30 Works

Data from: Hybrid crosses and the genetic basis of interspecific divergence in lifespan in Pristionchus nematodes

Cameron J. Weadick & Ralf J. Sommer
Characterizing the genetic basis of among-species variation in lifespan is a major goal of evolutionary gerontology research, but the very feature that defines separate species—the inability to interbreed—makes achieving this goal impractical, if not impossible, for most taxa. Pristionchus nematodes provide an intriguing system for tackling this problem, as female lifespan varies among species that can be crossed to form viable (though infertile) hybrids. By conducting reciprocal crosses among three species—two dioecious (long-lived P. exspectatus...

FT TFL1 bimolecular luciferase complementation assays

Detlef Weigel & William Ho
CORRECTION Ho, W.W.H., and Weigel, D. (2014). Structural Features Determining Flower-Promoting Activity of Arabidopsis FLOWERING LOCUS T. Plant Cell 26: 552-564. Published February 2014. DOI: https://doi.org/10.1105/tpc.113.115220. During the assembly of Supplemental Figure 7 and Figure 8, six luciferase images of individual leaves were inadvertently duplicated. These images served to illustrate the strength of interactions between FT and TFL1 proteins and their mutant variants with GRF and TCP proteins, as measured qualitatively in split luciferase assays...

Data from: Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known

Charles B. Fenster, Matthew Thomas Rutter, Angela J. Roles, Jeffrey K. Conner, Ruth G. Shaw, Frank Holcomb Shaw, Korbinian Schneeberger, Stephan Ossowski & Detlef Weigel
Despite the fundamental importance of mutation to the evolutionary process, we have little knowledge of the direct consequences of specific spontaneous mutations to the fitness of the organism. Combining results of whole-genome sequencing with repeated field assays of survival and reproduction, we quantify the combined effects on fitness of spontaneous mutations identified in Arabidopsis thaliana. We demonstrate that the effects are beneficial, deleterious or neutral depending on the environmental context. Some lines, bearing mutations disrupting...

Data from: Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping.

Beth A. Rowan, Vipul Patel, Detlef Weigel & Korbinian Schneeberger
The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The reassortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by the short-read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. Although sequencing costs have decreased precipitously in recent years, the costs of...

Data from: Landscape and oceanic barriers shape dispersal and population structure in the island nematode, Pristionchus pacificus

Katy Morgan, Angela McGaughran, Seelavarn Ganeshan, Matthias Herrmann & Ralf J. Sommer
Despite the biological importance and diversity of nematodes, little is known of the factors influencing their dispersal and shaping their evolutionary history. Populations of the cosmopolitan species Pristionchus pacificus are characterized by high genetic diversity and strong spatial structure, which contrasts with patterns detected in nematode species such as Caenorhabditis elegans. The environmentally heterogeneous volcanic Mascarene Islands provide an ideal setting for investigating fine-scale patterns of nematode migration and gene flow. Based on the analysis...

Data from: Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes beetles on La Réunion Island

Jan M. Meyer, Praveen Baskaran, Christian Quast, Vladislav Susoy, Christian Rödelsperger, Frank Oliver Glöckner & Ralf J. Sommer
Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island....

Data from: Environmental variables explain genetic structure in a beetle-associated nematode

Angela McGaughran, Katy Morgan & Ralf J. Sommer
The distribution of a species is a complex expression of its ecological and evolutionary history and integrating population genetic, environmental, and ecological data can provide new insights into the effects of the environment on the population structure of species. Previous work demonstrated strong patterns of genetic differentiation in natural populations of the hermaphroditic nematode Pristionchus pacificus in its La Réunion Island habitat, but gave no clear understanding of the role of the environment in structuring...

Data from: The genomic landscape at a late stage of stickleback speciation: high genomic divergence interspersed by small localized regions of introgression

Mark Ravinet, Kohta Yoshida, Shuji Shigenobu, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how...

