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Displaying 18 of 18 results for "CRISP1"
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Title Date Issued Date Released Description
crisp_dna
06-12-2014 06-12-2014
DNA alignment of the cysteine rich secretory protein (CRISP) toxin family
Gopherus_ND4_inputdata arp
03-30-2012 06-26-2012
SAMOVA genetic data file
PPM-Algeria-microsat-9loci-25pops-arp
05-31-2016 05-31-2016
microsatellite dataset in Arlequin format of 25 pine processionary moth populations sampled in Algeria
Anas crecca PCK1.arp
06-21-2012 09-24-2012
Resolved alleles for Anas crecca crecca (n = 50)and Anas crecca carolinensis (n = 50) for intron 8 of the PCK1 gene. This file is formatted for analyses in Arlequin, and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
Anas crecca GRIN1.arp
06-21-2012 09-24-2012
Resolved alleles for Anas crecca crecca (n = 50)and Anas crecca carolinensis (n = 50) for intron 13 of the GRIN1 gene. This file is formatted for analyses in Arlequin, and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
Anas crecca ENO1.arp
06-21-2012 09-24-2012
Resolved alleles for Anas crecca crecca (n = 50)and Anas crecca carolinensis (n = 50) for intron 8 of the ENO1 gene. This file is formatted for analyses in Arlequin, and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
Anas crecca ODC1.arp
06-21-2012 09-24-2012
Resolved alleles for Anas crecca crecca (n = 50)and Anas crecca carolinensis (n = 50) for intron 5 of the ODC1 gene. This file is formatted for analyses in Arlequin, and sequences are sorted between OW (A. c. crecca) and NW (A. c. carolinensis) samples.
Poecilia butleri cytochrome b data for all individuals in samova / arlequin geography format
04-18-2014 06-06-2014
These data contain the geographic information and should be placed in the same directory as the .arp file
rubus_photos1
07-10-2012 04-22-2013
Photographs of plants sampled at sites ARC, ARP, BBG, and BWP. Sample IDs can be seen within the images. Image format is .jpg.
Poecilia butleri cytochrome b data for all individuals in arlequin haplotype format
04-18-2014 06-06-2014
These data contain the haplotype information and should be placed in the same directory as the .arp file
LDna_simulation
01-16-2015 01-20-2015
Includes .par, .arp, the associated r-squared data sets and R-code to produce figures in Appendix S3 (LDna on simulated data).
Poecilia butleri cytochrome b data for all individuals in arlequin format
04-18-2014 06-06-2014
The haplotype data are in a second file which should be placed in the same directory as the .arp file
Poecilia butleri cytochrome b data for all individuals in samova / arlequin format
04-18-2014 06-06-2014
The haplotype data are in a second file which should be placed in the same directory as the .arp file
Raw micro-satellite data for 14 Rye populations
11-25-2015 11-25-2015
Raw micro-satellite data in arp format with original population names. The populations are grouped following the three classes described in the article at the end of the data file. Missing information is coded with a "?" and null alleles are coded with a "0".
Data from: Experimental evolution reveals balancing selection underlying coexistence of alternative male reproductive phenotypes
08-03-2016 11-11-2016
Heritable alternative reproductive phenotypes (ARPs), which differ in traits associated with competition for mates, occur across taxa. If polymorphism in the genes underlying ARPs is maintained by balancing selection, selection should return ARP proportions to their equilibrium if that equilibrium is perturbed. Here, we used an experimental evolution approach to directly test this prediction in male Rhizoglyphus robini, in which two heritable morphs occur: armoured fighters and more female-like, benign scramblers. Using selection lines nearly fixed for male morph, we constructed replicate populations consisting of 50% or 94% fighters, and allowed them to evolve for 14 generations in two types of environment: simple or spatially complex. We found that in both types of populations, the proportion of fighters converged on values within a narrow range of 0.70-0.83, although the rate of convergence was slower in the complex environment. Our results thus demonstrate balancing selection acting on polymorphism(s) underlying ARPs
Data from: Integrating fuzzy logic and statistics to improve reliabile definition of biogeographic regions and transition zones
06-28-2012 01-15-2013
The present study uses the amphibian species of the Mediterranean Region to develop a consistent procedure based on fuzzy sets with which biogeographic regions and biotic transition zones can be objectively detected and reliably mapped. Biogeographical regionalizations are abstractions of the geographical organization of life on Earth that provide frameworks for cataloguing species and ecosystems, for answering basic questions in biogeography, evolutionary biology and systematics, and for assessing priorities for conservation. On the other hand, limits between regions may form sharply defined boundaries along some parts of their borders, whereas elsewhere they may consist of broad transition zones. The fuzzy set approach provided a heuristic way to analyze the complexity of the biota within an area; significantly different regions were detected whose mutual limits were sometimes fuzzy, sometimes clearly crisp. Most of the regionalizations described in the literature for the Mediterranean Region present a certain degree of convergence when they are compared within the context of fuzzy interpretation, as many of the differences found between regionalizations are located in transition zones, according to our case study. Compared to other classification procedures based on fuzzy sets, the novelty of our method is that both fuzzy logic and statistics are used together in a synergy in order to avoid arbitrary decisions in the definition of biogeographic regions and transition zones.
