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419 results for “capture data”
Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales
Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776–1516 UCE loci across the five species. Across species, 53–77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales.
Data from: An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)
Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron–exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic scales for frogs, including outgroups ~100 Myr divergent from the ingroup. We recovered a large phylogenomic data set consisting of sequence alignments for 1047 of the 1260 transcriptome-based loci (~561 000 bp) and a large quantity of highly variable regions flanking the exons in transcripts (~70 000 bp), the latter improving substantially by only including ingroup species (~797 000 bp). We recovered both shorter (<100 bp) and longer exons (>200 bp), with no major reduction in coverage towards the ends of exons. We observed significant differences in the performance of blocking oligos for target enrichment and nontarget depletion during captures, and differences in PCR duplication rates resulting from the number of individuals pooled for capture reactions. We explicitly tested the effects of phylogenetic distance on capture sensitivity, specificity, and missing data, and provide a baseline estimate of expectations for these metrics based on a priori knowledge of nuclear pairwise differences among samples. We provide recommendations for transcriptome-based exon capture design based on our results, cost estimates and offer multiple pipelines for data assembly and analysis.
Data from: Comparison of photo-matching algorithms commonly used for photographic capture-recapture studies
Photographic capture–recapture is a valuable tool for obtaining demographic information on wildlife populations due to its noninvasive nature and cost-effectiveness. Recently, several computer-aided photo-matching algorithms have been developed to more efficiently match images of unique individuals in databases with thousands of images. However, the identification accuracy of these algorithms can severely bias estimates of vital rates and population size. Therefore, it is important to understand the performance and limitations of state-of-the-art photo-matching algorithms prior to implementation in capture–recapture studies involving possibly thousands of images. Here, we compared the performance of four photo-matching algorithms; Wild-ID, I3S Pattern+, APHIS, and AmphIdent using multiple amphibian databases of varying image quality. We measured the performance of each algorithm and evaluated the performance in relation to database size and the number of matching images in the database. We found that algorithm performance differed greatly by algorithm and image database, with recognition rates ranging from 100% to 22.6% when limiting the review to the 10 highest ranking images. We found that recognition rate degraded marginally with increased database size and could be improved considerably with a higher number of matching images in the database. In our study, the pixel-based algorithm of AmphIdent exhibited superior recognition rates compared to the other approaches. We recommend carefully evaluating algorithm performance prior to using it to match a complete database. By choosing a suitable matching algorithm, databases of sizes that are unfeasible to match "by eye" can be easily translated to accurate individual capture histories necessary for robust demographic estimates.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.
Data from: Genomic-scale capture and sequencing of endogenous DNA from feces
Genomic-level analyses of DNA from non-invasive sources would facilitate powerful conservation and evolutionary studies in natural populations of endangered and otherwise elusive species. However, the typical low quantity and poor quality of DNA that is extracted from non-invasive samples have generally precluded such work. Here we apply a modified DNA capture protocol that, when used in combination with massively-parallel sequencing technology, facilitates efficient and highly-accurate resequencing of megabases of specified nuclear genomic regions from fecal DNA samples. We validated our approach by comparing genetic variants identified from corresponding fecal and blood DNA samples of six western chimpanzees (Pan troglodytes verus) across more than 1.5 megabases of chromosome 21, chromosome X, and the complete mitochondrial genome. Our results suggest that it is now feasible to conduct genomic studies in natural populations for which constraints on invasive sampling have otherwise long been a barrier. The data we collected also provided an opportunity to examine western chimpanzee genetic diversity at unprecedented scale. Despite high mitochondrial genome diversity (pi = 0.585%), western chimpanzees have a low ratio (0.42) of X chromosomal (pi = 0.034%) to autosomal (chromosome 21 pi = 0.081%) sequence diversity, a pattern that may reflect an unusual demographic history of this subspecies.
Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97 075 highly reliable in silico SNPs. These SNPs were distributed across 14 909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2%, for in silico SNPs compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications.
