speciation; introgression; reproductive isolation; demographic history; selection; coalescent simulations; recombination rates; Population genetics; wild tomatoes; gene flow; divergence; natural selection
Florez-Rueda Ana M., Paris Margot, Schmidt Anja, Widmer Alex, Grossniklaus Ueli, Städler Thomas (2016), Genomic imprinting in the endosperm is systematically perturbed in abortive hybrid tomato seeds, in Molecular Biology and Evolution
, 33(11), 2935-2946.
Lin Tao, 26 other coauthors, Städler Thomas, Li Jingfu, Ye Zhibiao, Du Yongchen, Huang Sanwen (2014), Genomic analyses provide insights into the history of tomato breeding, in Nature Genetics
, 46(11), 1220-1226.
Qi Jianjian, Liu Xin, Shen Di, Miao Han, 18 other authors, Städler Thomas, Renner Susanne S., Kamoun Sophien, Lucas William J., Zhang Zhonghua, Huang Sanwen (2013), A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity, in Nature Genetics
, 45(12), 1510-1515.
Städler Thomas (2012), Molecular ecology in Vienna: hot topics in a chilly place, in EMBO REPORTS
, 13(6), 475-477.
Städler Thomas, Florez-Rueda Ana Marcela, Paris Margot (2012), Testing for "snowballing" hybrid incompatibilities in Solanum: impact of ancestral polymorphism and divergence estimates, in Molecular Biology and Evolution
, 29(1), 31-34.
Tellier A, Pfaffelhuber P, Haubold B, Naduvilezhath L, Rose LE, Städler T, Stephan W, Metzler D (2011), Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum, in PLOS ONE
, 6(5), keine-keine.
Tellier A, Fischer I, Merino C, Xia H, Camus-Kulandaivelu L, Städler T, Stephan W (2011), Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure, in HEREDITY
, 107(3), 189-199.
Lineage divergence and processes of speciation are of fundamental interest in evolutionary biology and population genetics, but are difficult to address in many natural systems because extant species may have diverged sufficiently to erode signatures of evolutionary processes that accompanied and/or caused the initial divergence. Under a genealogical (coalescent) perspective, DNA sequence data obtained from multiple unlinked loci contain footprints of demographic history and may reveal incidences of interspecific gene flow during the process of divergence. Understanding the demographic history of species is also of considerable importance for interpreting patterns of nucleotide polymorphism, site frequency spectra (SFS), and linkage disequilibrium (LD) at “candidate” loci that might be involved in adaptive traits or reproductive isolation. Moreover, recombination rates can vary dramatically across genomic regions, providing opportunities to test evolutionary models invoking the effects of directional and/or purifying selection. Finally, regions of very low recombination may facilitate the build-up of reproductive barriers and adaptive differentiation, but empirical data in plants to address these issues are still scarce. Here I propose a research project that builds on my previous studies in wild tomatoes (Solanum section Lycopersicon) with a similar focus, but that were limited to fewer species and markedly fewer loci. Wild tomatoes are ideally suited for such a project because of their recent divergence, differences in their mating system, and abundant genomic resources including estimates of recombination rate for hundreds of mapped nuclear markers. I plan to pursue three subprojects that each have their own conceptual framework, but rest on a common data set generated by sequencing 50-60 nuclear loci from seven nominal wild tomato species, two of them with a highly selfing mating system. Due to population subdivision and its genealogical consequences, the aim of characterizing nucleotide diversity and the SFS can be accomplished in the least biased manner by a scattered sampling scheme across each species’ geographic range. Nuclear loci from known regions of normal versus very low recombination rate, but without regard to putative function, will be sequenced with next-generation sequencing technology (454) to provide the raw data for the three subprojects. Project 1 concerns the demographic history and divergence processes of the seven nominal species, to be evaluated with extensive coalescent simulations under an approximate Bayesian computation (ABC) framework. Project 2 focuses on the direction and strength of correlation(s) between levels of silent nucleotide diversity, divergence to a non-tomato outgroup, and levels of recombination; these analyses assess the relative importance of directional and/or purifying selection on nucleotide diversity and divergence in linked regions, compared to neutral factors such as mutation and random genetic drift. By screening for genomic regions showing either higher or lower divergence levels between the focal species than expected given their inferred demographic history, project 3 aims to test the potential role of suppressed recombination in facilitating divergence and reproductive isolation. The proposed research will provide new insights into genome-wide patterns of diversity and divergence between multiple closely related, ecologically diverged plant species, as well as into the evolutionary processes generating those patterns. These issues are of fundamental biological interest and have now become amenable to study at a genome-wide scale, due to recent innovations in sequencing technology and theoretical advances in understanding the genealogical implications of different sampling schemes in subdivided species.