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Additional files for manuscript titled 'The double round-robin population unravels the genetic architecture of grain size in barley'

Additional file 1: Parental allele for barley orthologs of genes controlling grain size in rice Additional file 2: Cross-validation of quantitative trait loci (QTLs) detected for grain size characters in rice Additional file 3: Adjusted entry means of recombinant inbred lines of 45 HvDRR sub-populations

opencc-by-4.0Jul 2021View details →

Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code, Numerical and Primary data.

Uploaded under this Zenodo DOI is the following: 1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs). 2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files. 3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments.  4. Excel worksheets that contain the numerical source data for all qPCR bar plots.

opencc-zeroApr 2022View details →

Effects of genetic vs. environmental quality on condition-dependent morphological and life history traits in a neriid fly

Condition is assumed to reflect both genes and environment, enabling condition-dependent signals to reveal genetic quality. However, because the phenotypic effects of variation in genetic quality could be masked by environmental heterogeneity, the contribution of genetic quality to phenotypic variation in fitness-related traits and condition-dependent signals remains unclear. We compared effects of ecologically relevant manipulations of environmental quality (nutrient dilution in the larval diet) and genetic quality (one generation of inbreeding) on male and female morphology, life history and reproductive performance in the neriid fly Telostylinus angusticollis. We found that larval diet quality had strong, positive effects on male and female body size, male secondary sexual traits, and aspects of male and female reproductive performance. By contrast, inbreeding had weak effects on most traits, and no trait showed clear and consistent effects of both environmental and genetic quality. Indeed, inbreeding effects on body size and male competitive performance were of opposite sign in rich vs. poor larval diet treatment groups. Our results suggest that environmental quality strongly affects condition, but the effects of genetic quality are subtle and environment-dependent in this species. These findings raise questions about the genetic architecture of condition and the potential for condition-dependent traits to function as signals of genetic quality.

opencc-zeroApr 2022View details →

Genetic architecture of adaptive radiation across two trophic levels

Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20,000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology, and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed Quantitative Trait Locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.

Immune and genetic signature of HER2-driven breast carcinomas triggering anti-Yo paraneoplastic cerebellar degeneration

<ul> <li>Supplementary eTables from: Immune and genetic signature of HER2-driven breast carcinomas triggering anti-Yo paraneoplastic cerebellar degeneration: <ul> <li>eTables 1: Results of DESeq2 on the differential gene expression analysis between Yo-PCD and control tumours for all genes and for differentially expressed genes.</li> <li>eTables 2: Results of the Gene Ontology enrichment performed by clusterProfiler on genes over-expressed in Yo-PCD tumours</li> <li>eTables 3: Results of the Gene Ontology enrichment performed by clusterProfiler on genes under-expressed in Yo-PCD tumours</li> </ul> </li> <li>Gene counts</li> <li>Gene TPMs</li> </ul>

Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability

While selfing populations harbor little genetic variation limiting evolutionary potential, the causes are unclear. We experimentally evolved large, replicate populations of Mimulus guttatus for nine generations in greenhouses with or without pollinating bees and studied DNA polymorphism in descendants. Populations without bees adapted to produce more selfed seed yet exhibited striking reductions in DNA polymorphism despite large population sizes. Importantly, the genome-wide pattern of variation cannot be explained by a simple reduction in effective population size, but instead reflects the complicated interaction between selection, linkage, and inbreeding. Simulations demonstrate that the spread of favored alleles at few loci depresses neutral variation genome-wide in large populations containing fully selfing lineages. It also generates greater heterogeneity among chromosomes than expected with neutral evolution in small populations. Genome-wide deviations from neutrality were documented in populations with bees, suggesting widespread influences of background selection. After applying outlier tests to detect loci under selection, two genome regions were found in populations with bees, yet no adaptive loci were otherwise mapped. Large amounts of stochastic change in selfing populations compromise evolutionary potential and undermine outlier tests for selection. This occurs because genetic draft in highly selfing populations makes even the largest changes in allele frequency unremarkable.

