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publicNov 2023View details →

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

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publicDec 2025View details →

Data from: Multispecies pangenomes reveal a pervasive influence of population size on structural variation

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publicDec 2020View details →

Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture

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publicOct 2024View details →

Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders

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opencc-by-4.0Dec 2019View details →

Data set related to the manuscript "Ionic liquids under confinement: From systematic variations of the ion and pore sizes towards an understanding of structure and dynamics in complex porous carbons"

Graphical files in the agr format for all the figures in the main text of the manuscript entitled "Ionic liquids under confinement:  From systematic variations of the ion and pore sizes towards an understanding of structure and dynamics in complex porous carbons" (10.1021/acsami.9b16740). Example of input file for one of the systems simulated.

opencc-zeroDec 2017View details →

Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation

Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.

opencc-zeroDec 2018View details →

Data from: Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis

Premise of the study: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in rarity. Here, we compare genetic variation among varieties of Astragalus lentiginosus differing in range size. Additionally, we ask if genetic structure exists in A. l. var. piscinensis, a rare taxon consisting of several thousand individuals that persist on ~8 km2 of alkaline soil. Methods: We compared genetic variation among 11 varieties of A. lentiginosus differing in range size using a genotyping by sequencing (GBS) approach, which generated 11,475 single nucleotide polymorphisms (SNPs). We characterized genetic structure among subpopulations of A. l. var. piscinensis using a second GBS dataset of 7,274 SNPs and explored associations between genetic structure and environmental variation. Key results: We found no association between genetic variation and range size among varieties of A. lentiginosus. Additionally, despite the extremely small range of A. l. var. piscinensis, we report a well-defined genetic structure among subpopulations associated with microhabitat variation in soil composition. Conclusion: Our results suggest that fine scale genetic structure may exist within other rare Astragalus taxa and that rarity does not preclude the maintenance of genetic diversity in this genus. In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.

opencc-zeroOct 2019View details →

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

Aim: Wetland habitats, and the ecological restrictions imposed by them, structure patterns of genetic variation in constituent taxa. As such, genetic variation may reflect properties of the specific biomes species inhabit, or shared life history traits among species may result in similar genetic structure. We evaluated these hypotheses jointly by quantifying the similarity of genetic structure in three South American marsh rat species (Holochilus), and test how genetic variation in each species relates to biome‐specific environmental space and historical stability. Location: South America. Taxon: Rodentia. Methods: Using complementary analyses (Mantel tests, dbRDA, Procrustes, covariance structure of allele frequencies and environmental niche models [ENMs]) with 8,000–32,000 SNPs per species, we quantified the association between genomic variation and geographic and/or environmental differences. Results: Significant association between genetic variation and geography was identified for all species. Similarity in the strength of the association suggests connectivity patterns dictated by shared species‐traits predominate at the biome scale. However, substantial amounts of genetic variation are not explained by geography. Focusing on this portion of the variance, we demonstrate a significant quantitative association between genetic variation and the environmental space of a biome, and a qualitative association with varying regional stability. Specifically, historically stable areas estimated from ecological niche models are correlated with local levels of geographic structuring, suggesting that local biome‐specific histories affect population isolation/ connectivity.

opencc-zeroDec 2019View details →

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses

Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9% of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after 10 replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1102 SVs carried by 52.4 to 80.1% of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.

opencc-zeroFeb 2020View details →

Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability

The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon. Here, we explain this association by elucidating a mutational cascade, downstream of <a>th</a>e single cell division error of chromosome bridge formation, that rapidly generates extreme genomic complexity. We show that actomyosin forces are required for initial bridge breakage and mutagenesis, following which chromothripsis accumulates with aberrant interphase replication of bridge DNA. This is then followed by an unexpected burst of DNA replication in the next mitosis, generating extensive DNA damage. During this second cell division, broken bridge chromosomes frequently mis-segregate and form micronuclei, promoting additional chromothripsis. We <a>fu</a>rther show that this mutational cascade generates the continuing evolution and sub-clonal heterogeneity characteristic of many human cancers.

