Thomas Städler

• PhD
• Senior Researcher at ETH Zurich

The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)1,2 dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly accelerate its improvement³. Crucially, the devel...

The genetic analysis of potato is hampered by the complexity of tetrasomic inheritance. An ongoing effort aims to transform the clonally propagated tetraploid potato into a seed-propagated diploid crop, which would make genetic analyses much easier owing to disomic inheritance. Here, we construct and report the large-scale genetic and heterotic cha...

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutio...

Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits1,2. The solution to this problem is to identify all causal genetic variants and to measure their individual contributions3,4. Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 mi...

Most flowering plants must defend themselves against herbivores for survival and attract pollinators for reproduction. Although traits involved in plant defence and pollinator attraction are often localised in leaves and flowers, respectively, they will show a diffuse evolution if they share the same molecular machinery and regulatory networks. We...

Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as th...

Interest in understanding hybrid seed failure (HSF) has mushroomed, both in terms of identifying underlying molecular processes and their evolutionary drivers. We review phenotypic and molecular advances with a focus on the ‘effective ploidy’ concept, witnessing a recent revival after long obscurity. Endosperm misdevelopment has now been shown to u...

The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of sel...

Crosses between the wild tomato species Solanum peruvianum and S. chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent of origin dependent expression of alleles, is perturbed in hybrid endosperm, with many of the normally paternally expres...

Parental imbalances in the endosperm leading to impaired development and eventual hybrid seed failure are common causes of postzygotic isolation in flowering plants. Endosperm sensitivity to parental dosage is reflected by canonical phenotypes of 'parental excess' in reciprocal interploid crosses. Moreover, parental-excess traits are also evident i...

Crosses between the wild tomato species Solanum peruvianum and S. chilense result in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in hybrid endosperm, with many of the normally paternally expres...

Endosperm misdevelopment leading to hybrid seed failure is a common cause of postzygotic isolation in angiosperms and is observed in both interploidy and homoploid crosses between closely related lineages. Moreover, parental dosage is critical for successful endosperm and seed development, typically requiring a ratio of two maternal to one paternal...

Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome‐wide studies have found limited conservation of IGs among...

The number of male gametes produced is critical for reproductive success and varies greatly between and within species 1–3 . Evolutionary reduction of male gamete production has been widely reported in plants as a hallmark of the selfing syndrome, as well as in humans. Such a reduction may simply represent deleterious decay 4–7 , but evolutionary t...

The number of male gametes produced is critical for reproductive success and varies greatly between and within species. Evolutionary reduction of male gamete production has been widely reported in plants as a hallmark of the selfing syndrome, as well as in humans. Such a reduction may simply represent deleterious decay, but evolutionary theory pred...

Background and aims: Defective hybrid seed development in angiosperms might mediate the rapid establishment of intrinsic post-zygotic isolation between closely related species. Extensive crosses within and among three lineages of wild tomatoes (Solanum section Lycopersicon) were performed to address the incidence, developmental timing and histolog...

Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other flowering plants. We studied genome-wide changes associated with hybrid seed abortion in the closely related Solanum peruvianum and S. chilense where hybrid crosses yield high proportions of inviab...

Hybrid seed failure is a common reproductive barrier between plant species. For plant breeders, it represents a major obstacle to introgression of desirable traits from wild to domesticated species. Postzygotic barriers to hybridization have been well-documented among wild tomato species, and histological work showed that endosperm failure is the m...

Hybrid seed failure, a common postzygotic barrier in angiosperms, is likely mediated by abnormal endosperm development, highlighting the pivotal role of the endosperm for proper seed development. Epigenetic processes modulate the parent-of-origin specific expression of so-called “imprinted” genes in the endosperm, some of which may be important for...

The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence t...

Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ∼3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks d...

The international VIPCA conference on ‘Molecular Ecology’ took place in Vienna, Austria, in early February 2012. The meeting showcased the diversity of molecular tools and conceptual approaches at the disposal of practitioners in this flourishing field, which lies at the interface of ecology, evolution and molecular biology.

Two recent high-profile studies offered empirical evidence for a “snowballing” accumulation of postzygotic incompatibilities in Drosophila and Solanum (tomatoes). Here we present a reanalysis of the Solanum data that is motivated by population genetic principles. Specifically, the high levels of intraspecific nucleotide polymorphism in wild tomato...