Phenotypic plasticity and genetic diversity in a polyploid Arabidopsis complex

Polyploid species possess more than two sets of chromosomes and may show high gene redundancy, hybrid vigor and masking of deleterious alleles compared to their parent species. Following this, it is hypothesized that this makes them better at adapting to novel environments than their parent species, possibly due to phenotypic plasticity. The allopolyploid Arabidopsis suecica and its parent species A. arenosa and A. thaliana were chosen as a model system to investigate relationships between phenotypic plasticity, fitness and genetic variation. Particularly, we test if A. suecica is more plastic, show higher genetic diversity and/or have higher fitness than its parent species. Wild Norwegian populations of each species were analyzed for phenotypic responses to differences in availability of nutrient, water and light, while genetic diversity was assessed through analysis of AFLP markers. Arabidopsis arenosa showed a higher level of phenotypic plasticity and higher levels of genetic diversity than the two other species, probably related to its outbreeding reproduction strategy. Furthermore, a general positive relationship between genetic diversity and phenotypic plasticity was found. Low genetic diversity were found in the inbreeding A. thaliana. Geographic spacing of populations might explain the clear genetic structure in A. arenosa, while the lack of structure in A. suecica could be due to coherent populations. Fitness measured as allocation of resources to reproduction, pointed towards A. arenosa having lower fitness under poor environmental conditions. Arabidopsis suecica, on the other hand, showed tendencies towards keeping up fitness under different environmental conditions.

opencc-by-4.0May 2022View details →

The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances

Microsatellite dataset of the wood mouse (Apodemus sylvaticus) and the bank vole (Myodes glareolus). The dataset of the wood mouse is constituted of 194 samples and 7 microsatellite markers: WM_194ind_7STRs.txt The dataset of the bank vole is constituted of 199 samples and 8 microsatellite markers: BV_199ind_8STRs.txt Each locus is encoded in the three-digit format (e.g., 126126) and each column corresponds to a locus specified in the order at the beginning of the file, following the GENEPOP format. Pop indicates the beginning of a new location.   Locus name in WM_194ind_7STRs.txt Locus_1    AS-7-FAM Locus_2    AS-12-PET Locus_3    AS-20-NED Locus_4    AS-34-FAM Locus_5    GTTD9A-PET Locus_6    AS-11-VIC Locus_7    MS-AF-8-NED   Locus name in BV_199ind_8STRs.txt Locus_1    Cg13B8-F_FAM Locus_2    Cg6A1-F_VIC Locus_3    Cg3F12-F_PET Locus_4    Cg13H9-F_PET Locus_5    Cg2E2-F_VIC Locus_6    Cg3E10-F_FAM Locus_7    Cg2A4-F_FAM Locus_8    Cg3A8-F_NED

opencc-by-4.0Feb 2022View details →

Genetic basis of growth reaction to drought stress differs in contrasting high-latitude treeline ecotones of a widespread conifer

Raw and filtered SNP data and raw tree ring data of the analysed trees. R scripts for SNP filtering, phenotypic data and genotype-phenotype association analysis.

Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow

Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g., multiple large, old inversions that are FST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic.

Effects of insularity on genetic diversity within and among natural populations

We conducted a review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together "insularity"). Using populations from within the same studies, we were able to control for between-study variation in methodology, as well as demographic and life histories. Contradictory to typical expectations, insularity had relatively minor effects on GD within and among population, which points to the more important roles of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen – particularly in systems (i.e. studies) where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non-insular populations of the same system – suggesting an important role for the "scope" of influences on GD. These conclusions were more robust for within - population GD than among - population GD, although a number of biases might underlie this difference. Overall, our findings indicate that population-level genetic assumptions need to be tested rather than assumed in nature, particularly for topics highly relevant to current conservation management practices.

