43 Works

Data for: Population genomic insights into invasion success in the polyphagous agricultural pest, Halyomorpha halys

Elahe Parvizi, Manpreet K. Dhami, Juncong Yan & Angela McGaughran
Invasive species are increasingly threatening ecosystems and agriculture by rapidly expanding their range and adapting to environmental and human-imposed selective pressures. The genomic mechanisms that underlie such rapid changes remain unclear, especially for agriculturally important pests. Here, we use genome-wide polymorphisms derived from native, invasive, and intercepted samples and populations of the brown marmorated stink bug (BMSB), Halyomorpha halys, to gain insights into population genomics processes that have promoted the successful global invasion of this...

Additional file 14 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 14. All traits FWK pop. Plain text file containing the quantitative trait data of all individuals in the QTL population.

Additional file 8 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 8. 268,405 loc file. Plain text file containing the genotype codes for loci in the 268,405 parental map, in the format required for analysis using MAPQTL 6.0.

Additional file 8 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 8. 268,405 loc file. Plain text file containing the genotype codes for loci in the 268,405 parental map, in the format required for analysis using MAPQTL 6.0.

Additional file 9 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 9. All traits QTL pop. Plain text file containing the quantitative trait data of all individuals in the QTL population.

Additional file 10 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 10. 850,055 map file. Plain text file containing the map position (cM) of all loci on the 850,055 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 12 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 12. 850,055 loc file. Plain text file containing the genotype codes for loci in the 850,055 parental map, in the format required for analysis using MAPQTL 6.0.

Additional file 15 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 15: Table S4. Comprehensive parental linkage maps constructed in the Pinus radiata QTL and FWK pedigrees: A) 268,345; B) 268,405; C) 850,055; D) 850,096.

Additional file 16 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 16: Fig. S2. Synteny and collinearity between linkage groups 8 and 10 amongst the Pinus radiata parental linkage maps in this study. Vertical bars represent linkage groups, horizontal lines within bars show the position of markers within each group, lines between groups indicate homologous markers at the contig level. Scale bars shows cM (Kosambi). Fig. S1A shows perfect synteny and high collinearity between these linkage groups in three parental linkage maps. Fig. S2B...

Additional file 3 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 3: Table S3. Descriptive statistics for the phenotypic traits measured in the QTL and FWK Pinus radiata populations in this study.

Additional file 5 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 5. 268,345 map file. Plain text file containing the map position (cM) of all loci on the 268,345 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 6 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 6. 268,405 map file. Plain text file containing the map position (cM) of all loci on the 268,405 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 6 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 6. 268,405 map file. Plain text file containing the map position (cM) of all loci on the 268,405 linkage map, in the format required for analysis using MAPQTL 6.0.

Additional file 15 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 15: Table S4. Comprehensive parental linkage maps constructed in the Pinus radiata QTL and FWK pedigrees: A) 268,345; B) 268,405; C) 850,055; D) 850,096.

Data from: Latitudinal and altitudinal patterns of plant community diversity on mountain summits across the tropical Andes

Francisco Cuesta, Priscilla Muriel, Luis D. Llambí, Stephan Halloy, Nikolay Aguirre, Stephan Beck, Julieta Carilla, Rosa I. Meneses, Soledad Cuello, Alfredo Grau, Luis E. Gámez, Javier Irazábal, Jorge Jacome, Ricardo Jaramillo, Lirey Ramírez, Natalia Samaniego, David Suárez-Duque, Natali Thompson, Alfredo Tupayachi, Paul Viñas, Karina Yager, María T. Becerra, Harald Pauli & William D. Gosling
The high tropical Andes host one of the richest alpine floras of the world, with exceptionally high levels of endemism and turnover rates. Yet, little is known about the patterns and processes that structure altitudinal and latitudinal variation in plant community diversity. Herein we present the first continental-scale comparative study of plant community diversity on summits of the tropical Andes. Data were obtained from 792 permanent vegetation plots (1m2) within 50 summits, distributed along a...

