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opennotspecifiedDec 2017View details →

FIGURE 41 in A revision of the genus Lepidobrya Womersley (Collembola: Entomobryidae) based on morphology and sequence data of the genotype

FIGURE 41. Abundance in numbers per trap day of Lepidobrya mawsoni on Macquarie Island from December 1992 until December 1993.

opencc-by-4.0Oct 2016View details →

Dataset from 'Billino,J., Hennig, J., & Gegenfurtner K.R. (2016). Association between COMT genotype and the control of memory guided saccades: Individual differences in healthy adults reveal a detrimental role of dopamine. Vision Research. doi: 10.1016/j.visres.2016.10.001'

Dataset associated with the following publication: Billino,J., Hennig, J., & Gegenfurtner K.R. (2016). Association between COMT genotype and the control of memory guided saccades: Individual differences in healthy adults reveal a detrimental role of dopamine. Vision Research. doi: 10.1016/j.visres.2016.10.001 <a></a> -------------------------------------------------------------- The folder contains 4 data files and 1 description file providing column labels. The data file 'maindata.txt' contains the complete dataset including all analyzed parameters. The data file 'accuracybydelay.txt' contains accuracy data across delay conditions, providing the dataset for Figure 3A. The data file 'accuracybyamplitude.txt' contains accuracy data across target amplitude conditions, providing the dataset for Figure 3B. The data file 'singlesublanding.txt' contains landing positions of primary memory guided saccades from three subjects of different genotype groups, providing the dataset for Figure 3C. ------------------------------------------------------------- For further questions, please contact: jutta.billino[at]psychol.uni-giessen.de

opencc-by-4.0May 2024View details →

Locityper loci database, 1KGP genotypes and benchmarking data

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opencc-zeroJan 2024View details →

Genotype likelihoods for low-coverage whole-genome sequencing data of yellow warblers

The following datasets include the required input files used to empirically test population assignment in WGSassign on Yellow Warbler data. The file "yewa.known.ind105.ds_2x.beagle.gz" includes the filtered variants of 105 Yellow Warbler individuals output as genotype likelihoods and stored in a Beagle-formatted file. The ID file, "yewa.known.ind105.reference.IDs.txt", is a tab-delimited file with 2 columns, the first being the sample ID, and the second being the known reference population. The sample order in the ID file should match that of the input beagle file. To measure the assignment accuracy of WGSassign, we used leave-one-out cross validation using the input beagle file and our ID file.

opencc-by-4.0Dec 2023View details →

Contribution of parasite and host genotype to immunopathology of schistosome infections

The present dataset contains all the phenotype data (.csv files) and R scripts used for data analysis and generation of figures (Fig. 2-6) present in the manuscript entitled "Contribution of parasite and host genotype to immunopathology of schistosome infections."

opencc-by-4.0Mar 2024View details →

Iranian Sheep Genotypes

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opencc-by-4.0Jul 2024View details →

Defensive symbiont genotype distributions are linked to parasitoid attack networks - Dataset and scripts

