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In a 25-Mb interval on chromosome 1, where we reached almost entirely hotspot resolution (<8 kb), we estimated that females use more hotspots than males, although with lower activity per hotspots; the data presented here hints that this must also be true for chromosome 11 because we found recombination in more intervals in females than in males.
Kurabayashi et al. [ 13] found recombination only on one side of the RFB.
Studies in other pathogens [ 1, 21] have also found recombination and positive selection occurring in tandem, especially in genomic regions coding for proteins involved in pathogenicity.
2014) to develop microsatellite markers and found recombination footprints, a tremendous diversity and a strong population structure in a large collection of 114 isolates from different environments and locations (Table S1).
Earlier comparisons of different A. macleodii strains isolated from different geographical points (Lopez-Lopez et al. 2005; Ivars-Martinez et al. 2008a) found recombination among several distinct housekeeping genes.
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In addition to astrocytes, we find recombination in NG2+ cells of GFAP-NCre x PLP-CCre mice.
Pairwise comparison of subgroups 2, 3, and 4 did not find recombination or large fragment replacement, which suggests that all HP-PRRSVs originated from the same ancestor by gradual evolution.
The REDHORSE pipeline was followed to generate a "merged allele file" and to find recombinations.
The RD algorithm in REDHORSE employs an iterative procedure to find recombinations.
Generally, determining the phase of genotypes to find recombinations requires genetic information of three generations, or that of two generations with many children.
Similar to our simulated dataset one, we converted the "merged allele file" into a MSA fasta file and used this file to find recombinations by several programs.
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