Reply: facts, faeces and setting standards for the study of MHC genes using noninvasive samples

Lukas, Dieter; Vigilant, Linda

doi:10.1111/j.1365-294x.2005.02459.x

Cited by 17 publications

(18 citation statements)

References 23 publications

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“…We quantified the PCR error rate due to recombinant products originating from heteroduplex mismatch repair during cloning, as well as base nucleotide substitution during PCR (Kanagawa, 2003;Lukas and Vigilant, 2005). The probability of erroneous base substitution was estimated to be around 4.2 Â 10 À5 nucleotide substitution per site per duplication, which compares to 7.3 Â 10 À5 in a study by Kobayashi et al (1999).…”

Section: Pcr Proceduresmentioning

confidence: 99%

“…By comparing the results from different sets of primers, we assessed whether we have missed alleles due to mutations in primer annealing sites (see eg Lukas and Vigilant, 2005). The degenerate primers were designed by aligning all P. reticulata (guppy), P. picta, P. sphenops and X. maculatus DAB sequences published on GenBank, as well as those previously amplified in our lab (SM Cummings and C van Oosterhout, unpublished manuscript).…”

Section: Pcr Proceduresmentioning

confidence: 99%

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Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

2006

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This is the first study to quantify genomic sequence variation of the major histocompatibility complex (MHC) in wild and ornamental guppies, Poecilia reticulata. We sequenced 196-219 bp of exon 2 MHC class IIB (DAB) in 56 wild Trinidadian guppies and 14 ornamental strain guppies. Each of two natural populations possessed high allelic richness (15-16 alleles), whereas only three or fewer DAB alleles were amplified from ornamental guppies. The disparity in allelic richness between wild and ornamental fish cannot be fully explained by fixation of alleles by inbreeding, nor by the presence of non-amplified sequences (ie null alleles). Rather, we suggest that the same allele is fixed at duplicated MHC DAB loci owing to gene conversion. Alternatively, the number of loci in the ornamental strains has contracted during 4100 generations in captivity, a hypothesis consistent with the accordion model of MHC evolution. We furthermore analysed the substitution patterns by making pairwise comparisons of sequence variation at the putative peptide binding region (PBR). The rate of non-synonymous substitutions (dN) only marginally exceeded synonymous substitutions (dS) in PBR codons. Highly diverged sequences showed no evidence for diversifying selection, possibly because synonymous substitutions have accumulated since their divergence. Also, the substitution pattern of similar alleles did not show evidence for diversifying selection, plausibly because advantageous non-synonymous substitutions have not yet accumulated. Intermediately diverged sequences showed the highest relative rate of non-synonymous substitutions, with dN/dS414 in some pairwise comparisons. Consequently, a curvilinear relationship was observed between the dN/dS ratio and the level of sequence divergence.

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Section: Pcr Proceduresmentioning

confidence: 99%

Section: Pcr Proceduresmentioning

confidence: 99%

Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

2006

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“…A further concern is that an increasing trend towards using noninvasive or nondestructive samples for characterising genetic diversity may introduce more genotyping errors, as proficient characterisation of MHC alleles from minute amounts of potentially damaged DNA will be problematic (see Knapp, 2005 and reply from Lukas and Vigilant, 2005).…”

Section: Summary and Future Directionsmentioning

confidence: 99%

The evolutionary ecology of the major histocompatibility complex

2005

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The major histocompatibility complex (MHC) has become a paradigm for how selection can act to maintain adaptively important genetic diversity in natural populations. Here, we review the contribution of studies on the MHC in non-model species to our understanding of how selection affects MHC diversity, emphasising how ecological and ethological processes influence the tempo and mode of evolution at the MHC, and conversely, how variability at the MHC affects individual fitness, population dynamics and viability. We focus on three main areas: the types of information that have been used to detect the action of selection on MHC genes; the relative contributions of parasite-mediated and sexual selection on the maintenance of MHC diversity; and possible future lines of research that may help resolve some of the unanswered issues associated with MHC evolution.

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“…We also performed data screening to minimize the inclusion of PCR and cloning artifacts (spurious errors) in our data set. MHC sequences were confirmed when they were observed in at least two independent PCRs (Lukas and Vigilant, 2005;Cummings et al, 2010). To avoid analysis of PCR artefacts, we only considered variants as 'true' alleles if they occurred in at least two individuals.…”

Section: Samples Collection and Dna Extractionmentioning

confidence: 99%

“…total, 67 distinct sequence variants were identified using SSCP and sequencing ( (Lukas and Vigilant, 2005;Cummings et al, 2010). Accordingly, 36 sequence variants were validated and included in the subsequent analyses (sequences are deposited in GenBank, under accession numbers KJ143572−KJ143607).…”

Section: Mhc Class I Polymorphism Of E Multiocellata Inmentioning

confidence: 99%

MHC Class I Exon 4 in the Multiocellated Racerunners (Eremias multiocellata): Polymorphism, Duplication and Selection

Yuan¹,

Zeng²,

Guo³

2014

AHR

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The major histocompatibility complex (MHC) is a dynamic genetic region with an essential role in the adaptive immunity of jawed vertebrates. The MHC polymorphism is affected by many processes such as birth-anddeath evolution, gene conversion, and concerted evolution. Studies investigating the evolution of MHC class I genes have been biased toward a few particular taxa and model species. However, the investigation of this region in nonavian reptiles is still in its infancy. We present the first characterization of MHC class I genes in a species from the family Lacertidae. We assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 4 among 37 individuals of Eremias multiocellata from a population in Lanzhou, China. We generated 67 distinct DNA sequences using cloning and sequencing methods, and identified 36 putative functional variants as well as two putative pseudogene-variants. We found the number of variants within an individual varying between two and seven, indicating that there are at least four MHC class I loci in this species. Gene duplication plays a role in increasing copy numbers of MHC genes and allelic diversity in this species. The class I exon 4 sequences are characteristic of low nucleotide diversity. No signal of recombination is detected, but purifying selection is detected in β2-microglobulin interaction sites and some other silent sites outside of the function-constraint regions. Certain identical alleles are shared by Eremias multiocellata and E. przewalskii and E. brenchleyi, suggesting trans-species polymorphism. The data are compatible with a birth-and-death model of evolution.class II genes, have been the subjects of the majority of research in the fields of ecology and evolution (reviewed in Sommer, 2005; Milinski, 2006;Piertney and Oliver, 2006;Ujvari and Belov, 2011). This is because MHC includes the most polymorphic genes in vertebrate populations. Given the extraordinary richness and diversity of continuously evolving pathogens in the environment, it is not surprising that the MHC harbors the most polymorphic genes described thus far, with some loci, such as the human HLA-B locus, possessing more than 2000 alleles (de Bakker and Raychaudhuri, 2012). The number of genes in the MHC varies enormously between species, even between individuals of the same species (Malaga-Trillo et al., 1998;Figueroa et al., 2001). It has been noted that balancing selection is an evolutionary force that can maintain many haplotypes over long periods of evolutionary time. Genes that

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Reply: facts, faeces and setting standards for the study of MHC genes using noninvasive samples

Cited by 17 publications

References 23 publications

Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

Evolution of MHC class IIB in the genome of wild and ornamental guppies, Poecilia reticulata

The evolutionary ecology of the major histocompatibility complex

MHC Class I Exon 4 in the Multiocellated Racerunners (Eremias multiocellata): Polymorphism, Duplication and Selection

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