opencc-zeroMay 2020View details →

Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes

Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8–12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.

opencc-zeroDec 2012View details →

Data from: Variation in population structure and dynamics of montane forest tree species in Ethiopia guide priorities for conservation and research

The greatest extent of Afromontane environments in the world is found in Ethiopia. These areas support exceptional biodiversity, but forest cover and ecological integrity have declined sharply in recent decades. Conservation and management efforts are hampered in part by an inadequate understanding of the basic ecology of major tree species. We investigated population structure and inferred population dynamics from size frequency distributions of 22 forest tree species encountered in montane forests of Ethiopia. We collected new empirical data from four sites in the Bale Mountains, where some of the country's most extensive and least disturbed forests remain, and conducted a systematic review and analysis of all such studies that reported population structure for one or more of these species in Ethiopia. Thirteen widespread montane tree species showed a reverse-J size distribution, indicating a relatively stable population structure. Six other species had size-frequency distributions that indicate episodic recruitment and/or removal of certain size classes. Specific causes of these patterns are uncertain: they may involve timber harvesting, herbivory, fire, or natural disturbances, but patterns were inconsistent and locality dependent. For three other tree species, existing data are inadequate for any interpretation of population structure and dynamics. A species of particular conservation concern that emerged from this analysis was Hagenia abyssinica, which was found in all areas to consist only of larger individuals with no recent recruitment. For management and conservation purposes, the species in most urgent need of new research are those with inadequate or inconsistent data, and H. abyssinica..

opencc-by-4.0Dec 2016View details →

Data files for: Structural variation shapes the landscape of recombination in mouse

Supplementary data files for the manuscript "Structural variation shapes the landscape of recombination in mouse."

opencc-zeroOct 2023View details →

Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories, and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger-scale genomic variation. We employed long-read sequencing technologies to generate a chromosome-scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing datasets, we constructed the first pan-genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan-genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions, however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan-genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.

opencc-zeroApr 2024View details →

Striking variation in chromosome structure within Musa acuminata and its diploid cultivars

The majority of cultivated bananas originated from inter- and intra(sub)specific crosses between two wild diploid species, Musa acuminata and Musa balbisiana. Hybridization and polyploidization events during the evolution of bananas led to the formation of clonally propagated cultivars characterized by a high level of genome heterozygosity and reduced fertility. The combination of low fertility of edible clones and differences in the chromosome structure among M. acuminata subspecies greatly hampers the breeding of improved banana cultivars. Using comparative oligo painting we investigated large chromosomal rearrangements in a set of wild M. acuminata subspecies and cultivars that originated by natural crosses. Additionally, we analyzed chromosome structure of F1 progeny that resulted from crosses between Mchare bananas and wild M. acuminata 'Calcutta 4' genotype. Analysis of chromosome structure within M. acuminata revealed the presence of a large number of chromosomal rearrangements showing a correlation with banana speciation. Chromosome painting of F1 hybrids was complemented by Illumina resequencing, which enabled to identify the contribution of parental subgenomes to the diploid hybrid clones. Balanced presence of both parental genomes was revealed in all F1 hybrids with the exception of one clone, which contained only Mchare specific SNPs, and thus most probably originated from an unreduced diploid gamete of Mchare.

opencc-by-4.0Jan 2022View details →

Spatiotemporal variation of the 2010 Yushu Mw 6.9 earthquake sequence: Insight from the 3-D electrical resistivity structure

This dada set will be available in GRL, it was support by the Chinese Earthquake Administration, and it was also supported by the National Natural Science Foundation of China (Grant No. 41674081).

opencc-zeroApr 2022View details →

Spatial variation in human disturbances and their effects on forest structure and biodiversity across an Afromontane forest