Relative error for estimates of (a) the divergence time (τ) and (b) the migration rate (M = M12 = M21), for the maximum likelihood methods (D1–D4), MIMAR and the composite-likelihood methods (J1–J4). Relative error is calculated as (τest−τsim)/τsim where τest is the estimated value and τsim is the simulated value. Groups with significant difference...

Factor 2 as a percentage of the estimates of migration rate (M = M12 = M21) in the range Msim/2<Mest<Msim×2 as a function of the population mutation rate (θ), values of simulated migration rates (M12 = M21) and population recombination rates (ρ). (a) For the four maximum likelihood methods (D1–D4) and MIMAR, (b) for the four composite-likelihood me...

Factor 2 for estimates of the divergence time and migration rates ( M12 , M21 ) for the four composite-likelihood methods (J1–J4), ∂a∂i and for popABC with 6, 11 and 14 summary statistics (computed over 100 datasets). (TIF)

Distribution of relative error for (a) divergence time and for (b) migration rate depending on the population mutation rate (θ) for composite-likelihood method J4. For clarity, only relative errors lower than 15 are shown in (b). (TIF)

Relative error in the estimation of the migration rate (M12 in blue and M21 in red) depending on the simulated value of the migration rate for composite likelihood method J4. (a) For simulated divergence times smaller than 0.5, and (b) for simulated divergence times greater than 1. Note the difference in scale of the y-axes between (a) and (b). (TI...

Power analysis of the various JSFS coarsenings to estimate divergence time and migration rates for 100 datasets of 100 loci. RMSE are computed for estimates of the (a) divergence time (τ) and (b) migration rates (M12≠M21) for the four composite-likelihood methods (J1–J4) based on six vectors of summary statistics with different numbers elements. Th...

Supplementary information. (PDF)

Distribution of the relative error of (a) divergence time and of (b) migration rate depending on the population recombination rate (ρ) for composite-likelihood method J4. For clarity, only relative errors lower than 15 are shown in (b). (TIF)

Relative error for estimation of migration rate depending on the simulated value of the migration rate (M12 in blue and M21 in red) for composite method J2. (a) For simulated divergence times less than 0.5, and (b) for simulated divergence times greater than 1. Note the difference in scale of the y-axes between (a) and (b). (TIF)

Relative error in the estimation of migration rate depending on the simulated value of the migration rate (M12 in blue and M21 in red) for popABC estimates with 6 summary statistics. (a) For simulated divergence times smaller than 0.5, and (b) for simulated divergence times greater than 1. (TIF)

ANOVA table of analysis of error in the estimation of divergence times ( τ ). (PDF)

Analysis of regression between errors in estimates of migration rate (M12 = M21) and divergence time τ for the 9 methods tested. (a) D1–4 for the maximum likelihood methods, (b) J1–4 for the composite likelihood methods and (c) for MIMAR. Positive (negative) relative error indicates over (under)-estimation of the parameter. Regression coefficients...

Factor 2 as a percentage of the estimates of divergence time (τ) in the range τsim/2<τest<τsim×2 as a function of the population mutation rates (θ), values of simulated migration rates (M12 = M21) and population recombination rates (ρ). The Factor 2 (F2) is the proportion of data sets for which the estimated value (of τ or M) is at least half and a...

ANOVA table of analysis of error in the estimation of migration rates ( M12 = M21 ). (PDF)

Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older...

A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking int...

Multilocus sequencing studies assessing patterns of nucleotide polymorphism within and among closely related species provide valuable insights into the evolutionary processes involved in species divergence. We have employed the analytical framework of divergence population genetics in testing models of speciation in two species of wild tomatoes (cl...

Ever since Darwin's pioneering research, the evolution of self-fertilisation (selfing) has been regarded as one of the most prevalent evolutionary transitions in flowering plants. A major mechanism to prevent selfing is the self-incompatibility (SI) recognition system, which consists of male and female specificity genes at the S-locus and SI modifi...

Using coalescent simulations, we study the impact of three different sampling schemes on patterns of neutral diversity in structured populations. Specifically, we are interested in two summary statistics based on the site frequency spectrum as a function of migration rate, demographic history of the entire substructured population (including timing...

We present a multilocus sequencing study to assess patterns of polymorphism and divergence in the closely related wild tomato species, Solanum peruvianum and S. chilense (Solanum section Lycopersicon, Solanaceae). The data set comprises seven mapped nuclear loci (approximately 9.3 kb of analyzed sequence across loci) and four local population sampl...

