| 1. |
- Leclaire, Sarah, et al.
(författare)
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Plumage microbiota covaries with the major histocompatibility complex in blue petrels
- 2018
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X.
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Tidskriftsartikel (refereegranskat)abstract
- To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odour remains largely unclear. MHC class IIB molecules, which enable recognition and elimination of extracellular bacteria, have been suggested to influence odour indirectly by shaping odour-producing microbiota, i.e. bacterial communities. However, there is little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent-producing body surfaces. Here, using high-throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel (Halobaena caerulea), a seabird with highly developed olfaction that has been suggested to rely on oduor cues during an MHC-based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with high MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus in which some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical-producing microbiota in birds.
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| 2. |
- Stervander, Martin, et al.
(författare)
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High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
- 2020
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 29:19, s. 3578-3592
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Tidskriftsartikel (refereegranskat)abstract
- Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso larkAlauda razae, a species restricted to the 7 km(2)islet of Raso, Cape Verde, since similar to 1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by cosegregation of multiple haplotypes comprising 2-8 linked MHC-I loci. Within-locus homozygosity is high, contributing to low population-wide diversity. Conversely, each individual had comparably many alleles, 6-16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species' adaptive potential.
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| 3. |
- Vekemans, Xavier, et al.
(författare)
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Whole-genome sequencing and genome regions of special interest : Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility
- 2021
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:23, s. 6072-6086
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.
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| 4. |
- Biedrzycka, Aleksandra, et al.
(författare)
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Blood parasites shape extreme major histocompatibility complex diversity in a migratory passerine
- 2018
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083. ; 27:11
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Tidskriftsartikel (refereegranskat)abstract
- Pathogens are one of the main forces driving the evolution and maintenance of the highly polymorphic genes of the vertebrate major histocompatibility complex (MHC). Although MHC proteins are crucial in pathogen recognition, it is still poorly understood how pathogen-mediated selection promotes and maintains MHC diversity, and especially so in host species with highly duplicated MHC genes. Sedge warblers (Acrocephalus schoenobaenus) have highly duplicated MHC genes, and using data from high-throughput MHC genotyping, we were able to investigate to what extent avian malaria parasites explain temporal MHC class I supertype fluctuations in a long-term study population. We investigated infection status and infection intensities of two different strains of Haemoproteus, that is avian malaria parasites that are known to have significant fitness consequences in sedge warblers. We found that prevalence of avian malaria in carriers of specific MHC class I supertypes was a significant predictor of their frequency changes between years. This finding suggests that avian malaria infections partly drive the temporal fluctuations of the MHC class I supertypes. Furthermore, we found that individuals with a large number of different supertypes had higher resistance to avian malaria, but there was no evidence for an optimal MHC class I diversity. Thus, the two studied malaria parasite strains appear to select for a high MHC class I supertype diversity. Such selection may explain the maintenance of the extremely high number of MHC class I gene copies in sedge warblers and possibly also in other passerines where avian malaria is a common disease.
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| 5. |
- Kamiya, T., et al.
(författare)
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A quantitative review of MHC-based mating preference: the role of diversity and dissimilarity
- 2014
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083. ; 23:21, s. 5151-5163
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Forskningsöversikt (refereegranskat)abstract
- Sexual selection hypotheses stipulate that the major histocompatibility complex genes (MHC) constitute a key molecular underpinning for mate choice in vertebrates. The last four decades saw growing empirical literature on the role of MHC diversity and dissimilarity in mate choice for a wide range of vertebrate animals, but with mixed support for its significance in natural populations. Using formal phylogenetic meta-analysis and meta-regression techniques, we quantitatively review the existing literature on MHC-dependent mating preferences in nonhuman vertebrates with a focus on the role of MHC diversity and dissimilarity. Overall, we found small, statistically nonsignificant, average effect sizes for both diversity- and dissimilarity-based mate choice (r=0.113 and 0.064, respectively). Importantly, however, meta-regression models revealed statistically significant support regarding female choice for diversity, and choice for dissimilarity (regardless of choosy sex) only when dissimilarity is characterized across multiple loci. Little difference was found among vertebrate taxa; however, the lack of statistical power meant statistically significant effects were limited to some taxa. We found little sign of publication bias; thus, our results are likely to be robust. In light of our quantitative assessment, methodological improvements and fruitful future avenues of research are highlighted.
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| 6. |
- O'Connor, Emily, et al.
(författare)
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The Evolution of Highly Variable Immunity Genes Across a Passerine Bird Radiation
- 2016
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083.
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Tidskriftsartikel (refereegranskat)abstract
- In order to survive, individuals must be able to recognise and eliminate pathogens. The genes of the Major Histocompatibility Complex (MHC) play an essential role in this process in vertebrates as their diversity affects the repertoire of pathogens that can be recognised by the immune system. Emerging evidence suggests that birds within the parvorder Passerida possess an exceptionally high number of MHC genes. However, this has yet to be directly investigated using a consistent framework, and the question of how this MHC diversity has evolved has not been addressed. We used next generation sequencing to investigate how MHC class I gene copy number and sequence diversity varies across the Passerida radiation using twelve species chosen to represent the phylogenetic range of this group. Additionally, we performed phylogenetic analyses on this data to identify, for the first time, the evolutionary model that best describes how MHC class I gene diversity has evolved within Passerida. We found evidence of multiple MHC class I genes in every family tested, with an extremely broad range in gene copy number across Passerida. There was a strong phylogenetic signal in MHC gene copy number and diversity, and these traits appear to have evolved through a process of Brownian Motion in the species studied, i.e. following the pattern of genetic drift or fluctuating selection, as opposed to towards a single optimal value or through evolutionary ‘bursts’. By characterising MHC class I gene diversity across Passerida in a systematic framework, this study provides a first step towards understanding this huge variation.
