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opencc-zeroDec 2014View details →

Data from: Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems

Sex chromosomes have evolved many times in animals and studying these replicate evolutionary "experiments" can help broaden our understanding of the general forces driving the origin and evolution of sex chromosomes. However this plan of study has been hindered by the inability to identify the sex chromosome systems in the large number of species with cryptic, homomorphic sex chromosomes. Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling technology that can identify the sex chromosome systems in many species where traditional cytogenetic methods have failed. Using newly generated RAD-seq data from twelve gecko species, along with data from the literature, we reinterpret the evolution of sex-determining systems in lizards and snakes and test the hypothesis that sex chromosomes can routinely act as evolutionary traps. We uncovered between 17 and 25 transitions among gecko sex-determining systems. This is approximately ½ to ⅔ of the total number of transitions observed among all lizards and snakes. We find support for the hypothesis that sex chromosome systems can readily become trap-like and show that adding even a small number of species from understudied clades can greatly enhance hypothesis testing in a model-based phylogenetic framework. RAD-seq will undoubtedly prove useful in evaluating other species for male or female heterogamety, particularly the majority of fish, amphibian, and reptile species that lack visibly heteromorphic sex chromosomes, and will significantly accelerate the pace of biological discovery.

opencc-zeroDec 2013View details →

Data from: Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences

There is a lack of consensus on how next-generation sequence data should be considered for phylogenetic and phylogeographic estimates, with some studies excluding loci with missing data, while others include them, even when sequences are missing from a large number of individuals. Here we use simulations, focusing specifically on RAD sequences, to highlight some of the unforeseen consequence of excluding missing data from next-generation sequencing. Specifically, we show that in addition to the obvious effects associated with reducing the amount of data used to make historical inferences, the decisions we make about missing data (such as the minimum number of individuals with a sequence for a locus to be included in the study) also impact the types of loci sampled for a study. In particular, as the tolerance for missing data becomes more stringent, the mutational spectrum represented in the sampled loci becomes truncated such that loci with the highest mutation rates are disproportionately excluded. This effect is exacerbated further by factors involved in the preparation of the genomic library (i.e., the use of reduced representation libraries, as well as the coverage) and the taxonomic diversity represented in the library (i.e., the level of divergence among the individuals). We demonstrate that the intuitive appeals about being conservative by removing loci may be misguided.

opencc-by-4.0Nov 2023View details →

rAd-libraries barcode analysis underlying data

Open the record for dataset details and reuse information.

opencc-by-4.0Jun 2024View details →

Data for "Development and Evaluation of a New Correlated K-distribution Scheme for BCC_RAD Radiative Transfer Model"

Data and matlab scripts for plotting.

opencc-zeroApr 2022View details →

Plastome and RAD-seq of Polygonatum odoratum

Polygonatum odoratum (Mill.) Druce (Asparagaceae, Asparagales) is a widely cultivated medicinal herb in China. However, this useful herb is understudied despite being known as a medicinal resource with top grade medical and edible properties since long. In this study, P. odoratum and four cultivars were investigated. The variations in morphological characteristics and vegetative phases of each cultivars were observed. For genetic aspect, the plastid genome of P. odoratum varies in length from 154,569 bp to 155,491 bp, containing a large single-copy region of 83,486—84,459 bp, a small single-copy region of 18,292—18,471 bp, and two inverted repeats of 26,302—26,370 bp. A total of 131 genes were predicted, including 85 protein-coding, 38 tRNA, and eight rRNA genes. Genome comparisons revealed a slight variation in the sequence across the five accessions, but two highly variable regions (trnC-petN and rpl32-trnL) were detected when comparing the four different cultivars. For the RAD-seq markers, a total of 33.64 Gb of clean data, with an average value of 1.08 Gb per sample, were analyzed for presence of single nucleotide polymorphisms (SNPs). Well-resolved phylogenies of the P. odoratum cultivars are constructed; the non-monophyletic relationship in the plastome-based phylogenetic trees, yet monophyletic form in the RAD-based linkage map suggested possibility of hybrid cultivar for P. odoratum "Dazhu" (GDDZ), which was further supported by morphological observations. Quality assessment based on the standards of the Chinese Pharmacopoeia on Polygonati Odorati Rhizoma (POR) on the four cultivars used in this study recorded that PORs from P. odoratum 'Zhongzhu' (GDZZ) met the minimum criteria for the acceptance as raw material for medicinal drug production. This study has provided insights on the morphological variations, genetic background, and medicinal qualities of P. odoratum cultivars that could be explored for future genetic improvement as well as breeding programs of P. odoratum for POR production.