Context Human disturbances can have large impacts on forest structure and biodiversity, and thereby result in forest degradation, a property difficult to detect by remote sensing. Objectives To investigate spatial variation in anthropogenicdisturbances and their effects on forest structure and biodiversity. Methods In 144 plots of 20 x 20 m distributed across a forest area of 750 km2 in Southwest Ethiopia, we recorded: landscape variables (e.g., distance to forest edge), different human disturbances, forest structure variables, and species composition of trees and epiphyllous bryophytes. We then first assessed if landscape variables could explain the spatial distribution of disturbances. Second, we analysed how forest structure and biodiversity were influenced by disturbances. Results Human disturbances, such as coffee management and grazing declined with distance to forest edges and penetrated at least a kilometer into the forest. The slope was not related to disturbance levels, but several types of disturbances were less common at higher elevations. Among human disturbance types, coffee management reduced liana cover and was associated with altered species composition of trees. The presence of large trees and basal areas was not related to any of the disturbance gradients. Conclusions Although most anthropogenic disturbances displayed clear edge effects, surprisingly the variation in the chosen forest degradation indices was only weakly related to these disturbances. We suggest that the intersection between edge effects and forest degradation is very context-specific and relies much on how particular societies use the forests. For example, in this landscape coffee management seems to be a key driver.

opencc-zeroMay 2022View details →

Data from: Variations in bark structural properties affect both water loss and carbon economics in neotropical savanna trees in the Cerrado region of Brazil

Even after complete stomatal closure, plants lose water through the leaf cuticles and bark. This residual water conductance of leaves (gleaf-res) and stems (gbark) can negatively impact plant water balance and affect plant survival in seasonally dry environments. However, little is known about the costs and benefits associated with such water leaks, especially on stem level. Here, we characterized the structural and functional determinants of the variability in gbark across tropical savanna species to elucidate how variations in this trait are related to contrasting growth strategies. The high variability in gbark across species was associated with morphoantomical properties of the outer bark (thickness, density, and lenticel investment), and such characteristics influenced both stem transpiration and respiration, suggesting the existence of a trade-off between water conservation and oxygen permeability, which reflected contrasting growth and dehydration tolerance strategies. For instance, species with higher gbark and gleaf-res presented a fast resource acquisition strategy but were more prone to drought-induced mortality by hydraulic failure. However, model simulations revealed that the relative contribution of gleaf-res and gbark to overall water balance depended on whether leaves were less or more resistant to cavitation than the stems. Synthesis. By combining correlative studies, experimental results, and a modeling exercise, we provide a new understanding of the costs and benefits associated with the variability in gbark across tropical savanna species, and a new perspective for studies of water relations and carbon economics in species from a hyperdiverse savanna.

opencc-zeroMay 2022View details →

Body size variation in polyplacophoran mollusks: geographic clines and community structure along the Southeastern Pacific

Aim: To evaluate the latitudinal pattern of body size within and among chiton species employing phylogenetically structured analyses, and to examine the role of geographic variation in temperature, productivity and oxygen availability as potential environmental drivers. Location: Coastal habitats of the Southeastern Pacific along a latitudinal range of nearly 6,000 km, from the Equator to Patagonia (~ 2º to 56º S). Time Period: Present (2011 – 2017). Major taxa: 31 species of polyplacophoran mollusks. Methods: We measured the body length of 6,162 individuals collected in 62 sites, and reconstructed the phylogeny of this group based on two mitochondrial and one nuclear gene regions. We combined this information with data of sea surface temperature, chlorophyll-a concentration –as a proxy of primary productivity– and dissolved oxygen, and assessed which variables best explain the variation in size both within and among species employing phylogenetic generalised least squares (PGLS) and a model comparison approach. Main conclusions: Our analyses show that body size increases consistently with latitude, both within and among species, following Bergmann's rule. Variation in sea surface temperature along the latitudinal gradient provided a substantially better fit than chlorophyll-a and dissolved oxygen. Our results support the temperature-size rule for this lineage and suggest that similar processes could underlie the emergence of intra and interspecific gradients in body size of polyplacophorans. At the community level, chiton species richness was higher at intermediate latitudes and positively correlated with body size variation, suggesting that heterogeneity in size may reduce interspecific competition and contribute to species coexistence in this group. Overall, our study demonstrates that historical events, macroecological adaptive trends and local processes at the community level contribute to the distribution and size variation of polyplacophoran species along the Southeastern Pacific.