see also S5B Fig). The negative log base 10 transformed P values for SNPs on chromosome 4 are plotted against their physical positions. The dashed horizontal line indicates the P value separating the 1,000 genome-wide most significant SNPs, among which 83.8% are located in the vicinity of the SPL9 QTL cluster. The SPL9 missense SNP E242Q that was found to be responsible for QTL LLN4_2 is highlighted by a red circle. Yellow boxes in the lower part of the panel depict the location of QTL LLN4_1A, LLN4_1B and LLLN4_2 (SPL9). The bottom panel shows a sliding window analysis along chromosome 4 of weighted FST between the 2 groups of strains from the Azores, grp1 and grp2, which were found as highly differentiated in the SPL9 QTL cluster region (see also Fig 5B). The horizontal dashed line shows the genome-wide 95th percentile of weighted FST. (B) PCA of the 838 outlier SNPs detected by pcadapt analysis that were located within the SPL9 QTL cluster region, in 753 worldwide strains. Two groups of strains were highly differentiated from each other (grp1 –blue, grp2 –red) and from the other strains (gray and black). Strains with recombinations in the SPL9 QTL cluster are shown in black. (C) Nucleotide diversity (π) and Tajima’s D in the region of the pcadapt peak surrounding the SPL9 QTL cluster and the GBG outside of the peak for grp1 (blue) and grp 2 (red) strains from the Azores. (D) Geographic distribution of C. hirsuta strains within the Azores archipelago. The pie charts show the proportions of strains from the different groups in our sample colored according to Fig 5B (blue—grp1; red—grp2; black—recombinant in the SPL9 QTL cluster; gray—others). Strains from grp1 and grp2 were exclusively sampled on the Azores and show a nonuniform distribution with highest frequencies in the east and the west, respectively. Map layers were made with Natural Earth and [142]. (E) Phenological field data of C. hirsuta plants from 4 islands along the west–east transect colored according to alleles for the functional missense SNP E242Q of SPL9 (blue—Az1; red—not Az1; yellow—heterozygous;). Plants were classified for developmental stage from 1 (very young seedling) to 6 (advanced seed shedding). On Flores, Faial, and Pico, SPL9Az1-harboring strains were found in more advanced stages of development than strains carrying an alternative allele (*** P F) Weather station data from the Azores indicates reduced precipitation in the east when compared to the west. Data from 1970–2020 were analyzed in sliding windows of 11 days with 5-day stride and in each window the fraction of days with rain (> 0 mm) out of the total number of observed days was calculated. The fraction of days with rain in each window is shown by the points, and the lines show smoothing splines fitted to the data to reveal the trends. Note how on Santa Maria, in the east, from April until October, the fraction of days with rain is as low or lower than the lowest annual value for Flores and Faial in the west. The data underlying the graphs shown in the figure can be found at https://doi.org/10.5281/zenodo.7907435. GBG, genomic background; PCA, principal component analysis; QTL, quantitative trait locus; SPL9, SQUAMOSA PROMOTER BINDING PROTEN-LIKE 9.</p

Linkage map of the Ox-Az1-RIL population.

We study natural DNA polymorphisms and associated phenotypes in the Arabidopsis relative Cardamine hirsuta. We observed strong genetic differentiation among several ancestry groups and broader distribution of Iberian relict strains in European C. hirsuta compared to Arabidopsis. We found synchronization between vegetative and reproductive development and a pervasive role for heterochronic pathways in shaping C. hirsuta natural variation. A single, fast-cycling ChFRIGIDA allele evolved adaptively allowing range expansion from glacial refugia, unlike Arabidopsis where multiple FRIGIDA haplotypes were involved. The Azores islands, where Arabidopsis is scarce, are a hotspot for C. hirsuta diversity. We identified a quantitative trait locus (QTL) in the heterochronic SPL9 transcription factor as a determinant of an Azorean morphotype. This QTL shows evidence for positive selection, and its distribution mirrors a climate gradient that broadly shaped the Azorean flora. Overall, we establish a framework to explore how the interplay of adaptation, demography, and development shaped diversity patterns of 2 related plant species.</div

Sample location and Illumina sequencing information of all 752 <i>C</i>. <i>hirsuta</i> natural strains.

Sample location and Illumina sequencing information of all 752 C. hirsuta natural strains.</p

Positions for new assembled regions of the reference chromosome 8.

Positions for new assembled regions of the reference chromosome 8.</p