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opencc-zeroDec 2016View details →

Data from: Multi-DICE: R package for comparative population genomic inference under hierarchical co-demographic models of independent single-population size changes

Population genetic data from multiple taxa can address comparative phylogeographic questions about community-scale response to environmental shifts, and a useful strategy to this end is to employ hierarchical co-demographic models that directly test multi-taxa hypotheses within a single, unified analysis while benefiting in statistical power from aggregating datasets. This approach has been applied to classical phylogeographic datasets such as mitochondrial barcodes as well as reduced-genome polymorphism datasets that can yield 10,000s of SNPs, produced by emergent technologies such as RAD-seq and GBS. A strategy for the latter had been accomplished by adapting the site frequency spectrum to a novel summarization of population genomic data across multiple taxa called the aggregate site frequency spectrum (aSFS), which potentially can be deployed under various inferential frameworks including approximate Bayesian computation, random forest, and composite likelihood optimization. Here, we introduce the R package Multi-DICE, a wrapper program that exploits existing simulation software for straight-forward and flexible execution of hierarchical model-based inference using the aSFS, which is derived from genomic-scale data, as well as mitochondrial data. We validate several novel software features such as applying alternative inferential frameworks, enforcing a minimal threshold of time surrounding event pulses, and specifying flexible hyperprior distributions. In sum, Multi-DICE provides comparative analysis within the familiar R environment while allowing a high degree of user customization, and will thus serve as a valuable tool for comparative phylogeography and population genomics.

opencc-zeroDec 2017View details →

Data from: Heritability estimates from genome wide relatedness matrices in wild populations: application to a passerine, using a small sample size

Genomic developments have empowered the investigation of heritability in wild populations directly from genome wide relatedness matrices (GRM). Such GRM based approaches can in particular be used to improve or substitute approaches based on social pedigree (PED-social). However, measuring heritability from GRM in the wild has not been widely applied yet, especially using small samples and in non-model species. Here, we estimated heritability for four quantitative traits (tarsus length, wing length, bill length and body mass), using PED-social and a pedigree corrected by genetic data (PED-corrected) and GRM from a small sample (n = 494) of blue tits from natural populations in Corsica genotyped at nearly 50,000 filtered SNPs derived from RAD-seq. We also measured genetic correlations among traits and we performed chromosome partitioning. Heritability estimates were slightly higher when using GRM compared to PED-social, and PED-corrected yielded intermediate values, suggesting a minor underestimation of heritability in PED-social due to incorrect pedigree links, including extra-pair paternity, and to lower information content than the GRM. Genetic correlations among traits were similar between PED-social and GRM but credible intervals were very large in both cases, suggesting a lack of power for this small dataset. Although a positive linear relationship was found between the number of genes per chromosomes and the chromosome heritability for tarsus length, chromosome partitioning similarly showed a lack of power for the three other traits. We discuss the usefulness and limitations of the quantitative genetic inferences based on genomic data in small samples from wild populations.

opencc-zeroDec 2013View details →

Data from: Genome size variation affects song attractiveness in grasshoppers: evidence for sexual selection against large genomes

Genome size is largely uncorrelated to organismal complexity and adaptive scenarios. Genetic drift as well as intragenomic conflict have been put forward to explain this observation. We here study the impact of genome size on sexual attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers show particularly large variation in genome size due to the high prevalence of supernumerary chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance and fitness costs if present in high numbers. We ranked male grasshoppers by song characteristics that are known to affect female preferences in this species and scored genome sizes of attractive and unattractive individuals from the extremes of this distribution. We find that attractive singers have significantly smaller genomes, demonstrating that genome size is reflected in male courtship songs and that females prefer songs of males with small genomes. Such a genome size dependent mate preference effectively selects against selfish genetic elements that tend to increase genome size. The data therefore provide a novel example of how sexual selection can reinforce natural selection and can act as an agent in an intragenomic arms race. Furthermore, our findings indicate an underappreciated route of how choosy females could gain indirect benefits.

opencc-zeroDec 2014View details →

Data from: Ploidy and domestication are associated with genome size variation in Palms

PREMISE OF THE STUDY: The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe. METHODS: Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci. KEY RESULTS: The coconut genome is large—averaging 5.966 pg—and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes. CONCLUSIONS: Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.

opencc-zeroDec 2014View details →

Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water

Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.

opencc-zeroDec 2019View details →

Data from: Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (Ne), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had little effect on either fitness correlate, which were determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low Ne and long-term isolation can represent important sources of variation and be capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

opencc-zeroApr 2016View details →

Data used for ALife 2016 paper "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes"

The results files in this directory contain the evolved critical mutation rates, exponential or quadratic curves produced by curve-fitting using the given data in R, and biological data used for comparison in the following paper: Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-Length Genomes, accepted for publication in ALife 2016: Proceedings of the 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV)

opencc-by-4.0May 2017View details →

Data used for submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover"

Datasets generated and presented in the submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover".

opencc-by-4.0May 2017View details →

Data used for submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover".

Datasets generated and presented in the submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover". Includes the results of statistical analysis.

opencc-by-4.0May 2017View details →

Data used for submission entitled "Critical Mutation Rate has an Exponential Dependence on Population Size for Eukaryotic-length Genomes with Crossover".

