Sequence analysis of MHC DRB alleles in domestic cats from the United Kingdom

Kennedy, L. J.; Ryvar, R.; Gaskell, Rosalind M.; Addie, Diane; Willoughby, Kim; Carter, Stuart; Thomson, Wendy; Ollier, William; Radford, Alan

doi:10.1007/s00251-002-0465-5

Cited by 66 publications

(68 citation statements)

References 12 publications

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“…All these methods have different advantages, but we used the alternative method of reference strand conformation analysis (RSCA). As an automated method, RSCA is suitable for screening large populations reliably, with excellent between-run repeatability even for large fragments (less than 500 bp), and can separate alleles that differ by a single nucleotide (Ramon et al 1998;Kennedy et al 2002).…”

Section: (A) Study Speciesmentioning

confidence: 99%

Cryptic preference for MHC-dissimilar females in male red junglefowl,Gallus gallus

et al. 2008

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An increasing number of studies test the idea that females increase offspring fitness by biasing fertilization in favour of genetically compatible partners; however, few have investigated or controlled for corresponding preferences in males. Here, we experimentally test whether male red junglefowl, Gallus gallus, prefer genetically compatible females, measured by similarity at the major histocompatibility complex (MHC), a key gene complex in vertebrate immune function. Theory predicts that because some degree of MHC heterozygosity favours viability, individuals should prefer partners that carry MHC alleles different from their own. While male fowl showed no preference when simultaneously presented with an MHC-similar and an MHC-dissimilar female, they showed a 'cryptic' preference, by allocating more sperm to the most MHC-dissimilar of two sequentially presented females. These results provide the first experimental evidence that males might respond to the MHC similarity of a female through differential ejaculate expenditure. By revealing that cryptic male behaviours may bias fertilization success in favour of genetically compatible partners, this study demonstrates the need to experimentally disentangle male and female effects when studying preferences for genetically compatible partners.

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Section: (A) Study Speciesmentioning

confidence: 99%

Cryptic preference for MHC-dissimilar females in male red junglefowl,Gallus gallus

et al. 2008

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“…Several previous studies reported that relatively high proportions of obtained sequences could be artifacts of PCR amplifications or cloning (Kennedy et al 2002;Longeri et al 2002;Bryja et al 2005). Herein, we used motif-specific PCR, SSCP analysis, and direct sequencing to detect DRB-2 alleles in Ussuri sika deer for the first time.…”

Section: Discussionmentioning

confidence: 99%

“…Previous analyses showed that relatively high proportions of obtained sequences could be artifacts of PCR amplifications (Bryja et al 2005). We considered a new sequence variant as a new allele only when it met the criteria proposed by Kennedy et al (2002): The allele must be identified either in two separate PCRs from the same individual or from PCRs from at least two different individuals. Nomenclature of Ussuri sika deer (Ceni DRB) sequences followed Swarbrick et al (1995).…”

Section: Sequence Characterizations and Phylogenetic Analysismentioning

confidence: 99%

Allelic characterization of the second DRB locus of major histocompatibility complex class II in Ussuri sika deer (Cervus nippon hortulorum): highlighting the trans-species evolution of DRB alleles within Cervidae