This R project includes data and scripts for paper - Defensive symbiont genotype distributions are linked to parasitoid attack networks Script for analysis:     Run all the scripts in order, to get all analyses and results in this paper.      Script_0_package_install_load.R:          Installs and loads the necessary R packages required for all subsequent scripts.         This R project     Script_1_Extract_from_Table_S2.R         Extracts information from:             Table_S2.csv (located in /Rawdata/)    Data_4_Aphid_sequences.fas         Generates 10 files for further analyses:             Aphid relatedness distance:               Aphid_phylogenetic_relatedness_16species.csv               Aphid_phylogenetic_relatedness_22species.csv               Aphid_phylogenetic_relatedness_31species.csv             Hamiltonella - Aphid Matrices:               Hamiltonella_Aphid_matrix_16species.csv               Hamiltonella_Aphid_matrix_22species.csv               Hamiltonella_Aphid_matrix_31species.csv             Parasitoid - Aphid Matrices:               Para_Aphid_matrix_16species.csv               Para_Aphid_matrix_22species.csv             Plant - Aphid Matrices:               Plant_Aphid_matrix_16species.csv               Plant_Aphid_matrix_31species.csv     Script_2_BarPlot_Fig1.R:          Generates Fig. 1 using:              Data_11_Parasitoid_genus_aphid_22_species_Fig.1.csv  Data_12_Plant_genus_aphid_31_species_Fig.1.csv         The bar order in Fig. 1 is arranged by proportion, which is not directly supported in the ggplot2 package in R. Therefore, we need manually reordered if using the first plot code; or, manually colour it using the second plot code.      Script_3_MMRR_analysis.R         Uses 10 distance/distribution matrices of Parasitoid, Plant, Hamiltonella, and Aphid relationships to compute matrix correlations with the MMRR (Multiple Matrix Regression with Randomization) model.     Script_4_Species_linkage_Fig2_FigS4.R         Uses 7 distribution matrices of Parasitoid, Plant, and Hamiltonella relationships with Aphids (excluding Aphid genetic distance matrices) to generate the species linkage diagrams for Fig. 2 and Fig. S4, For aesthetic purposes, unconnected sample points have been moved.     Script_5_MMRR_Fig3_FigS5.R         Plots the MMRR correlations using the 10 distance/distribution matrices for Parasitoid, Plant, Hamiltonella, and Aphid relationships (Fig. 3 & Fig. S5).      Script_6_parasitoid_specialization_Fig4.R         Computes specialization levels using the H2 Index for:             Parasitoid-Aphid             Aphid-Hamiltonella             Parasitoid-Hamiltonella relationships          Generates Figure 4.     Script_7_Ecologicial_indices&plots_Table1_FigS3.R         Uses 7 distribution matrices of Parasitoid, Plant, and Hamiltonella relationships with Aphids (excluding Aphid genetic distance matrices) to:             Calculate ecological indices (Richness, Shannon Index, Simpson Index).             Use linear models to analyze the relationships between Parasitoid/Plant-Aphid and Aphid-Hamiltonella communities.            Outputs results for Table 1 and Figure S3.     Script_8_Bubble_plot_FigS2.R         This script using              Hamiltonella_Aphid_matrix_31species.csv          and two phylogeny trees              Data_8_Aphid_species_phylogeny.txt &              Data_9_Hamiltonella_phylogeny.txt         To create a Cophylogeny tree of Hamiltonella strains and aphid species that we identified in this study and previously known strains. (Fig. S2)     Script_9_DADA2_pipeline.R         This script is the DADA2 pipeline used to processing the raw COI sequencing data into ASV (Amplicon Sequence Variant) count files. After processing, the ASV files required manual curation to link each ASV with a distinct parasitoid and aphid species name based on BLAST results. In our updated version, we have provided both the raw data (BioProject PRJNA1139364) as well as the manually curated files (Data_1 and Data_2) which includes the ASV species names. All subsequent analyses can be reproduced using the curated datasets (Data_1 and Data_2), ensuring clarity and replicability for users.         We have incorporated the SRA Toolkit to streamline the process. This allows users to download raw SRR sequencing files directly and convert them into FASTQ files, which can then be input into the DADA2 pipeline. The pipeline produces two ASV count files, one for each sequencing run.   Raw data and inofrmation:     Table_S2.csv         The Dataset from Supplementary Table S2: After manual pooling the Parasitoid/Aphid species based on the Data_1,2 and 6.             