Figure 2 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition

Figure 2. Bayesian consensus tree resulting from the LW-Rh and Wg gene alignments (871 bp). Coloured dots on the branches indicate the values of posterior probability (PP): green dots represent values between 1.00 and 0.95, yellow dots between 0.94 and 0.90, and red dots ≤ 0.89. The nodes are indicated with numbers. Values above and below the branches represent the ancestral genome size (GS; 1C-values, in picograms) at particular nodes: in blue is the value generated by the maximum likelihood (ML) [asterisks are related to confidence interval (CI) values shown in Supporting Information, Table S4]; orange is the value generated by maximum parsimony (MP); and black, given below the branches, is the value generated by Bayesian inference (BI). Genome size data (1C-values) were obtained in the present work (pink dots) or taken from the literature (grey dots).

Figure 1 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition

Figure 1. Fluorescence intensity histograms obtained from three different species, with Drosophila melanogaster as internal standard, stained with propidium iodide (PI; A–C) or 4,6-diamidino-2-phenylindole (DAPI; D–F). The x-axis corresponds to the scale of fluorescence intensity, and the y-axis represents the number of nuclei with that fluorescence intensity.

Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling

Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C peaks represent diploid cells, and 4C peaks represent cells in the G2 phase of the cell cycle, with replicated DNA. Standard used: Solanum pseudocapsicum 2C = 2.61 pg. A, Himacerus apterus female with 2n = 36 + XX and 2C = 9.71 pg. B, Nabis maoricus female with 2n = 16 + XX and 2C = 4.21 pg.

Figure 2 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling

Figure 2. Nuclear DNA content stained with propidium iodide (PI) compared with relative nuclear DNA content stained with 4′,6-diamidino-2-phenylindole (DAPI). The line represents the trend in GC content, with a minimum of 33.34% and a maximum of 37.83%. Each pair of black and white symbols represents one specimen, as follows: circles, females; squares, males; white symbols, DAPI; black symbols, PI.

Figure 1 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling

Figure 1. Chromosomes of Nabidae species studied, stained with Giemsa (A, D, F, G, M) or with an 18S ribosomal DNA (rDNA) probe (red) applied via fluorescence in situ hybrization (FISH) (B, C, E, H–L, N–P). A, B, Nabis punctatus ♀ 2n = 16 + XX, mitotic metaphase. C, Himacerus apterus ♀ 2n = 36 + XX, mitotic metaphase. D, Nabis rugosus ♂ 2n = 16 + XY + 1 metaphase I, specimen with an additional chromosome (arrow). E, Nabis maoricus ♀ 2n = 18 + XX, mitotic metaphase. F, N. maoricus ♂ 2n = 16 + XY, postpachytene, with sex chromosomes superspiralized. G, H, Nabis biformis ♀ 2n = 16 + XX, mitotic metaphase, with two 18S rDNA signals on each X chromosome. I, Nabis limbatus ♀ 2n = 16 + XX, mitotic metaphase, species with the most distal 18S rDNA signal. J, N. rugosus ♂ 2n = 16 + XY, mitotic metaphase, species with the two 18S rDNA signals on Y chromosome. K, Prostemma guttula ♂ 2n = 26 + XY, metaphase II. L, N. maoricus ♂ 2n = 16 + XY, metaphase II, with Y chromosome showing no 18S rDNA signal. M, N, Prostemma aeneicolle ♀ 2n = 26 + XX, mitotic metaphase. O, H. apterus ♀ 2n = 36 + XXXX, mitotic metaphase, with terminal 18S rDNA signals on four X chromosomes originated by fragmentation. P, N. maoricus ♀ 2n = 18 + XXX, mitotic metaphase, with one X chromosome fragmented outside of the 18S rDNA position. Arrowheads indicate 18S rDNA signal; X and Y are the sex chromosomes. Scale bars: 10 μm.

Figure 3 in The tight genome size of ants: diversity and evolution under ancestral state reconstruction and base composition

Figure 3. Mean genome size (in picograms and megabase pairs) estimated for Formicidae subfamilies. The phylogenetic tree generated in the present study was redrawn, with collapsed branches corresponding to species of the same subfamily.

Figure 4 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling

Figure 4. Comparison of three alternative hypotheses on the ancestral 2n number of chromosomes of Nabidae: fusions, proposed by Nokkala et al. (2007); autosomal polyploidy, suggested by Kuznetsova & Maryańska-Nadachowska (2000) and supported by nuclear DNA content data from the present study; and the hypothetical fission theory. Abbreviations: 2C, nuclear DNA content; F, autosomal fusions; Fis, fissions; P, polyploidy.

opencc-by-4.0Dec 2023View details →

Genome size predicts diatom abundance in the polar ocean

This repository contains the datasets, code, and results for: Roberts et al. 2024. Genome size predicts diatom abundance in the polar ocean.

opencc-zeroFeb 2022View details →

Novel genomic insights into body size evolution in cetaceans and a resolution of Peto's Paradox

Cetaceans (whales, dolphins, and porpoises) have undergone a radical transformation from the typical terrestrial mammalian body plan to a streamlined one while exhibited dramatic inter-specific size ranges. However, the molecular mechanisms underlying the diversifying evolution of cetacean body size are largely unknown. Here, by using genome and phenotypic data from 22 cetaceans, we seek to investigate the genome-wide gene-phenotype correlation and to explore the genetic basis under the high diversity of body size in cetaceans. Results of the functional enrichment showed that body size-related genes in cetaceans were enriched in pathways associated with immunity, cell growth, and metabolism, suggesting their potential roles in the diversifying evolution of body size in cetaceans. A series of genes was also found coevolution with body size that are mainly involved in immune surveillance, tumor suppression function, and development of 'cheater' tumors. This in turn suggests that the genes play a role in tumor control and thus resolve Peto's paradox, a finding that the expansion in body size and thereby cell number does not correlate with increases in cancer incidence in larger whales. The present study could provide novel insights into the evolution of great body size variation in cetaceans.