Extensive polymorphism and geographical variation at a positively selected MHC class II B gene of the lesser kestrel (<i>Falco naumanni</i>)

Alcaide, Miguel; Edwards, Scott V.; Negro, Juan J.; Serrano, David; Tella, José Luis

doi:10.1111/j.1365-294x.2008.03791.x

Cited by 116 publications

(150 citation statements)

References 90 publications

(155 reference statements)

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“…Temporal shifts of selection, affected by temporal changes in prey availability or prey preference, may also have led to patterns of variation that we detected. In some taxa, patterns of variation at MHC genes are substantially different from those of neutral loci [71,72]. For example, differentiation of MHC loci among populations of grey seals is associated with habitat differences [71].…”

Section: (B) Geographical Variation In Dietmentioning

confidence: 99%

Effects of geographical heterogeneity in species interactions on the evolution of venom genes

2015

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Geographical heterogeneity in the composition of biotic interactions can create a mosaic of selection regimes that may drive the differentiation of phenotypes that operate at the interface of these interactions. Nonetheless, little is known about effects of these geographical mosaics on the evolution of genes encoding traits associated with species interactions. Predatory marine snails of the family Conidae use venom, a cocktail of conotoxins, to capture prey. We characterized patterns of geographical variation at five conotoxin genes of a vermivorous species, Conus ebraeus, at Hawaii, Guam and American Samoa, and evaluated how these patterns of variation are associated with geographical heterogeneity in prey utilization. All populations show distinct patterns of prey utilization. Three 'highly polymorphic' conotoxin genes showed significant geographical differences in allelic frequency, and appear to be affected by different modes of selection among populations. Two genes exhibited low levels of diversity and a general lack of differentiation among populations. Levels of diversity of 'highly polymorphic' genes exhibit a positive relationship with dietary breadth. The different patterns of evolution exhibited by conotoxin genes suggest that these genes play different roles in prey capture, and that some genes are more greatly affected by differences in predator-prey interactions than others. Moreover, differences in dietary breadth appear to have a greater influence on the differentiation of venoms than differences in the species of prey.

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Section: (B) Geographical Variation In Dietmentioning

confidence: 99%

Effects of geographical heterogeneity in species interactions on the evolution of venom genes

2015

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“…Positive colonies were amplified using universal M13 forward and reverse primers (M13F: 5 0 -GTAAAACGAC-GGCCAG-3 0 ; M13R: 5 0 -CAGGAAACAGCTATGAC-3 0 ) and 6-8 clones per individual were randomly selected for sequence analysis. Following the standards described in Alcaide et al (2008), rare cloned sequences found only once and differing by o3 bp from a redundant sequence of the same PCR product were considered as PCR artifacts and assumed to have been sampled already. As recombination of cloned PCR products can result in additional artifacts, comparisons were conducted between cloned sequences and direct sequencing of uncloned PCR products to get reliable polymorphic sites.…”

Section: Amplification and Sequencingmentioning

confidence: 99%

“…The exon and intron boundaries were defined following the annotated genes in the reference saker genome. In addition, we analyzed exonic variation in two well-characterized gene systems with known exonic variations in vertebrates linked to phenotypic diversity and pathogen resistance, the melanocortin-1-receptor (MC1R; Zhan et al, 2012) and major histocompatibility complex (MHC) Class II B (Alcaide et al, 2008).…”

Section: Contrasting Roles Of Exonic and Intronic Snps X Zhan Et Almentioning

confidence: 99%

Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species

et al. 2014

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Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species.

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“…Southern hybridization methods have been used to estimate the number of genes and alleles/locus for the class I and II loci thereby providing a rough estimate of overall genetic variation at the MHC (Emara et al, 1992;Westerdahl et al, 2000;Freeman-Gallant et al, 2002;Richardson and Westerdahl, 2003;Alcaide et al, 2008). PCR-based techniques such as reference strand-mediated conformational analysis, single strand conformation polymorphism and denaturing gradient gel electrophoresis (DGGE) are also effective in estimating the number of alleles, especially when locus-specific primers are available (Ramon et al, 1998;Goto et al, 2002;Westerdahl et al, 2004;Knapp, 2005;Alcaide et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

A locus-wide approach to assessing variation in the avian MHC: the B-locus of the wild turkey

Chaves

Faile

Hendrickson³

et al. 2010

Heredity

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Studies of major histocompatibility complex (MHC) diversity in non-model vertebrates typically focus on structure and sequence variation in the antigen-presenting loci: the highly variable and polymorphic class I and class IIB genes. Although these studies provide estimates of the number of genes and alleles/locus, they often overlook variation in functionally related and co-inherited genes important in the immune response. This study utilizes the sequence of the MHC B-locus derived from a commercial turkey to investigate MHC variation in wild birds. Sequences were obtained for nine interspersed MHC amplicons (non-class I/II) from each of 40 birds representing 3 subspecies of wild turkey (Meleagris gallopavo). Analysis of aligned sequences identified 238 single-nucleotide variants approximately onethird of which had minor allele frequencies 40.2 in the sampled birds. PHASE analysis identified 70 prospective MHC haplotypes in the wild turkeys, whereas a combined analysis with commercial birds identified almost 100 haplotypes in the species. Denaturing gradient gel electrophoresis (DGGE) of the class IIB loci was used to test the efficacy of single-nucleotide polymorphism (SNP) haplotyping to capture locus-wide variation. Diversity in SNP haplotypes and haplotype sharing among individuals was directly reflected in the DGGE patterns. Utilization of a reference haplotype to sequence interspersed regions of the MHC has significant advantages over other methods of surveying diversity while identifying high-frequency SNPs for genotyping. SNP haplotyping provides a means to identify both divergent haplotypes and homozygous individuals for assessment of immunological variation in wild and domestic populations.

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Extensive polymorphism and geographical variation at a positively selected MHC class II B gene of the lesser kestrel (Falco naumanni)

Cited by 116 publications

References 90 publications

Effects of geographical heterogeneity in species interactions on the evolution of venom genes

Effects of geographical heterogeneity in species interactions on the evolution of venom genes

Exonic versus intronic SNPs: contrasting roles in revealing the population genetic differentiation of a widespread bird species

A locus-wide approach to assessing variation in the avian MHC: the B-locus of the wild turkey

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