We employed a multilocus approach to examine the effects of population subdivision and natural selection on DNA polymorphism in 2 closely related wild tomato species (Solanum peruvianum and Solanum chilense), using sequence data for 8 nuclear loci from populations across much of the species' range. Both species exhibit substantial levels of nucleot...

We analyzed the effects of mating system and recombination rate on single nucleotide polymorphisms using 14 single-copy nuclear loci from single populations of five species of wild tomatoes (Solanum section Lycopersicon). The taxa investigated comprise two self-compatible (SC) and three self-incompatible (SI) species. The observed reduction in nucl...

The small aquatic snail Potamopyrgus antipodarum is an important invading species in Europe, Australia and North America. European populations are generally believed to derive from accidental introductions from New Zealand, probably dating back to the mid-19th century. We have employed mitochondrial DNA sequences to test the proposed New Zealand or...

Multilocus studies assessing patterns of nucleotide polymorphism within and among closely related species provide access to genealogical information bearing on demographic and geographic aspects of their speciation history. However, the technical difficulties in obtaining sufficient sequence data have severely limited this approach thus far, especi...

Abstract Multilocus studies assessing patterns of nucleotide polymorphism within and among closely related species provide access to genealogical information bearing on demographic and geographic aspects of their speciation history. However, the technical difficulties in obtaining sufficient sequence data have severely limited this approach thus fa...

Because of their extremely low nucleotide mutation rates, plant mitochondrial genes are generally not expected to show variation within species. Remarkably, we found nine distinct cytochrome b sequence haplotypes in the gynodioecious alpine plant Silene acaulis, with two or more haplotypes coexisting locally in each of three sampled regions. Moreov...

Evolutionary ecology includes aspects of community structure, trophic interactions, life-history tactics, and reproductive modes, analyzed from an evolutionary perspective. Freshwater environments often impose spatial structure on populations, e.g. within large lakes or among habitat patches facilitating genetic and phenotypic divergence. Tradition...

Experimental studies on freshwater organisms are frequently easier, especially with planktonic species, than comparable studies on terrestrial organisms. Beside a general overview on aspects characteristic for freshwater environments, the chapter provides introductions and background for the twelve other chapters of the book.

Freshwater gastropods can reproduce by both uniparental and biparental means. In particular, self-fertilization in the hermaphrodite pulmonates (Basommatophora) and apomictic parthenogenesis in prosobranchs are viable alternatives to biparental sexuality in several species. The coexistence of different mating systems within and among extant populat...

Simple sequence repeats (SSRs, or microsatellites) have been constantly gaining importance as single-locus DNA markers in population genetics and behavioural ecology. We tested a PCR-based strategy for finding microsatellite loci in anonymous genomes, which avoids genomic library construction and screening, and the need for larger amounts of DNA. I...

We estimated outcrossing rates and correlated matings in a natural population of the hermaphroditic freshwater snail Ancylus fluviatilis, using progeny arrays and polymorphic allozyme markers. This design circumvents drawbacks of earlier studies, and yields maximum likelihood estimates of outcrossing rates at both the individual and population leve...

Freshwater gastropods (Basommatophora and Prosobranchia) harbor a variety of mating systems. In particular, apomictic parthenogenesis in prosobranchs and self-fertilization in the hermaphrodite pulmonates may be viable alternatives to outcrossing sexuality in a number of species. The coexistence of different mating systems in extant populations pro...

[formerly EXPERIENTIA]

INTRODUCTION: FRESHWATER INVERTEBRATES AS MODEL SYSTEMS IN POPULATION ECOLOGY AND GENETICS Page 423-424 Population biology draws on several subdisciplines of biology, such as population ecology, population genet- ics, and life history theory. It is a rapidly growing, diversifying field at the nexus of general and community ecology, of genetics, bi...

The number of cases where the phenomena of hybridization and gene introgression have been found in species interactions is steadily increasing, in both plant and animal taxa. During the last few years, many examples have been detected even in otherwise well-known freshwater animal taxa. We discuss the topic with respect to ecology and evolutionary...

Polyploidy and its genetical, ecological, and evolutionary consequences in hermaphrodites have predominantly been studied in vascular plants, but the condition also occurs in animals, such as freshwater pulmonate snails (Basommatophora). Representatives of this group have been preserved in fossil deposits, but the paucity and plasticity of morpholo...

We did breeding experiments with the polyploid hermaphroditic freshwater snail Ancylus fluviatilis to determine outcrossing rates at the level of individuals. The study was in response to electrophoretic work on the genetic structure of natural populations which suggested only a limited extent of cross-fertilization. Snails were sampled from popula...