Find research datasets worth reusing

opencc-by-4.0Oct 2022View details →

Genome-wide association and multi-trait analyses characterize the common genetic architecture of heart failure

Genome-wide association study summary statistics.

opencc-by-sa-4.0Mar 2017View details →

Interplay between Genetics, Epigenetics & Exposures- Proposed Algorithm for Pediatric Cancer Development

opencc-by-4.0Dec 2016View details →

Cross-correlations and symmetries in genetic sequences

Data sets and supporting material used in the manuscript "The common origin of symmetry and structure in genetic sequences" by G. Cristadoro , M. Degli Esposti , E. G. Altmann https://arxiv.org/abs/1710.02348 Output of calculations can be seen in the file: Notebook.html In order to repeat calculations or explore different choices: <ol> <li>Download all files to the same directory</li> <li>Uncompress the "data.tar.gz" file (e.g., using tar -xzvf data.tar.gz)</li> <li>Open the Notebook using Python 3.0 in Jupyter (www.jupyter.org)</li> </ol>

opencc-by-4.0Nov 2017View details →

ASreml code and Data from the study "Between-population differences in the genetic and maternal components of body mass in roe deer"

This repository contains the source code (ASremL input files) and the data used to perform the QG analyses (univariate, bivariate, random regression animal models) in the study "Between-population differences in the genetic and maternal components of body mass in roe deer". Quéméré E et al.

opencc-zeroApr 2024View details →

EST-SSR genotyping data from: Ecotype variation in the endemic tree Callicarpa subpubescens on small oceanic islands: Genetic, phenotypic, and environmental insights

Callicarpa subpubescens, endemic to the Ogasawara Islands, is suggested to have multiple ecotypes in the Hahajima Islands, specifically in the central part of the Ogasawara Islands. In this study, associations between genetic groups and spatial distribution, habitat, leaf morphology, size structure, and flowering time of each genetic group were investigated on Hahajima and the satellite Imoutojima Islands. Genetic groups were identified using EST-SSR markers, revealing four ecotypes named based on morphological features: Dwarf (D), Glabrescent (G), Tall (T), and Middle (M), with M being a result of the hybridization of G and T. Ecotype D, adapted to dry environments, is characterized by small tree size, dense thick leaves with abundant hairs, and is distributed in dry scrub. Ecotype G, adapted to understory of mesic forests, lacks leaf hairs. Ecotype T, adapted to the canopy of mesic forests, has hairy leaves and is tall in tree height. Ecotype M, adapted to the canopy of mesic scrub or edges of mesic forests, has hairy leaves but with a shorter tree height than ecotype T. Flowering peaks differed among all ecotype pairs except G and M, but the flowering times more or less overlapped among all ecotypes, suggesting that pre-mating isolation among ecotypes is not perfect. Post-mating isolation is considered absent, as there were no differences in the results, germination, and survival rates of one-year seedlings among inter- and intra-ecotype crossings. The existence of such ecotypes provides valuable insights into the ongoing speciation processes adapting to the oceanic island environments.

opencc-zeroApr 2024View details →

Data from: Genetic variation in growth and leaf traits associated with local adaptation to climate in yellow birch (Betula alleghaniensis Britton)

Understanding patterns of variation in functional traits of hardwood trees is crucial for conserving and managing North American temperate forests under climate change. This study examined provenance variation of yellow birch (Betula alleghaniensis Britton) in growth, biomass allocation, leaf morphology, and stable carbon isotope composition. Trees were grown from ten seed sources originating from across Canada and the northern USA. Height and diameter were not significantly related to climate at seed origin, suggesting that variation may be better explained by site factors, such as soil pH and soil moisture. In contrast, carbon isotope composition and leaf morphological traits were significantly correlated to climate variables including temperature, precipitation, and solar radiation. Provenances from warmer, drier localities tended to have higher stable carbon isotope ratio (δ13C), greater specific leaf area, and narrower leaf width than their counterparts from cooler, wetter climates. Thus, variation in leaf morphological traits appears to be involved in adaptation of yellow birch to variation in temperature and moisture availability across the species' range. Our results suggest that there may exist potential for selection and breeding of drought resistant yellow birch genotypes to aid in reforestation under climate change.

opencc-by-4.0Apr 2024View details →

StArt_Protocol - Phytoparasitic nematodes of Musa spp. with emphasis on sources of genetic resistance: a systematic review