opencc-zeroDec 2012View details →

Data from: "RAD Sequencing for SNP Discovery in Two Populations of Bighorn Sheep (Ovis canadensis)" in Genomic Resources Notes accepted 1 April 2013 - 31 May 2013

In this work we present the development of a large set of single nucleotide polymorphisms (SNPs) discovered in two populations of bighorn sheep (Ovis canadensis). To do so we used restriction-site associated DNA (RAD) sequencing of four individuals from each population. Through alignment of reads to the domestic sheep (Ovis aries) genome we discovered >83,000 SNPs, of which >38,000 are suitable for assays such as an Illumina SNP chip. These loci will allow for fine-mapping of loci associated with horn size, and examination of the consequences of the genetic rescue including mapping genes underling differences in life-history characteristics.

opencc-zeroDec 2015View details →

Data from: PSMC (pairwise sequentially Markovian coalescent) analysis of RAD (restriction site associated DNA) sequencing data

The pairwise sequentially Markovian coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Although originally designed for whole-genome data, we here use simulations to investigate its applicability to reference genome-aligned restriction site associated DNA (RAD) data. We find that RAD data can potentially be used for PSMC analysis, but at present with limitations. The key factor is the proportion (p) of the genome that the RAD data covers. In our simulations, a proportion of 10% can still retain a substantial amount of coalescent information, whereas for 1% estimation becomes unreliable. The performance depends strongly on mutation rate (μ) and recombination rate (r) and is proportional to μ*p/r. When the value of this term is low, increasing the amount of data and number of iterations helps restoring the power of the estimation. We subsequently analyse one whole-genome-sequenced and 17 RAD-sequenced three-spined sticklebacks (Gasterosteus aculeatus) from a lake in Greenland. The whole-genome sequence suggests a relatively recent expansion and decline within ca. 4000–40 000 generations ago, possibly reflecting postglacial expansion and founding of the lake population. RAD data, where chromosomes from 10 individuals are combined, identify a similar pattern. Our study provides guidance about the use of PSMC analysis and suggests measures that can improve its utility for RAD data. Finally, the study shows that RAD loci in general contain coalescent information that can be used for developing more targeted methods.

opencc-zeroDec 2016View details →

Data from: Estimation of contemporary effective population size and population declines using RAD sequence data

Large genomic datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Using a linkage disequilibrium-based analysis, individual sampling (i.e., n ≥ 30) had the greatest effect on Ne estimation and the detection of population-size declines, with declines reliably detected across scenarios approximately 10 generations after they began. Coalescent-based inference required fewer sampled individuals (i.e., n = 15), and instead was most influenced by the size of the SNP dataset, with 25,000 to 50,000 SNPs required for accurate detection of population trends and at least 20 generations after decline began. The number of samples available and targeted number of RADseq loci are important criteria when choosing between these methods. Neither method suffered any apparent bias due to the effects of allele dropout typical of RAD data. With an understanding of the limitations and biases of these approaches, researchers can make more informed decisions when designing their sampling and analyses. Overall, our results reveal that demographic inference using RADseq data can be successfully applied to infer recent population size change and may be important tools for population monitoring and conservation biology.

opencc-zeroDec 2016View details →

Data from: RAD sequencing and genomic simulations resolve hybrid origins within North American Canis

Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes, in combination with genomic simulations, to test hypotheses of hybrid origins of Canis types in eastern North America. A principal components analysis revealed no evidence to support eastern wolves, or any other Canis type, as the product of grey wolf × western coyote hybridization. In contrast, simulations that included eastern wolves as a distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves and eastern coyotes. Our results support the eastern wolf as a distinct genomic cluster in North America and help resolve hybrid origins of Great Lakes wolves and eastern coyotes. The data provide timely information that will shed new light on the debate over wolf conservation in eastern North America.