Data from: Activation of the Arabidopsis thaliana immune system by combinations of common ACD6 alleles

Marco Todesco, Sang-Tae Kim, Eunyoung Chae, Kirsten Bomblies, Maricris Zaidem, Lisa M. Smith, Detlef Weigel & Roosa A. E. Laitinen
A fundamental question in biology is how multicellular organisms distinguish self and non-self. The ability to make this distinction allows animals and plants to detect and respond to pathogens without triggering immune reactions directed against their own cells. In plants, inappropriate self-recognition results in the autonomous activation of the immune system, causing affected individuals to grow less well. These plants also suffer from spontaneous cell death, but are at the same time more resistant to...

Learning from dynamic traits: Seasonal shifts yield insights into ecophysiological tradeoffs across scales from macroevolutionary to intra-individual

Chase Mason, Michael C. LaScaleia, Danielle R. De La Pascua, J. Grey Monroe & Eric W. Goolsby
Premise of the Research. Phylogenetic comparative methods provide a powerful approach for exploring the macroevolution of plant functional traits. Such approaches can uncover trait-trait correlations through evolutionary time, as well as provide evidence of the role of traits in adaptation across environmental gradients. For continuous traits, most phylogenetic comparative approaches to date employ a single trait value per species, often a mean of sampled individuals, or alternatively incorporate intraspecific variation as a distribution around such...

Data from: Transposon variants and their effects on gene expression in Arabidopsis

Xi Wang, Detlef Weigel & Lisa M. Smith
Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA-mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation...

Data from: A serial multiplex immunogold labeling method for identifying peptidergic neurons in connectomes

Réza Shahidi, Elizabeth A. Williams, Markus Conzelmann, Albina Asadulina, Csaba Verasztó, Sanja Jasek, Luis A. Bezares-Calderón & Gáspár Jékely
Electron microscopy-based connectomics aims to comprehensively map synaptic connections in neural tissue. However, current approaches are limited in their capacity to directly assign molecular identities to neurons. Here, we use serial multiplex immunogold labeling (siGOLD) and serial-section transmission electron microscopy (ssTEM) to identify multiple peptidergic neurons in a connectome. The high immunogenicity of neuropeptides and their broad distribution along axons, allowed us to identify distinct neurons by immunolabeling small subsets of sections within larger series....

Data from: First insights into the nature and evolution of antisense transcription in nematodes

Christian Rödelsperger, Kevin Menden, Vahan Serobyan, Hanh Witte & Praveen Baskaran
Background: The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in gene regulation has moved into focus of research. To characterize genome-wide patterns of antisense transcription and to study their evolutionary conservation, we sequenced a strand-specific RNA-seq library of the nematode Pristionchus pacificus. Results: We identified 1112 antisense configurations of which the largest group represents 465 antisense transcripts...

Data from: What causes mating system shifts in plants? Arabidopsis lyrata as a case study

Barbara K. Mable, Joerg Hagmann, Sang-Tae Kim, Aileen Adam, Elizabeth Kilbride, Detlef Weigel & Marc Stift
The genetic breakdown of self-incompatibility (SI) and subsequent mating system shifts to inbreeding has intrigued evolutionary geneticists for decades. Most of our knowledge is derived from interspecific comparisons between inbreeding species and their outcrossing relatives, where inferences may be confounded by secondary mutations that arose after the initial loss of SI. Here, we study an intraspecific breakdown of SI and its consequences in North American Arabidopsis lyrata to test whether: (1) particular S-locus haplotypes are...

Data from: Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

François Vasseur, Louise Fouqueau, Dominique De Vienne, Thibault Nidelet, Cyrille Violle & Detlef Weigel
Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude...

Data from: Independent FLC mutations as causes of flowering time variation in Arabidopsis thaliana and Capsella rubella

Ya-Long Guo, Marco Todesco, Jörg Hagmann, Sandip Das & Detlef Weigel
Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain...

Data from: Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.

Nagarjun Vijay, Jelmer W. Poelstra, Axel Künstner & Jochen B. W. Wolf
Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism π, alternative splicing), technological processing (sequencing error ε, library normalization) and bioinformatic workflow (de novo vs....

Data from: Adaptive diversification of growth allometry in the plant Arabidopsis thaliana

François Vasseur, Moises Exposito-Alonso, Oscar J. Ayala-Garay, George Wang, Brian J. Enquist, Denis Vile, Cyrille Violle & Detlef Weigel
Seed plants vary tremendously in size and morphology. However, variation and covariation between plant traits may at least in part be governed by universal biophysical laws and biological constants. Metabolic Scaling Theory (MST) posits that whole-organismal metabolism and growth rate are under stabilizing selection that minimizes the scaling of hydrodynamic resistance and maximizes the scaling of resource uptake. This constrains variation in physiological traits and in the rate of biomass accumulation, so that they can...

Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology

Kohta Yoshida & Jun Kitano
Karyotype, including the chromosome and arm numbers, is a fundamental genetic characteristic of all organisms and has long been used as a species-diagnostic character. Additionally, karyotype evolution plays an important role in divergent adaptation and speciation. Centric fusion and fission change chromosome numbers, whereas the intra-chromosomal movement of the centromere, such as pericentric inversion, changes arm numbers. A probabilistic model simultaneously incorporating both chromosome and arm numbers has not been established. Here, we built a...

Geographic parthenogenesis in the brown alga Scytosiphon lomentaria (Scytosiphonaceae): Sexuals in warm waters and parthenogens in cold waters

Masakazu Hoshino
Geographic parthenogenesis, a phenomenon where parthenogens and their close sexual relatives inhabit distinct geographic areas, has been considered an interesting topic in evolutionary biology. Reports of geographic parthenogenesis from land and freshwater are numerous, however, this occurrence has been rarely reported from the sea. Brown algae are mostly marine and are thought to include numerous obligate parthenogens; still, little is known about the distribution, origin, and evolution of parthenogens in this group. Here we report...

Data from: The recombination landscape in Arabidopsis thaliana F2 populations

Detlef Weigel, K. Bomblies, Joffrey Fitz, Roosa A. E. Laitinen, Norman Warthmann, Levi Yant & Patrice A. Salome
Recombination during meiosis shapes the complement of alleles segregating in the progeny of hybrids, and has important consequences for phenotypic variation. We examined allele frequencies as well as crossover locations and frequencies in over 7000 plants from 17 F2 populations derived from crosses between 18 Arabidopsis thaliana accessions. We observe segregation distortion between parental alleles in over half of our populations. The potential causes of distortion include variation in seed dormancy and lethal epistatic interactions....

Data from: Multi-locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events, and rare out-crossing

Katy Morgan, Angela McGaughran, Laure Villate, Matthias Herrmann, Hanh Witte, Gabi Bartelmes, Jacques Rochat & Ralf J. Sommer
Pristionchus pacificus, recently established as a model organism in evolutionary biology, is a cosmopolitan nematode that has a necromenic association with scarab beetles. The diverse array of host beetle species and habitat types occupied by P. pacificus make it a good model for investigating local adaptation to novel environments. The presence of P. pacificus on La Réunion Island, a young volcanic island with a dynamic geological history and a wide variety of ecozones, facilitates such...

Data from: Neuronal connectome of a sensory-motor circuit for visual navigation

Nadine Randel, Albina Asadulina, Luis A. Bezares-Calderón, Csaba Verasztó, Réza Shahidi, Gáspár Jékely, Elizabeth A Williams & Markus Conzelmann
Animals use spatial differences in environmental light levels for visual navigation; however, how light inputs are translated into coordinated motor outputs remains poorly understood. Here we reconstruct the neuronal connectome of a four-eye visual circuit in the larva of the annelid Platynereis using serial-section transmission electron microscopy. In this 71-neuron circuit, photoreceptors connect via three layers of interneurons to motorneurons, which innervate trunk muscles. By combining eye ablations with behavioral experiments, we show that the...

Data from: Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

Bonnie A. Fraser, Axel Künstner, David N. Reznick, Christine Dreyer & Detlef Weigel
Convergent evolution represents one of the best lines of evidence for adaptation, but few cases of phenotypic convergence are understood at the genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad provide a classic example of phenotypic convergent evolution, where adaptation to low or high predation environments has been found for a variety of traits. A major advantage of this system is the possibility of long-term experimental studies in nature, including transplantation from high...

Data from: Neandertal and Denisovan DNA from Pleistocene sediments

Viviane Slon, Charlotte Hopfe, Clemens L. Weiss, Fabrizio Mafessoni, Marco De La Rasilla & Carles Lalueza-Fox
Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA...

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