2013

Animal Cells and Systems

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(2013) Allelic characterization of the second DRB locus of major histocompatibility complex class II in Ussuri sika deer (Cervusnippon hortulorum): highlighting the trans-species evolution of DRB alleles within Cervidae, Animal Cells and Systems, 17:4, 269-276, DOI: 10.1080/19768354.2013 MHC (major histocompatibility complex)-DRB variability reflects evolutionarily relevant and adaptive processes within and between populations, and is suitable for the investigation of a wide range of questions in evolutionary ecology. Using motif-specific polymerase chain reaction (PCR), single-stranded conformation polymorphism (SSCP) analyses and direct sequencing, 15 DRB-2 alleles were identified from 43 Ussuri sika deer. Extensive sequence variation was detected at peptide-binding region (PBR) or positively selected sites (PSS) sites among DRB loci, which were proved to be maintained by positive selection. DRB-2 loci of the Ussuri sika deer were strikingly similar to those of red deer after comparing sequences. In phylogenetic analysis, DRB-2 alleles of Ussuri sika deer were not monophyletic with respect to red deer, white-tailed deer, fallow deer, and roe deer sequences. Two DRB-2 alleles of the species tended to cluster together with those of white-tailed deer or red deer with high bootstrap values, respectively. Considering that sika and red deer are closely related, and their hybridization is occasionally seen in areas of range overlap, and their mtDNAs are paraphyletic to white-tailed deer, fallow deer, and other Cervus species, we suggested that these similarities result from trans-species evolution rather than convergent evolution.

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“…The 0.1% threshold was chosen because increasing the threshold resulted in a loss of alleles independently detected in the Ion Torrent and Miseq sequencing experiments, while decreasing the threshold resulted in an increase in erroneous sequences found between replicate samples in this study. We discarded any sequences that were not found in replicate samples unless observed in at least two other individuals after calculating repeatability (Kennedy et al 2002;Galan et al 2010). We calculated repeatability in this study as 1−APD (average percent difference; Yuhki & O'Brien 1990).…”

Section: Mhc Typing Via Next-generation Sequencingmentioning

confidence: 99%

Differential patterns of diversity at microsatellite, MHC, and TLR loci in bottlenecked South Island saddleback populations

Knafler¹,

Grueber²,

Sutton³

et al. 2017

NZ J Ecol

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For populations that experienced historical population bottlenecks, subsequent contemporary bottlenecks may continue to degrade genetic diversity at loci that are still variable. However, it is currently unclear how different types of contemporary bottlenecks may affect diversity at functional versus neutral loci. In this study, we examine genetic diversity of microsatellite, major histocompatibility complex (MHC), and toll-like receptor (TLR) loci of three New Zealand South Island saddleback (Philesturnus carunculatus) populations: Big Island, Kaimohu Island and Motuara Island. One population, Motuara, experienced two sets of contemporary bottlenecks (translocation event followed by a disease-outbreak and population crash) and was sampled in three different years. For all populations and sampling periods, we compare patterns of diversity across the three sets of loci to infer the effects of contemporary bottlenecks. We found that translocation-induced bottlenecks resulted in greater losses of microsatellite than MHC diversity, whereas temporal (encompassing a potential disease-induced bottleneck) fluctuations in diversity were greater for MHC markers than microsatellite loci. Both translocation-and disease-induced contemporary bottlenecks affected TLR diversity to a greater extent than diversity of either microsatellites or MHC. We found significant temporal changes in the frequencies of two TLR1LA alleles on Motuara Island (coincident with the population crash), but no further subsequent change. These alleles differ by an amino acid variant (associated with the leucine-rich repeat region of TLR1LA). Since TLR1LA may initiate an innate immune response in the presence of haemosporidia parasites, it is possible that a selection event has contributed to the observed patterns at TLR1LA. Our results indicate that patterns of genetic diversity loss at microsatellite, MHC and TLR loci are not equally affected by contemporary population bottlenecks, and may be influenced by bottleneck type.

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Sequence analysis of MHC DRB alleles in domestic cats from the United Kingdom

Cited by 66 publications

References 12 publications

Cryptic preference for MHC-dissimilar females in male red junglefowl,Gallus gallus

Cryptic preference for MHC-dissimilar females in male red junglefowl,Gallus gallus

Allelic characterization of the second DRB locus of major histocompatibility complex class II in Ussuri sika deer (Cervus nippon hortulorum): highlighting the trans-species evolution of DRB alleles within Cervidae

Differential patterns of diversity at microsatellite, MHC, and TLR loci in bottlenecked South Island saddleback populations

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