Protocolo do StArt da revisão sistemática Phytoparasitic nematodes of Musa spp. with emphasis on sources of genetic resistance: a systematic review

opencc-zeroApr 2024View details →

Data from: Genetic diversity in tempo determines foraging range in ants

The foraging behavior of a colony arises from the activity of individual workers. In this paper we explore the phenotypic differences among the workers of the western harvester ant, Pogonomyrmex occidentalis in order to understand the temporal pattern of foraging in colonies. We know that the genetic diversity of colonies influences the temporal pattern of foraging: with greater genetic diversity colonies begin foraging earlier and forage for greater duration. We test two mechanisms to account for this pattern. The Temperature Hypothesis predicts that early foragers will be more active at lower temperatures than late foragers and will be the first workers to initiate foraging. Late foragers will be more active at high temperatures. The Tempo Hypothesis predicts that early foragers will be the first to forage because they have the higher overall tempo of activity at all temperatures. We measure the movement activity of samples of early and late foragers from 32 colonies over a range of temperatures from 9-37̊C. We find that early workers are more active at all temperatures than late workers, supporting the Tempo Hypothesis. Early and late foragers tend to belong to different patrilines, suggesting that there is a genetic basis for the difference in the tempo of behavior. We also find that colonies that have greater number of patrilines, due to greater mating frequency by the queen, have a greater range temporal range of foraging.

opencc-by-4.0Apr 2024View details →

Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes - Identifying the host taxon of a previously undescribed plasmid

We investigated the taxonomic association of an unknown plasmid within a plaque biofilm of a patient diagnosed with stage 3 periodontitis. We combined long- and short- read sequencing to identify a complete plasmid with minimal homology to any sequence in the RefSeq database. The plasmid carried several predicted genes for mobilization and toxin-antitoxin systems. We designed MGE-FISH probes for the plasmid and combined this MGE-FISH stain with an 18-genera HiPR-FISH panel. Images are labeled by collection time such that the laser order for a given field of view (fov) is: 488nm Lambda, 514nm Lambda, 561nm Lambda, 633nm Airyscan, 405nm Lambda. We used Flye (https://github.com/fenderglass/Flye) to assemble the plasmid using long read Nanopore sequencing only and we used OPERA-MS (https://github.com/CSB5/OPERA-MS) to do hybrid assembly with Illumina short reads and Nanopore long reads. The assemblies are in the fasta files and the reads that map to the assemblies are in the fastq files.

opencc-by-4.0Apr 2024View details →

Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes - Combined MGE and taxonomic mapping

We used rRNA-FISH to stain five common oral genera, Veillonella, Streptococcus, Corynebacterium, Lautropia, and Neisseria, each with a different fluorophore, and we used MGE-FISH to stain the termL gene of the active prophage with a sixth fluorophore. We assembled contigs using combined long- and short-read sequencing and identified a highly abundant plasmid. Alignment of this contig to the plasmid database (PLSDB) showed that the plasmid had previously been observed in Prevotella nigrescens (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_018127865.1/). We selected two genes from the contig with metallo-β-lactamase (MBL) domains as targets for MGE-FISH (https://www.uniprot.org/uniprotkb/V8CNR4/entry, https://www.uniprot.org/uniprotkb/V8CNR9/entry). We stained both putative MBL genes (pMBL) with the same color using MGE-FISH. For taxonomic mapping, we broadened our target panel by employing HIPR-FISH. We selected a target panel of 18 genera that are highly abundant and prevalent in human plaque. We designed a HiPR-FISH spectral encoding using a 5-fluorophore combinatorial barcoding scheme, whereby each fluorophore represents a binary bit, providing 31 possible barcodes (2^5 - 1 = 31). The fluorophore for MGE-FISH was spectrally distinct from those of HiPR-FISH, enabling simultaneous implementation of both methods. Images are labeled by collection time such that the laser order for a given field of view (fov) is: 488nm Lambda, 514nm Lambda, 561nm Lambda, 633nm Airyscan, 405nm Lambda. We used OPERA-MS (https://github.com/CSB5/OPERA-MS) to do hybrid assembly with Illumina short reads and Nanopore long reads. The assemblies are in the fasta files and the reads that map to the assemblies are in the fastq files.