Epistatic selection on a selfish Segregation Distorter supergene: drive, recombination, and genetic load

Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive- the driver and the target- linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal, multilocus, male meiotic drive system, Segregation Distorter (SD) in the fruit fly, Drosophila melanogaster. In African populations, the predominant SD chromosome variant, SD-Mal, is characterized by two overlapping, paracentric inversions on chromosome arm 2R and nearly perfect (~100%) transmission. We study the SD-Mal system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying Sd, the main driving allele, and one or more factors within the double inversion. While most SD-Mal chromosomes are homozygous lethal, SD-Mal haplotypes can recombine with other, complementing haplotypes via crossing over, and with wildtype chromosomes via gene conversion. SD-Mal chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, SD-Mal haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of SD haplotypes in different populations around the world, and have implications for supergene evolution broadly.

opencc-by-4.0May 2022View details →

"Do you want to know who you are?" The rise of genetic ancestry testing and the search for genealogies: an anonymized survey from Sweden

Full, anonymized survey data on genetic genealogy, ancestry and identity conducted by the Swedish Genealogical Society as part of a research project funded by the HERA joint research program "Uses of the Past"

Figure 4 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 4 Holotype of Andrias jiangxiensis sp. nov. (KIZ 037731) in preservative A–C: Holotype of A. jiangxiensis sp. nov., in dorsal (A), lateral (B), and ventral (C) views. D, E: Dorsal (D) and ventral (E) views of head of holotype of A. jiangxiensis sp. nov. F, G: Ventral view of the left hand (F) and left foot (G) of the holotype of A. jiangxiensis sp. nov. Photos by Chen-Qi Lu.

Figure 7 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 7 The habitat of Andrias jiangxiensis sp. nov. in Daqi Mountain, Jing'an County, Jiangxi, China A, B: Summer (A) and winter (B) scene of 8–10 meters-wide stream with excellent vegetation coverage. C: Abreeding cave for A. jiangxiensis sp. nov. found in a backwater bay of the stream. Red arrow indicates the exit of the cave. D: Enlarged area near the exit of the cave. Dashed circles in cyan indicate six larvae of A. jiangxiensis sp. nov., and the ones in white indicate the co-occurring shrimps and fishes. Photos by Mu-Rong Yi.

Figure 3 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 3 Genetic distinctiveness of CGS from clade U2 found in Jing'an County, Jiangxi, China A: Asimplified phylogeny based on COI of mtDNA modified from Yan et al. (2018), in which clade U2 represents haplotypes found in Jing'an County, Jiangxi. The clade to which A. davidianus belongs remains uncertain. Clade Dindicates the haplotypes of A. sligoi according to the analyses by Turvey et al. (2019). B: Maximum Likelihood (ML) network based on genomic SNPs for six clades. Light purple background marks the 28 individuals of clade U2. C, D: PcoA plots based on genomic SNPs for six clades. E: Genetic clustering (K=2–8, best K=7) based on genomic SNPs from six clades by ADMIXTURE analysis. Asterisks label 18 wild-caught individuals including larvae, juveniles, and adults from Daqi Mountain, diamonds in light purple indicate 10 farm-bred individuals. Colors in all figures correspond with the mtDNA clades.

Figure 2 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 2 Results of field-monitoring surveys in Daqi Mountain, Jiangxi Jiulingshan National Nature Reserve (Sep. 2020–Mar. 2022) A: Capture per person-hour of juveniles and adults during Sep. 2020–Mar. 2022. B, C: Activity periods of newborn larvae displayed by capture per person-hour in 2021 and 2022.

Figure 6 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 6 Ontogenetic variation in coloration pattern A: Coloration of dorsum with spotted pattern in a juvenile with body length of ~20 cm. B: Coloration of dorsum having larger patch patterns in an adult with body length over 50 cm. Photos by Mu-Rong Yi.

Figure 5 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 5 The holotype of Andrias jiangxiensis sp. nov. (KIZ 037731) in life A–C: Coloration of dorsum of whole body (A), head (B), and enlarged view (C) of left periocular area. Photos by Chen-Qi Lu.

Figure 1 in Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities.

Figure 1 Map of survey localities in Jing'an County, northwest of Jiangxi, China The west part of black dashed line displays the historical distribution areas of CGS, upstream of River Liao. Red dashed line circles Daqi Mountain, which is closed to the public. Grey triangles indicate 16 sites surveyed without detection of individuals, while the red triangle and red line display the searching sites with detections.