Data from: Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass
Recent molecular phylogenetic studies of polyploid plants have successfully clarified complex patterns of reticulate evolution. In this study of Elymus repens, an allohexaploid member of the wheat tribe Triticeae, chloroplast and nuclear DNA data reveal an extreme reticulate pattern, revealing at least five distinct gene lineages coexisting within the species, acquired through a possible combination of allohexaploidy and introgression from both within and beyond the Triticeae. Earlier cytogenetic studies of E. repens suggested that Hordeum (genome H) and Pseudoroegneria (St) were genome donors to E. repens. Chloroplast DNA data presented here (from the rpoA gene and from the region between trnT and trnF) identify three potential maternal genome donors (Pseudoroegneria, Thinopyrum, and Dasypyrum), and information from previous molecular work suggests that, of these, Pseudoroegneria is the most likely maternal donor. Nuclear starch synthase gene data indicate that both Hordeum and Pseudoroegneria have contributed to the nuclear genome of E. repens, in agreement with cytogenetic data. However, these data also show unexpected contributions from Taeniatherum, and from two additional donors of unknown identity. One of the sequences of unknown origin falls within the Triticeae, but is not closely associated with any of the sampled diploid genera. The second falls outside of the clade containing Triticeae and its outgroup Bromus, suggesting the acquisition of genetic material from a surprisingly divergent source. Bias toward the amplification of certain starch synthase variants has complicated attempts to thoroughly sample from within individuals, but the data clearly indicate a complex pattern of reticulate evolution, consistent not only with allohexaploidy, but also with introgression from unexpectedly divergent sources.
Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms
Recent advances in high-throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of non-model organisms. To multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in-solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR-generated probes (SCPP) protocol requires no specialized equipment, is highly flexible, and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25-100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.
Data from: Acquired versus innate prey capturing skills in super-precocial live-bearing fish
Live-bearing fish start hunting for mobile prey within hours after birth, an example of extreme precociality. Because prenatal, in utero, development of this behaviour is constrained by the lack of free-swimming sensory-motor interactions, immediate success after birth depends on innate, evolutionarily acquired patterns. Optimal performance however requires flexible adjustment to an unpredictable environment. To distinguish innate from postnatally developing patterns we analysed over 2000 prey capture events for 28 metallic livebearers (Girardinus metallicus; Poeciliidae), during their first 3 days after birth. We show that the use of synchronous pectoral fin beats for final acceleration and ingestion is fixed and presumably innate. It allows for direct, symmetrical control of swimming speed and direction, while avoiding head yaw. Eye movements and body curvatures, however, change considerably in the first few days, showing that eye-tail coordination requires postnatal development. The results show how successful prey captures for newborn, live-bearing fish are based on a combination of fixed motor programmes and rapid, postnatal development.
Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture
The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.
Data assessing survival variation between capture methods in white-tailed deer
<p>Understanding what variables affect ungulate neonate survival is imperative to successful conservation and management of the species. Predation is commonly cited as a cause-specific source of mortality and ecological covariates often influence neonate survival. However, variation in survival estimates related to capture methodology has been documented with opportunistically captured neonates generally displaying greater survival than those captured via aid of vaginal implant transmitters (VITs), likely because of increased left truncation observed in the opportunistically captured datasets. Our goal was to assess if 3- and 6-month survival estimates varied by capture method while simultaneously assessing if capture method affected model selection and interpretation of ecological covariates for white-tailed deer neonates captured from three study sites from 2014 to 2015 in North Dakota and South Dakota, USA. We found survival varied by capture method for 3-month neonate survival with opportunistically captured neonates displaying up to 26% greater survival than their counterparts captured via VITs; however, this relationship was not present for 6-month survival. We also found model selection and subsequent interpretation of ecological covariates varied when analyzing datasets comprised of neonates captured via VITs, neonates captured opportunistically, and all neonates combined regardless of capture method. When interpreting results from our VIT only analysis for 3-month survival, we found survival varied by three time intervals and was lowest in the first two weeks of life. Capture method did not affect 6-month survival, which was most influenced by total precipitation occurring during 3 – 8 weeks of a neonate's life and percent canopy cover found at a neonate's capture site. Our results support previous research that capture method must be accounted for when deriving survival estimates for ungulate neonates as it can impact derived estimates and subsequent interpretation of results. </p>
Data from: Next-generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)
Historical museum specimens are invaluable for morphological and taxonomic research, but typically the DNA is degraded making traditional sequencing techniques difficult to impossible for many specimens. Recent advances in Next-Generation Sequencing, specifically target capture, makes use of short fragment sizes typical of degraded DNA, opening up the possibilities for gathering genomic data from museum specimens. This study uses museum specimens and recent target capture sequencing techniques to sequence both Ultra-Conserved Elements (UCE) and exonic regions for lineages that span the modern spiders, Araneomorphae, with a focus on Palpimanoidea. While many previous studies have used target capture techniques on dried museum specimens (for example, skins, pinned insects), this study includes specimens that were collected over the last two decades and stored in 70% ethanol at room temperature. Our findings support the utility of target capture methods for examining deep relationships within Araneomorphae: sequences from both UCE and exonic loci were important for resolving relationships; a monophyletic Palpimanoidea was recovered in many analyses and there was strong support for family and generic-level palpimanoid relationships. Ancestral character state reconstructions reveal that the highly modified carapace observed in mecysmaucheniids and archaeids has evolved independently.