Data from: dispersal restriction and facilitation in species with differing tolerance to development: a landscape genetics study of native and introduced lizards

Aim: The development of natural habitats into urban land uses has greatly accelerated in the recent past due to human activities. This habitat development disrupts species' natural dispersal processes and can lead to both direct and indirect impacts on dispersal. Whether human activities result in restricted or facilitated dispersal may depend on a species' development tolerance; however, this premise has not been tested. We examined the impact of urbanization and road networks on the dispersal of three lizard species in the context of their development tolerance. Location: Curaçao Methods: To quantify species' development tolerance, we modelled three lizard species abundances at sites based on surrounding landscape development. Using microsatellite genotypes, we conducted individual-based resistance surface analyses and modelled the effect of habitat development on genetic admixture to assess indirect dispersal restriction and facilitation. We explored direct facilitation of dispersal using network analysis of mitochondrial haplotypes. Results: Phyllodactylus martini, a native gecko species, was the least tolerant of development and experienced indirect dispersal restriction due to roads, according to resistance surface analyses. Anolis lineatus, a native anole species, exhibited a neutral relationship with development. Resistance surfaces and Structure analyses showed that A. lineatus faced indirect dispersal restrictions from roads and developed areas, while mitochondrial haplotype networks suggested they benefited from occasional human-facilitated long-distance dispersal events. Hemidactylus mabouia, an introduced gecko species, was the most tolerant of development, and experienced no dispersal restriction, but mitochondrial haplotypes suggest direct long-distance dispersal facilitation. Main conclusions: Our findings highlight development tolerance as a key predictor of dispersal impact for these species and future work should test whether these patterns are upheld in other systems. Understanding how human activities affect species' dispersal will aid in managing introduced species while promoting connectivity for native species navigating dispersal challenges in dynamic landscapes.

Ecological, genetic and geographical divergence explain differences in sunbird (Nectariniidae) colouration

Bird plumages are among the most elaborate ornaments, displaying almost all colours of the rainbow. Why and how birds are so colourful remains an open question with multiple and sometimes competing hypotheses. Different colours in different patches might have different functions and thus result from different forms of selection (e.g., natural vs. sexual selection). Here we test three hypotheses that might explain colour differences: (1) species isolation, (2) light environment, and (3) Brownian motion. We show that both natural and sexual selection affect the evolution of sunbird colouration, but that their extent and direction differs between sexes, by species interactions, and for different patches across the body. Even though overlap in the light environment explains part of colour differences in species, no colour metric (brightness and chroma) correlates to the light environment. It is likely that these results, where multiple forms of selection influence colouration in different ways, are more general across birds, highlighting the need to investigate bird colouration as a network of individual but inter-connected colour patches.

Data from: Small but connected islands can maintain populations and genetic diversity under climate change

In response to the striking effects of environmental change, conservation strategies often include the identification of conservation areas that can effectively maintain vulnerable species. Consequently, identifying system-specific conditions that maintain the demographic and genetic viability of species of conservation concern is essential. Connectivity plays a critical role in the persistence of populations. Islands have been model systems to understand connectivity and metapopulation processes and have emerged as particularly favorable targets for conservation. While islands can be isolated from mainland disturbances, it is unknown what degree of isolation is necessary to avoid unfavorable changes but remain sufficiently connected to maintain population viability. To test this question, we explored connectivity within the Apostle Islands, an archipelago of 22 islands within Lake Superior, by comparing historical and contemporary trends in ice bridge connectivity and by simulating the effect of reduced connectivity within this system. We developed a demographically informed individual-based model to explicitly test the role of connectivity to influence the persistence and genetic diversity of American marten (Martes americana), a forest carnivore at risk across its southern range boundary. We found that genetic diversity was resilient to moderate changes in ice cover, but a complete loss of connectivity resulted in rapid genetic erosion. Despite genetic erosion, populations persisted as long as nominal connectivity occurred between islands. Our work suggests that connectivity will decline, but martens would be resilient to moderate changes, and, in the short term, the Apostle Islands can act as a refuge along this species' southern range boundary. Identifying thresholds in connectivity that maintain populations but allow for isolation from disturbance will be necessary to identify suitable areas for species conservation across space and time.

Data from: Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish

Recent work has revealed the importance of contemporary evolution for shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically-important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead / resident rainbow trout (Oncorhynchus mykiss). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size-structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident O. mykiss populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.

opencc-by-4.0Feb 2014View details →

Data from: Admixture facilitates genetic adaptations to high altitude in Tibet

Genotype data for the 69 high altitude Sherpa individuals from   Jeong C, Alkorta-Aranburu G, Basnyat B, Neupane M, Witonsky DB, Pritchard JK, Beall CM, Di Rienzo A. Admixture facilitates genetic adaptations to high altitude in Tibet. Nat Commun. 2014;5:3281. doi: 10.1038/ncomms4281. PMID: 24513612; PMCID: PMC4643256.   Files are in PLINK binary format.

