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We evaluated the significance of the following explanatory variables: Other genetic studies of mouse MHC class II genes are of laboratory or wild-derived inbred strains for example, Saha et al. The multiplicity of parasites in natural populations may lead to maintenance of multiple MHC variants because of balancing selection based on heterozygote advantage or spatiotemporal variation in selection pressure for example, reviewed in Garrigan and Hedrick, ; Piertney and Oliver, Positively selected codons identified by random effects likelihood REL , fixed effects likelihood FEL and single likelihood ancestral counting SLAC are shown as black squares, by OmegaMap as grey squares, negatively selected codons as shaded squares and antigen-binding codons as asterisks. Antigen-binding codons ABS and codons under selection are shown below the alignments. To compare the strength of positive versus negative selection across different groups of sequences, we estimated whether the proportion of positively versus negatively selected codons was significantly different between groups, and if so, in which direction. If such balancing selection is sufficiently strong and persistent, multiple variants may be maintained through speciation events, resulting in trans-species polymorphism TSP; Klein, manifested by incongruence between gene and species trees. Similarly, the second recoded data set gave maximal FCT.

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H-2Aa shows higher allelic polymorphism, faster allelic turnover due to higher mutation rates, stronger positive selection at antigen-binding sites and higher population structuring than H-2Eb. They lie only 18 kb, and 0. To assess population differentiation within the subspecies and to compare between them, we used two-sided tests comparing the two groups of locality samples 10 permutations in FSTAT Goudet, However, there are at least two reasons for analysing more MHC genes. The authors recommend considering all three methods and following the consensus. The output was used to run three different maximum likelihood methods for detection of selection: Standardized values were calculated by dividing the original values by the maximal values Hedrick,

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To assess population differentiation within the subspecies and to compare between them, we used two-sided tests comparing the two groups of locality samples 10 permutations in FSTAT Goudet, Captain Sidney Burbank supervised the construction of Fort Duncan, which was named after Colonel James Duncan, who had fought in the Mexican War, after the Mexican-American War, trade flourished under the protection of the fort. Shelby , en route to offer his troops' service to Maximilian in Mexico, stopped at Fort Duncan and buried in the Rio Grande the last Confederate flag to have flown over his men. In the wild, Mus musculus is polytypic: If such balancing selection is sufficiently strong and persistent, multiple variants may be maintained through speciation events, resulting in trans-species polymorphism TSP; Klein, manifested by incongruence between gene and species trees. The multiplicity of parasites in natural populations may lead to maintenance of multiple MHC variants because of balancing selection based on heterozygote advantage or spatiotemporal variation in selection pressure for example, reviewed in Garrigan and Hedrick, ; Piertney and Oliver, Gene and allele nomenclature follow Klein et al. JS primers were used to detect expression of particular alleles, as their priming sites are inside exon 2, whereas the MusDRB primers, which have priming sites in adjacent introns, served to control for genomic DNA contamination.

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To control at least partially for this, we included gene identity nested within species identity as a random intercept of the model. Chavez admitted to having given false information in According to SSCP patterns we identified alleles that were identical with the alleles present in our locality samples.

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