opencc-zeroDec 2017View details →

Data from: Delimiting species of marine gastropods (Turridae, Conoidea) using RAD-sequencing in an integrative taxonomy framework

Species delimitation in poorly-known and diverse taxa is usually performed based on monolocus, DNA barcoding-like approaches, while multilocus data are often used to test alternative species hypotheses in well-studied groups. We combined both approaches to delimit species in the Xenuroturris / Iotyrris complex, a group of venomous marine gastropods from the Indo-Pacific. First, COI sequences were analyzed using three methods of species delimitation, ABGD, PTP and GMYC to propose primary species hypotheses (PSH). Second, RAD-seq data were also obtained and an IQ-tree phylogenetic tree produced. We tested the impact of the level of missing data on the robustness of the phylogenetic tree obtained with the RAD-seq data. Alternative species partitions revealed with the COI dataset were also tested using the RAD-seq data and the BFD method. The congruence between the species hypotheses proposed with the mitochondrial gene and the clades in the RAD-seq tree, together with the morphological variability of the shell and the radula and the distribution pattern, was used to turn the PSH into secondary species hypotheses (SSH). Allopatric PSH defined with the COI gene were interpreted to correspond to intraspecific structure. Most of the species are found sympatrically in the Philippines, and only one is confidently identified as a new species and described as Iotyrris conotaxis n. sp. The results obtained demonstrate the efficiency of the combined monolocus/multilocus approach to delimit species.

opencc-zeroDec 2018View details →

Supplementary material 2 from: Grewe F, Lagostina E, Wu H, Printzen C, Lumbsch HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91-113. https://doi.org/10.3897/mycokeys.43.29093

Overview of RADseq results after individual steps of RAD analyses :

Figure 3 from: Grewe F, Lagostina E, Wu H, Printzen C, Lumbsch HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91-113. https://doi.org/10.3897/mycokeys.43.29093

Figure 3 Genomic variation by non-parametric DAPC. ADAPC plot of the densities of U.antarctica (blue) and U.aurantiacoatra (green) on the first retained discriminant function B Bar plot of group membership probabilities.

Figure 2 from: Grewe F, Lagostina E, Wu H, Printzen C, Lumbsch HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91-113. https://doi.org/10.3897/mycokeys.43.29093

Figure 2 Pairwise Gst, G'st and D distribution. Pairwise values of Nei's Gst (green), Hedrick's G'st (blue) and Jost's D (yellow) are plotted by their frequency.

Figure 1 from: Grewe F, Lagostina E, Wu H, Printzen C, Lumbsch HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91-113. https://doi.org/10.3897/mycokeys.43.29093

Figure 1 Phylogenetic tree inferred from the U.antarctica and U.aurantiacoatraRADseq data. The clades of each species are highlighted by brackets. Bootstrap values are indicated at the branches. The unit of branch length is substitutions per site. Note that branches leading to both major clades were abbreviated by 0.4 substitutions per site.

opencc-zeroDec 2018View details →

Supplementary material 1 from: Grewe F, Lagostina E, Wu H, Printzen C, Lumbsch HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91-113. https://doi.org/10.3897/mycokeys.43.29093

Origin of samples used for this study :

Figure 4 from: Grewe F, Lagostina E, Wu H, Printzen C, Lumbsch HT (2018) Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91-113. https://doi.org/10.3897/mycokeys.43.29093

Figure 4 Clustered fineRADstructure co-ancestry matrix. A Full dataset including U.antarctica collected on the Antarctic Peninsula in addition to U.antarctica and U.aurantiacoatra collected on King George Island and Elephant Island B Reduced dataset with all U.antarctica and U.aurantiacoatra collected on King George Island and Elephant Island. Two major clades are corresponding to the two species U.antarctica (top-left) and U.aurantiacoatra (bottom-right). The top and left trees were calculated from the co-ancestry matrix to sort the individuals by their population structure. The matrix is diagonally split into the top-right half showing raw data and the bottom-left half displaying aggregated data.