Genetic architecture of heritable leaf microbes

Background Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown, yet fundamental to the community assembly of host-associated microbiomes, and with implications for the eco-evolutionary dynamics of microbes and hosts. Using Ipomoea hederacea, Ivy-leaved morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome, and how these two sources of genetic variation contributed to microbe heritability. Results We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation were important in contributing to microbe heritability, and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some microbes in the leaf microbiome. Conclusions The genetic architecture of plant-associated microbiomes depends on both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. Our results demonstrate the roles of different scales of host genetic variation in the assembly of a natural microbiome. The genetic basis and heritability of a host's microbial phenotype is important for host evolution and ecology because microbes can affect host fitness, and because it can influence reciprocal selection between hosts and microbiomes. Additionally, when host-associated microbiomes have heritability, then this suggests they have the capacity to evolve as other host traits might, with potentially adaptive functions.

Genome-wide single nucleotide polymorphisms reveal the genetic diversity and population structure of Creole goats from northern Peru

Goat farming constitutes a significant source of income for farmers in northern Peru. There is currently an absence of information about the genetics of Peruvian Creole goats that would enable us to understand their origins and genetic spread. The objective of this study was to estimate the genetic diversity of Creole goats from northern Peru using SNP markers. This study involved the collection of 192 male Creole goats from three key goat production regions in northern Peru. These goat samples were genotyped using the GGPGoat70k SNP panel. To explore the genetic influence of other breeds on Peruvian Creole goats, our dataset was combined with previously published SNP genotypes. External data set includes multiple breeds genotypes sampled from Argentina, Brazil, Spain, and Alpine breed from Italy, France, and Switzerland. After quality control 52,832 autosomal SNPs were used to assess genetic diversity in the Peruvian goats. For the population structure analysis of the merged data 20,513 common SNPs were used. Estimations for expected heterozygosity (He), observed heterozygosity (Ho), and inbreeding coefficient (FIS) were computed for the Peruvian groups. AMOVA, principal component analysis and ADMIXTURE were conducted to evaluate the population structure in the two data sets, Peru and merged. The results revealed a considerable genetic diversity, with Ho values ranging from 0.40 to 0.41 for the Peruvian sampling groups, and inbreeding coefficient was notably low for Peruvian goat. The population structure analysis demonstrated a distinction (p< 0.05) from other breeds. These findings suggest a level of genetic differentiation of the Peruvian goat population among other breeds, although further research is needed considering samples from other Peruvian areas. We expect this study will contribute to define genetic management strategies to prevent the loss of genetic diversity in Peruvian goat populations and for upcoming advancements in this field.

Data from: Patterns of constitutive and induced herbivore defense are complex, but share a common genetic basis in annual and perennial monkeyflower

Despite multiple ecological and evolutionary hypotheses that predict patterns of phenotypic relationships between plant growth, reproduction, and constitutive and/or induced resistance to herbivores, these hypotheses do not make any predictions about the underlying molecular genetic mechanisms that mediate these relationships. We investigated how divergent plant life-history strategies in the yellow monkeyflower and a life-history altering locus, DIV1 influence plasticity of phytochemical herbivory resistance traits in response to attack by two herbivore species with different diet breadth. Life-history strategy (annual vs. perennial) and the DIV1 locus significantly influenced levels of constitutive herbivory resistance, as well as resistance induction following both generalist and specialist herbivory. Perennial plants had higher total levels of univariate constitutive and induced defense than annuals, regardless of herbivore type. Annuals induced less in response to generalist herbivory than did perennials, while induction response was equivalent across the ecotypes for specialist herbivory. The effects of the DIV1 locus on levels of constitutive and induced defense were dependent on genetic background, the annual versus perennial haplotype of DIV1, and herbivore identity. The patterns of univariate induction due to DIV1 were non-additive and did not always match expectations based on patterns of divergence for annual/perennial parents. For example, perennial plants had higher levels of constitutive and induced defense than did annuals, but when the annual DIV1 was present in the perennial genetic background induction response to herbivory was higher than for the perennial parent lines. Patterns for multivariate defense arsenals generally echoed those of univariate, with annual and perennial monkeyflowers and those with alternative versions of DIV1 differing significantly in constitutive and induced resistance. Like univariate resistance, induced multivariate defense arsenals were affected by herbivore identity. Our results highlight the complexity of the genetic mechanisms underlying plastic response to herbivory. While a genetic locus underlying substantial phenotypic variation in life-history strategy and constitutive defense also influences defense plasticity, the induction response also depends on genetic background. This result demonstrates the potential for some degree of evolutionary independence between constitutive and induced defense, or induced defense and life-history strategy, in monkeyflowers.

Data from: Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens

The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, Melitaea diamina, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.