No: the number of this sample             City: The city that collected this sample             Location: the location of sample collection             Sample category: Aphid mummies or alive aphids             Sample code: the name of sample (self defined)             Collection year: when this sample was collected             Aphid taxa / Wasp taxa / Plant species /Hamiltonella strain: The Aphid/Parasitoid/Plant/Hamiltonella species              Sequencing method: Illumina or Sanger sequencing                Sequencing date: the date of sending this sample to sequencing             Data source: From this study or from Wu et al. 2022: Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species     Data_1_Deep_sequencing_data_block_1.xlsx & Data_2_Deep_sequencing_data_block_2.xlsx          Sample: The sample name from Illumina sequencing, which can later be found on GenBank (BioProject PRJNA1139364).         Aphid: The detected aphid species for each sample.         Parasitoid: The detected parasitoid species.         The remaining columns contain ASV (Amplicon Sequence Variant) data derived from high-throughput barcoding sequencing.         Data1 and Data_2 are the manually curated versions of the BioProject PRJNA1139364 with added species names for each ASV.      Data_3_Parasitoid sequences.fas &      Data_4_Aphid sequences.fas &      Data_5_Hamiltonella sequences.fas,         FASTA files for:             Parasitoid species             Aphid species             Hamiltonella strains         These sequences were used for phylogenetic reconstruction and subsequent analyses.     Data_6_Parasitoid_Aphid_pooled_table.xlsx          Contains the OTU (Operational Taxonomic Unit) manual pooling results for Parasitoid and Aphid species based on 99% (4 base pair) sequence similarity:             Parasitoid pooling together group & Aphid pooling together group: Original names from Illumina sequencing.             Original name: Representative sequences for each group.             Pooled species name: Final species names used in all analyses.             Pooled sequences: Final representative sequences used in all analyses.             The result of manual pooling see the Table_S2.csv     Data_7_Parasitoid_species_phylogeny.txt & Data_8_Aphid_species_phylogeny.txt & Data_9_Hamiltonella_phylogeny.txt          Phylogenetic trees for:             Parasitoid species             Aphid species             Hamiltonella strains         These trees were generated using the PhyML tool on the ATGC Montpellier platform, original fasta file was Data_3, 4 & 5.     Data_10_aphid_host_info.csv          Provides aphid host information for generating Figure 2 and Figure S4:         Aphid: Names of aphid species included in this study.         Host: Host categories:             1: Herb aphids             2: Grass aphids             3: Tree aphids         Host_category: Detailed descriptions of host categories.     Data_11_Parasitoid_genus_aphid_22_species_Fig.1.csv & Data_12_Plant_genus_aphid_31_species_Fig.1.csv          Reduced matrices used for Figure 1, created by merging data from:             OTUs associated with the same parasitoid species.             Plant species belonging to the same genus.     7 Distribution Matrices (from Script_1_Extract_from_Table_S2.R)         Hamiltonella-Aphid Matrices:            Hamiltonella_Aphid_matrix_16species.csv             Hamiltonella_Aphid_matrix_22species.csv             Hamiltonella_Aphid_matrix_31species.csv         Parasitoid-Aphid Matrices:             Para_Aphid_matrix_16species.csv             Para_Aphid_matrix_22species.csv         Plant-Aphid Matrices:             Plant_Aphid_matrix_16species.csv             Plant_Aphid_matrix_31species.csv         Structure:             Rows represent aphid species.             Columns represent Hamiltonella strains, parasitoid species, or host plant species linked to each aphid species.         Usage: These matrices were used to generate Figures 2, 3, 4, Figures S2, S3, S4, S5, and for MMRR tests, ecological indices, and H2 index calculations.     3 Aphid phylogenetic relatedness matrices derived from Script_1_Extract_from_Table_S2.R         Aphid_phylogenetic_relatedness_16species.csv         Aphid_phylogenetic_relatedness_22species.csv         Aphid_phylogenetic_relatedness_31species.csv         These matrices provide phylogenetic distance information, showing pairwise genetic distances between the 31 aphid species included in this study.     SraRunTable.csv         The BioProject (PRJNA1139364) information downloaded directly from Genbank.