Multi Modal Workload Data Capture Experiment 1
<p>EEG, Video, Game Video and IMU dataset 1st experiment</p>
Development of a site fidelity index based on capture-recapture data at population level
<p>R codes and dataset supporting the results of this article</p>
Code and data for the article "Feasible deployment of carbon capture and storage and the requirements of climate targets"
<p>Here, we present data and code for our study “Feasible deployment of carbon capture and storage and the requirements of climate targets” (2024), where we project feasible ranges of carbon capture and storage (CCS) deployment in this century based on historical evidence of CCS deployment and other policy-driven technologies.</p>
Development of a site fidelity index based on population capture-recapture data
<p>Raw data supporting the results of the scientific article</p>
Data from: Sequence capture of ultraconserved elements from bird museum specimens
New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.
Data from: Drone‐based structure‐from‐motion photogrammetry captures grassland sward height variability
Grasslands deliver a range of ecosystem services, including the provision of food and biodiversity, and regulation of soil carbon storage and hydrology. Monitoring schemes are needed to quantify spatial changes in these multiple functions alongside ecosystem degradation. Sward height is widely recognised as a key spatial variable in the provision of these services. Current manual monitoring approaches are labour intensive, and often fail to capture spatial patterns of important features, including sward height. Proximal sensing from small aerial drones carrying lightweight cameras can be transformed into surface height models using image‐based structure‐from‐motion and Multi‐View Stereo‐based approaches; this presents a new opportunity for monitoring the spatial structure of grassland sward height. We combined aerial photographs with field survey data and an open‐source image‐based modelling‐processing workflow to generate sward height measurements for a field comprising mainly Lolium perenne (perennial ryegrass) and Trifolium pratense (red clover). We compared the derived measurements with in situ data captured on the same day using traditional agronomic sward height techniques to determine the quality of the drone‐derived surface model product for sward characterisation. The SfM and Multi‐View Stereo‐based surface model had a mean absolute sward height measurement error of between 3.7 and 4.2 cm. To produce field observations with equivalent quality would require up to 550 sward height measurements for the study site (area: 8,059 m2), which is not feasible over larger extents required for conservation of key species or agronomic purposes. Synthesis and applications. We demonstrate how the collection of precise and detailed information on the spatial structure of grasslands can be made over management‐relevant extents. Aerial digital photographs can be transformed into surface models using an image‐based modelling approach: structure‐from‐motion and Multi‐View Stereo techniques. Image‐based measurements of sward heights were compared with manual sward height data captured on the same day. This novel source of vegetation spatial information could improve sward management for conservation and agronomy applications. The approach supports frequent surveys, at user‐controlled revisit times, and delivers data for spatial monitoring of key grassland functions and services.
Data from: Portable bacteria-capturing chip for direct surface-enhanced Raman scattering identification of urinary tract infection pathogens
Acute urinary tract infections (UTIs) are one of the most common nosocomial bacterial infections, which affect almost 50% of the population at least once in their lifetime. UTIs may lead to lethal consequences if they are left undiagnosed and untreated properly. Early, rapid and accurate uropathogens detection methods play a pivotal role in clinical process. In this work, a portable bacteria-grasping surface-enhanced Raman scattering (SERS) chip for identification of three species of uropathogens (E. coli CFT 073, P. aeruginosa PAO1, and P. mirabilis PRM1) directly from culture matrix was reported. The chip was firstly modified with a positively-charged NH3+ group, which enable itself grasp the negatively-charged bacterial cells through the electrostatic adsorption principle. After the bacterial cells were captured by the chip, concentrated Ag nanoparticles (NPs) were used to obtain their Raman fingerprint spectra with recognizable characteristic peaks and good reproducibility. With the help of chemometric method such as discriminant analysis (DA), the SERS based chip allows a rapid, successful identification of three species of UTI bacteria with a minimal bacterial concentration (105 cells/mL) required for clinical diagnostics. In addition, this chip could spot the bacterial SERS fingerprints information directly from LB culture medium and artificial urine without sample pre-treatment. The portable bacteria-grasping SERS based chip provides a possibility for fast and easy detection of uropathogens, and viability of future development in healthcare applications.
Data from: Sequence capture versus restriction site associated DNA sequencing for shallow systematics
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture datasets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq datasets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of datasets and inferences with those of prior work. In RAD-Seq datasets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a dataset to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among datasets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas. We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography.
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International Brain Laboratory public data
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OpenNeuro
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