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| 7. |
- Richardson, David, et al.
(författare)
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MHC diversity in two Acrocephalus species: the outbred Great reed warbler and the inbred Seychelles warbler
- 2003
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Ingår i: Molecular Ecology. - 0962-1083. ; 12:12, s. 3523-3529
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Tidskriftsartikel (refereegranskat)abstract
- The Great reed warbler (GRW) and the Seychelles warbler (SW) are congeners with markedly different demographic histories. The GRW is a normal outbred bird species while the SW population remains isolated and inbred after undergoing a severe population bottleneck. We examined variation at Major Histocompatibility Complex (MHC) class I exon 3 using restriction fragment length polymorphism, denaturing gradient gel electrophoresis and DNA sequencing. Although genetic variation was higher in the GRW, considerable variation has been maintained in the SW. The ten exon 3 sequences found in the SW were as diverged from each other as were a random sub-sample of the 67 sequences from the GRW. There was evidence for balancing selection in both species, and the phylogenetic analysis showing that the exon 3 sequences did not separate according to species, was consistent with transspecies evolution of the MHC.
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| 8. |
- Schrey, A W, et al.
(författare)
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Broad-scale latitudinal patterns of genetic diversity among native European and introduced house sparrow (Passer domesticus) populations.
- 2011
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Ingår i: Molecular Ecology. - 0962-1083. ; 20, s. 1133-1143
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Tidskriftsartikel (refereegranskat)abstract
- Introduced species offer unique opportunities to study evolution in new environments, and some provide opportunities for understanding the mechanisms underlying macroecological patterns. We sought to determine how introduction history impacted genetic diversity and differentiation of the house sparrow (Passer domesticus), one of the most broadly distributed bird species. We screened eight microsatellite loci in 316 individuals from 16 locations in the native and introduced ranges. Significant population structure occurred between native than introduced house sparrows. Introduced house sparrows were distinguished into one North American group and a highly differentiated Kenyan group. Genetic differentiation estimates identified a high magnitude of differentiation between Kenya and all other populations, but demonstrated that European and North American samples were differentiated too. Our results support previous claims that introduced North American populations likely had few source populations, and indicate house sparrows established populations after introduction. Genetic diversity also differed among native, introduced North American, and Kenyan populations with Kenyan birds being least diverse. In some cases, house sparrow populations appeared to maintain or recover genetic diversity relatively rapidly after range expansion (<50 years; Mexico and Panama), but in others (Kenya) the effect of introduction persisted over the same period. In both native and introduced populations, genetic diversity exhibited large-scale geographic patterns, increasing towards the equator. Such patterns of genetic diversity are concordant with two previously described models of genetic diversity, the latitudinal model and the species diversity model.
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| 9. |
- Westerdahl, Helena
(författare)
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No evidence of an MHC-based female mating preference in great reed warblers
- 2004
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Ingår i: Molecular Ecology. - 0962-1083. ; 13:8, s. 2465-2470
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Tidskriftsartikel (refereegranskat)abstract
- Female mate-choice based on genetic compatibility is an area of growing interest. The major histocompatibility complex (MHC) genes are likely candidates for such mate-choice since these highly polymorphic genes may both increase offspring viability and also provide direct cues for mate-choice. In great reed warblers, females actively choose a breeding partner out of a handful of males that they visit and evaluate; thus, female preference for compatible or heterozygous MHC genes could have evolved. Here, I investigate whether great reed warbler females preferentially mate with males with dissimilar MHC class I alleles or with males that are heterozygous at MHC class I. Despite favourable conditions, a thorough screening method and a large sample size, there was no evidence of an MHC-based female mating preference based on either genetic compatibility or heterozygosity in this population. Power analyses of the data sets revealed that relatively small differences (15% and 8%, respectively) between true and random pairs should have been detected.
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| 10. |
- Westerdahl, Helena, et al.
(författare)
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Sex ratio variation among broods of great reed warblers Acrocephalus arundinaceus
- 1997
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Ingår i: Molecular Ecology. - 0962-1083. ; 6:6, s. 543-548
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Tidskriftsartikel (refereegranskat)abstract
- The sex of 746 great reed warbler fledglings (from 175 broods) was determined by the use of single primer polymerase-chain reaction. The reliability of the technique was confirmed as 104 of the fledglings were subsequently recorded as adults of known sex. The overall sex ratio did not differ from unity. Variation in sex ratios between broods was larger than expected from a binomial distribution. Female identity explained some of the variation of brood sex ratio indicating that certain females consistently produced sex ratios that departed from the average value in the population. The theory of sex allocation predicts that parents should adjust the sex ratio of their brood to the relative value of sons and daughters and this may vary in relation to the quality of the parents or to the time of breeding. In the great reed warbler, the proportion of sons was not related to time of breeding, or to any of five female variables. Of five male variables, males with early arrival date tended to produce more daughters. The sex ratio of fledglings that were a result of extra-pair fertilizations did not differ from that of legitimate fledglings. Hence, there is currently no evidence of that female great reed warblers invest in a higher proportion of sons when mated with attractive males.
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