opencc-zeroNov 2021View details →

Genotyping validates the efficacy of photographic identification in a capture-mark-recapture study based on the head scale patterns of the prairie lizard (Sceloporus consobrinus)

Population studies often incorporate capture-mark-recapture (CMR) techniques to gather information on long-term biological and demographic characteristics. A fundamental requirement for CMR studies is that an individual must be uniquely and permanently marked to ensure reliable reidentification throughout its lifespan. Photographic identification involving automated photographic identification software has become a popular and efficient non-invasive method for identifying individuals based on natural markings. However, few studies have a) robustly assessed the performance of automated programs by using a double-marking system or b) determined their efficacy for long-term studies by incorporating multi-year data. Here, we evaluated the performance of the program Interactive Individual Identification System (I3S) by cross-validating photographic identifications based on the head scale pattern of the prairie lizard (Sceloporus consobrinus) with individual microsatellite genotyping (N=863). Further, we assessed the efficacy of the program to identify individuals over time by comparing error rates between within-year and between-year recaptures. Recaptured lizards were correctly identified by I3S in 94.1% of cases. We estimated a false rejection rate (FRR) of 5.9% and a false acceptance rate (FAR) of 0%. By using I3S we correctly identified 97.8% of within-year recaptures (FRR=2.2%; FAR=0%) and 91.1% of between-year recaptures (FRR=8.9%; FAR=0%). Misidentifications were primarily due to poor photo quality (N=4). However, two misidentifications were caused by indistinct scale configuration due to scale damage (N=1) and ontogenetic changes in head scalation between capture events (N=1). We conclude that automated photographic identification based on head scale patterns is a reliable and accurate method for identifying individuals over time. Because many lizard or reptilian species possess variable head squamation, this method has potential for successful application in many species.

opencc-zeroNov 2021View details →

Strong genotype-by-genotype interactions between aphid-defensive symbionts and parasitoids persist across different biotic environments

The dynamics of coevolution between hosts and parasites are influenced by their genetic interactions. Highly specific interactions, where the outcome of an infection depends on the precise combination of host and parasite genotypes (G × G interactions), have the potential to maintain genetic variation by inducing negative frequency-dependent selection. The importance of this effect also rests on whether such interactions are consistent across different environments or modified by environmental variation (G × G × E interaction). In the black bean aphid, Aphis fabae, resistance to its parasitoid Lysiphlebus fabarum is largely determined by the possession of a heritable bacterial endosymbiont, Hamiltonella defensa, with strong G × G interactions between H. defensa and L. fabarum. A key environmental factor in this system is the host plant on which the aphid feeds. Here, we exposed genetically identical aphids harbouring three different strains of H. defensa to three asexual genotypes of L. fabarum and measured parasitism success on three common host plants of A. fabae, namely Vicia faba, Chenopodium album and Beta vulgaris. As expected, we observed the pervasive G × G interaction between H. defensa and L. fabarum, but despite strong main effects of the host plants on average rates of parasitism, this interaction was not altered significantly by the host plant environment (no G × G × E interaction). The symbiont-conferred specificity of resistance is thus likely to mediate the coevolution of A. fabae and L. fabarum, even when played out across diverse host plants of the aphid.

opencc-zeroDec 2021View details →

A method for identifying environmental stimuli and genes responsible for genotype-by-environment interactions from a large-scale multi-environment data set

It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. In this study, we developed a data-driven approach termed Environmental Covariate Search Affecting Genetic Correlations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (Glycine max) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when they were involved. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields. This dataset provides the data used in this study and supplementary tables cited in the manuscript.

opencc-zeroJan 2022View details →

Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences

The data presented here are those used in the paper : CAYUELA H., JACOB S., SCHTICKZELLE N., VERDONCK R., PHILIPPE H., LAPORTE M., HUET M., BERNATCHEZ L., LEGRAND D. Transgenerational plasticity of dispersal-related traits in a ciliate: genotype-dependency and fitness consequences. Oikos. DOI: 10.1111/oik.08846 Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally-induced phenotypic variation across generations, and can influence adaptation. To date, the genetic control of TGP, its long-term stability, and its potential costs remain largely unknown, mostly because empirical demonstrations of TGP across many generations in several genetic backgrounds are scarce. In the paper of Cayuela et al., we examined how genotype determines the TGP of phenotypic traits related to dispersal, a fundamental process in ecology and evolution. We used an experimental approach in Tetrahymena thermophila, a ciliate model-species, to determine if and how phenotypic changes expressed following a dispersal treatment are inherited over multiple generations. The data include morphological and movement traits, dispersal rates, and cell growth data measured before and after dispersal trials. We considered different genotypes and different populations within each genotype.