Plant dispersal strategies of high tropical alpine communities across the Andes

Carolina Tovar, Inga Melcher, Buntarou Kusumoto, Francisco Cuesta, Antoine Cleef, Rosa Isela Meneses, Stephan Halloy, Luis Daniel Llambi, Stephan Beck, Priscilla Muriel, Ricardo Jaramillo, Jorge Jacome & Julieta Carilla
• Dispersal is a key ecological process that influences plant community assembly. Therefore, understanding whether dispersal strategies are associated with climate is of utmost importance, particularly in areas greatly exposed to climate change. We examined alpine plant communities located in the mountain summits of the tropical Andes across a 4000 km latitudinal gradient. We investigated species dispersal strategies and tested their association with climatic conditions and their evolutionary history. • We used dispersal-related traits (dispersal...

Additional file 17 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 17: Table S5. Matrix of Pearson’s phenotypic correlation coefficients between growth and wood property traits analysed in the Pinus radiata QTL population. Two tailed P-values *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.

Additional file 2 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 2: Table S2. SNP ranking criteria used for the Pinus radiata QTL and FWK mapping populations.

Additional file 18 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 18: Fig. S3. Genomic predictive ability for diameter at breast height (DBH) and wood density (WD) as a function of training population size (A) and number of markers (B) used in random cross-validations of 81 Pinus radiata genotypes from the FWK population. Error bars correspond to standard deviations across 100 random cross-validations for each set of parameters. Analyses in (A) were based on all markers (M = 9353). The training population size in...

Additional file 4 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 4: Fig. S1. Frequency distributions for the phenotypic traits measured in the QTL and FWK Pinus radiata populations in this study. QTL population: (A) Ring area (mm2); (B) Density (kg/m3) Silviscan; (C) Radial cell diameter (μm); (D) Tangential cell diameter (μm); (E) Fibre coarseness (μm/m); (F) Cell wall thickness (μm); (G) Specific surface area (m2/kg); (H) Microfibril angle (degrees); (I) Modulus of elasticity (GPa); (J) Density prediction for first 5 mm core (maximum...

Additional file 7 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 7. 268,345 loc file. Plain text file containing the genotype codes for loci in the 268,345 parental map, in the format required for analysis using MAPQTL 6.0.

High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Abstract Background The growing availability of genomic resources in radiata pine paves the way for significant advances in fundamental and applied genomic research. We constructed robust high-density linkage maps based on exome-capture genotyping in two F1 populations, and used these populations to perform quantitative trait locus (QTL) scans, genomic prediction and quantitative analyses of genetic architecture for key traits targeted by tree improvement programmes. Results Our mapping approach used probabilistic error correction of the marker...

Data from: Vegetation trends over eleven years on mountain summits in NW Argentina

Julieta Carilla, Stephan Halloy, Soledad Cuello, Alfredo Grau, Agustina Malizia & Francisco Cuesta
As global climate change leads to warmer and dryer conditions in the central Andes, alpine plant communities are forced to upward displacements following their climatic niche. Species range shifts are predicted to have major impacts on alpine communities by reshuffling species composition and abundances. Using a standardized protocol, we surveyed alpine plant communities in permanent plots on four high Andean summits in NW Argentina, which range from 4040 to 4740 m a.s.l. After a baseline...

Additional file 13 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 13. 850,096 loc file. Plain text file containing the genotype codes for loci in the 850,096 parental map, in the format required for analysis using MAPQTL 6.0.

Additional file 13 of High density linkage maps, genetic architecture, and genomic prediction of growth and wood properties in Pinus radiata

Jules S. Freeman, Gancho T. Slavov, Jakob B. Butler, Tancred Frickey, Natalie J. Graham, Jaroslav Klápště, John Lee, Emily J. Telfer, Phillip Wilcox & Heidi S. Dungey
Additional file 13. 850,096 loc file. Plain text file containing the genotype codes for loci in the 850,096 parental map, in the format required for analysis using MAPQTL 6.0.

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