DNA alignment for the genus Leucadendron phylogeny
05-15-2014 10-07-2014
This alignment is the concatenation of nine markers that were used to reconstruct the phylogeny of the genus Leucadendron in the paper cited above. Those markers were amplified for 81 Leucadendron taxa collected in natural populations in the South-African fynbos, except for three external groups which were collected in the Kirstenbosch Botanical Garden: Paranomus spathulatus, Mimetes cucullatus and Leucospermum erubescens. A detailed map of the alignment is given below: Positions 1 - 618 : AS1 marker which contains an exon of 618bp. Positions 619 - 1046 : PPR-like marker which contains an exon of 233bp and a 3'-UTR of 195bp. Positions 1047 - 1800 : SVR7 marker which contains an exon of 652bp and a 3'-UTR of 102bp. Positions 1801 - 2181 : CAF1-6 marker which only contains an exon of 381bp. Positions 2182 - 2795 : the classical ITS marker. Positions 2796 - 3591 : ATINT1 marker which contains an exon of 665bp and a 3'-UTR of 131bp. Positions 3592 - 3868 : APO2 marker which contains only an exon of 277bp. Positions 3869 - 4207 : APG6 marker which contains only an exon of 339bp. Positions 3208 - 4865 : ATPHAN marker which contains only an exon of 658bp The methodology used to design the following markers: PPR-like, CAF1-6, ATINT1, APO2, APG6 and ATPHAN is described in (Tonnabel et al. 2013). The AS1 marker was designed in (Illing et al. 2009). Tonnabel, J., Olivieri, I., Mignot, A., Rebelo, A., Justy, F., Santoni, S., Caroli, S., Sauné, L., Bouchez, O. & Douzery, E.J.P. (2014) Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach, Molecular Phylogenetics and Evolution, 70, 37-46. Illing, N., Klak, C., Johnson, C., Brito, D., Negrao, N., Baine, F., van Kets, V., Ramchurn K.R., Seoighe, C. & Roden, L. (2009) Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae. Development genes and evolution, 219, 331-338.
DNA alignment for the genus Leucadendron phylogeny
01-01-9999 05-21-2014
This alignment is the concatenation of nine markers that were used to reconstruct the phylogeny of the genus Leucadendron in the paper cited above. Those markers were amplified for 81 Leucadendron taxa collected in natural populations in the South-African fynbos, except for three external groups which were collected in the Kirstenbosch Botanical Garden: Paranomus spathulatus, Mimetes cucullatus and Leucospermum erubescens. A detailed map of the alignment is given below: Positions 1 - 618 : AS1 marker which contains an exon of 618bp. Positions 619 - 1046 : PPR-like marker which contains an exon of 233bp and a 3'-UTR of 195bp. Positions 1047 - 1800 : SVR7 marker which contains an exon of 652bp and a 3'-UTR of 102bp. Positions 1801 - 2181 : CAF1-6 marker which only contains an exon of 381bp. Positions 2182 - 2795 : the classical ITS marker. Positions 2796 - 3591 : ATINT1 marker which contains an exon of 665bp and a 3'-UTR of 131bp. Positions 3592 - 3868 : APO2 marker which contains only an exon of 277bp. Positions 3869 - 4207 : APG6 marker which contains only an exon of 339bp. Positions 3208 - 4865 : ATPHAN marker which contains only an exon of 658bp The methodology used to design the following markers: PPR-like, CAF1-6, ATINT1, APO2, APG6 and ATPHAN is described in (Tonnabel et al. 2013). The AS1 marker was designed in (Illing et al. 2009). Tonnabel, J., Olivieri, I., Mignot, A., Rebelo, A., Justy, F., Santoni, S., Caroli, S., Sauné, L., Bouchez, O. & Douzery, E.J.P. (2014) Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach, Molecular Phylogenetics and Evolution, 70, 37-46. Illing, N., Klak, C., Johnson, C., Brito, D., Negrao, N., Baine, F., van Kets, V., Ramchurn K.R., Seoighe, C. & Roden, L. (2009) Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae. Development genes and evolution, 219, 331-338.