Data from: Genome-wide sequence-based genotyping supports a nonhybrid origin of Castanea alabamensis

The genus Castanea in North America contains multiple tree and shrub taxa of conservation concern. The two species within the group, American chestnut (Castanea dentata) and chinquapin (C. pumila sensu lato), display remarkable morphological diversity across their distributions in the eastern United States and southern Ontario. Previous investigators have hypothesized that hybridization between C. dentata and C. pumila has played an important role in generating morphological variation in wild populations. A putative hybrid taxon, Castanea alabamensis, was identified in northern Alabama in the early 20th century; however, the question of its hybridity has been unresolved. We tested the hypothesized hybrid origin of C. alabamensis using genome-wide sequence-based genotyping of C. alabamensis, all currently recognized North American Castanea taxa, and two Asian Castanea species at >100,000 single-nucleotide polymorphism (SNP) loci. With these data, we generated a high-resolution phylogeny, tested for admixture among taxa, and analyzed population genetic structure of the study taxa. Bayesian clustering and principal components analysis provided no evidence of admixture between C. dentata and C. pumila in C. alabamensis genomes. Phylogenetic analysis of genome-wide SNP data indicated that C. alabamensis forms a distinct group within C. pumila sensu lato. Our results are consistent with the model of a nonhybrid origin for C. alabamensis. Our finding of C. alabamensis as a genetically and morphologically distinct group within the North American chinquapin complex provides further impetus for the study and conservation of the North American Castanea species.

Screening coffee genotypes for brown eye spot resistance in Brazil

Several researchers have attempted to develop coffee plants that are resistant to brown eye spot (BES); however, no coffee cultivars are resistant to the disease. In the present study, a blend of strains from Cercospora coffeicola was inoculated into 19 Brazilian commercial cultivars and 41 accessions from the Germplasm Collection of Minas Gerais to evaluate the genetic resistance ability within the population and select superior genotypes for the breeding program. After predicting the genotypic values of the studied material, the evaluations number necessary for selecting genotypes with accuracy and efficiency was determined based on the data of severity to BES. The action of defense mechanisms plant was also investigated by assessing the levels of total soluble phenolic compounds and soluble lignin in contrasting genotypes for disease susceptibility. Based on the results, the accession MG 1207 Sumatra, had an intrinsic genetic capacity to maintain low levels of severity to BES. The genotype MG 1207 Sumatra can substantially contribute to the development of new cultivars, which may lead to the reduced use of pesticides. According to the accuracy and efficiency results obtained, four evaluations BES severity are sufficient to achieve accuracy, providing expressive genetic gains. Finally, the levels of lignin and phenolic compounds were not found to be associated with the resistance of coffee genotypes to BES.

SNP genotypes for healthy and CIM-affected GSDs

German shepherd dogs (GSDs) are predisposed to an inherited motility disorder of the esophagus, termed congenital idiopathic megaesophagus (CIM), in which swallowing is ineffective and the esophagus is enlarged. Affected puppies are unable to properly pass food into their stomachs and consequently regurgitate their meals and show a failure to thrive, often leading to euthanasia. Here, we generated genome-wide SNP profiles for healthy and CIM-affected GSDs using the Illumina CanineHD BeadChip, containing 220,853 SNPs.

Association of physical activity and APOE genotype with longitudinal cognitive change in early PD

Objective: To determine whether greater physical activity could modify the negative association of APOE ε4 with longitudinal cognitive changes in early Parkinson's disease (PD) and to uncover the disease-specific mechanism for explaining such benefits of physical activity. Methods: We used data from the Parkinson's Progression Markers Initiative cohort. Because self-reported physical activity, measured by the Physical Activity Scale of the Elderly, was initiated at 2 years after enrollment, this longitudinal analysis was based on assessments performed at years 2, 3, and 4. Cognitive function was measured annually with the Montreal Cognitive Assessment (MoCA). Dopamine transporter (DAT) imaging was performed at years 2 and 4. We assessed the interactive associations between physical activity and the APOE ε4 allele on the longitudinal changes in MoCA scores and striatal DAT activities. Results: A total of 173 early PD patients (age 63.3±10.0 years; 27% APOE ε4 carriers) were included. The APOE ε4 allele showed a steeper rate of cognitive decline than the non-APOE ε4 allele (estimate -1.33; 95% CI, -2.12 to -0.47; p=0.002). However, there was a significant interaction between physical activity and APOE ε4, such that higher physical activity was related to slower APOE ε4-related cognitive decline (estimate 0.007; 95% CI, 0.003 to 0.011; p=0.001). No significant interaction was found between physical activity and the APOE ε4 allele regarding the change in striatal DAT activities. Conclusion: Increased physical activity attenuated APOE ε4-related vulnerability to early cognitive decline in PD patients. This protective effect did not appear to be mediated by striatal dopaminergic function. Classification of evidence: This study provides Class II evidence that increased physical activity was associated with decreased APOE ε4-related early cognitive decline in PD patients.

Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.

opencc-zeroMar 2022View details →

Schistosoma mansoni raw genotype calls from exome data

Schistosoma mansoni, a snail-vectored, blood fluke that infects humans, was introduced into the Americas from Africa during the Trans-Atlantic slave trade. As this parasite shows strong specificity to the snail intermediate host, we expected that adaptation to S. American Biomphalaria spp. snails would result in population bottlenecks and strong signatures of selection. We scored 475,081 single nucleotide variants (SNVs) in 143 S. mansoni from the Americas (Brazil, Guadeloupe, and Puerto Rico) and Africa (Cameroon, Niger, Senegal, Tanzania, and Uganda), and used these data to ask: (i) Was there a population bottleneck during colonization? (ii) Can we identify signatures of selection associated with colonization? And (iii) what were the source populations for colonizing parasites? We found a 2.4-2.9-fold reduction in diversity and much slower decay in linkage disequilibrium (LD) in parasites from East to West Africa. However, we observed similar nuclear diversity and LD in West Africa and Brazil, suggesting no strong bottlenecks and limited barriers to colonization. We identified five genome regions showing selection in the Americas, compared with three in West Africa and none in East Africa, which we speculate may reflect adaptation during colonization. Finally, we infer that unsampled African populations from central African regions between Benin and Angola, with contributions from Niger, are likely the major source(s) for Brazilian S. mansoni. The absence of a bottleneck suggests that this is a rare case of a serendipitous invasion, where S. mansoni parasites were preadapted to the Americas and were able to establish with relative ease.

opencc-zeroMar 2022View details →

Impatiens glandulifera SNP and SilicoDArT genotyping data

We conducted genomic characterization based on SNP and SilicoDArT markers on the invasive Himalayan balsam (Impatiens glandulifera) plants originating from the native and non-native regions of their distribution. When genetic relationships were explored by PCoA based on SNP and SilicoDArT marker data, the first, second and third principal coordinates explained altogether 37.4% and 31.0% of the variability, respectively. Samples from the UK, Canada and Pakistan grouped together, while Indian plants were clearly distinct based on SNP markers but relatively close to the UK-Canada-Pakistan group based on SilicoDArT markers. Constructed trees differentiated the individuals into clusters resembling the patterns observed by PCoA. The Bayesian BAPS analysis revealed that the individuals were distributed in seven clusters, representing samples from each of the four Finnish populations, India, Pakistan and the combination of the UK and Canada. Similar clustering was visible in the constructed UPGMA tree. The Indian cluster did not display any ancestral gene flow with the others, while the Pakistani cluster showed ancestral gene flow only with the combined UK and Canada cluster. Furthermore, the latter cluster displayed ancestral gene flow with the Finnish populations varying from 0% to 3.1%. The AMOVA analysis showed that 45% and 26% of genetic variation was present among the I. glandulifera groups/populations and the rest within them based on SNP and SilicoDArT markers, respectively. Overall, the Bayesian BAPS analysis and the following gene flow network were the most informative tools for resolving relationships among native and introduced plants.

opencc-zeroMar 2022View details →

Field data and microsatellite genotypes of Cercidiphyllum japonicum

Field data and genotypes at five microsatellite loci of 281 Cercidiphyllum japonicum adults of a population distributed over a ca. 80 ha along a stream and 755 C. japonicum current-year seedlings sampled at approximate center of the populatoin. The population is located in Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan.