Identification of plastid genotypes in Oenothera subsect. Munzia by restriction fragment length polymorphisms (RFLPs)

 Five discrete plastid genotypes (plastomes), designated I–V and typified by Oenothera Hookeri, biennis, Lamarckiana, parviflora and argillicola respectively, have been previously characterized within the European subsect. Euoenothera. The evolutionarily more-derived plastome types (I, II and V) are generally less tolerant of new hybridization events than the ancestral types (III and IV), and were first identified based on their incompatibility reactions with standard hybrid nuclei. Restriction maps for all five plastomes are available for the enzymes PvuII, SalI, KpnI and PstI (Gordon et al. 1982). The present study employs PvuII and KpnI restriction digests to compare 28 of the 45 species of subsect. Munzia with Euoenothera plastomes I–V. The results of plastome RFLP fingerprinting show uniform divergence of the South American taxa from their European congeners; all share the previously documented 45-kb inversion in the large single-copy region reported by Hachtel et al. (1991). However, at least six new plastome types have evolved within subsect. Munzia, giving rise to small-fragment size differences of 0.1–0.7 kb. In two of these cases (Oe. featherstonei and Oe. longiflora) unique fragments occurred. For Oe. featherstonei the unique KpnI fragment resulted from a novel 2.2 kb insertion, whereas in Oe. longiflora an additional PvuII restriction site has been created. Received: 2 June 1998 / Accepted: 14 July 1998     

Genic Heterozygosity and Protein Polymorphism among Local Populations of OENOTHERA BIENNIS

Twenty enzyme loci were studied in 44 Illinois populations of Oenothera biennis; four were polymorphic. Most of the variation was distributed between populations. Fifty-nine percent of the populations had one genotype, 27% two genotypes and the remaining 16% from three to five genotypes; the average was 1.50. The proportion of genetic diversity present in single populations is.38 of that present in the state. Members of single populations were uniformly heterozygous for 1 to 4 loci. The mean heterozygosity per population ranged from 0 to 20%. For Illinois populations collectively, heterozygosity averaged 4.5%. There was much gene frequency heterogeneity between populations. The true standardized genetic variance among populations for alleles at polymorphic loci varied from.40 to.78. Populations from Cook County were much more similar inter se than those downstate, had fewer genotypes and polymorphic loci, and had less heterozygosity than downstate populations. The mean normalized genetic identity among Cook County populations was.987 versus.947 for downstate populations. The mean number of genotypes per population in Cook County was 1.06 versus 2.40 in downstate populations. There was only one polymorphic locus in Cook County, VLP. The genetic structure of Oe. biennis suggests that single populations are colonized by one, or at best a few individuals. Cook County populations are judged to be less variable than downstate populations because the mean age of the populations probably is less than that of those downstate.     

Development of polarity in the ovules of the F2-progeny of theOenothera hybridalbicans · hhookeri

In the F₂-progeny of hybrids from crosses betweenOenothera biennis orsuaveolens andOe. hookeri with theRenner-complexesalbicans and^hhookeri, the development of callose pattern in meiocytes and megaspore tetrads is the same as in the F₁ and the parentOe. hookeri. During the development of the megaspore tetrads and the embryo sacs primary and secondary heteropolarity as well as homopolarity is observed. Estimates for the initial frequency of homo- and heteropolar tetrads at the end of the degeneration of megaspores in the tetrads immediately before the start of embryo sac development could be calculated. The F₂-plants can be arranged in three groups, distinguished by the frequency of the two polarity types. One of these groups behaves similar to the parentOe. hookeri, the two others have more homopolar tetrads. The segregation can be interpreted as recombination of genes, which influence the development of the polarity in the ovules. This is possible by crossing-over of genes between the twoRenner-complexes of the hybrid.     

Europäische Wildarten von Oenothera. III

Zusammenfassung Neu beschrieben werdenOenothera biennis var.angustifolia von Mannheim und die heterogameOe. nuda aus dem Bas Dauphiné.Eine im Gebiet der oberen Loire eingebürgerte Form derstrigosa-Gruppe wird als derOe. hungarica Borb. (Oe. Bauri Boedijn) nahestehend, wenn nicht mit ihr identisch erkannt.Zur Kenntnis vonOe. parviflora L.,ammophila Focke,syrticola Bartlett,rubricuspis, nova von Zinna, sowie der synthetischen Artenalbipercurva, Issleri (=rubicurva), Hölscheri (=rubiundata) wird einiges Neue beigebracht.AusOe. nova von Zinna (quaerens·paravelans) geht viel häufiger als ausOe. Lamarckiana eine Translokationsmutante vomrubrisepala-Typus hervor. Auch in der Nachkommenschaft der (biennis x Zinna) albiparavelutina ist einerubrisepala entstanden, wie sie bei (biennis x Lamarckiana) albivelutina noch nie beobachtet worden ist. Oe. nova von Zinna ist nicht, wie bisher vermutet, identisch mitOe. erythrosepala Borb. (die zu,Lamarckiana gehört) und wird in Zukunft alsOe. coronifera bezeichnet werden.Die Entstehung neuer Arten durch Kreuzung wird wieder erörtert.Auf die verschiedene Lage der Taxonomie der Oenotheren in Europa und in den Vereinigten Staaten wird hingewiesen.Die Chromosomenformeln der europäischen Komplexe werden mit denen der nächststehenden amerikanischen verglichen.Mit 17 TextabbildungenDer Deutschen Forschungsgemeinschaft bin ich für Unterstützung verpflichtet. Elisabeth Schiemann proleptisch zum 75. Geburtstag gewidmet.     

Notes on the genusOenothera subsect.Oenothera (Onagraceae) in the Czech Republic

Up-to-date results of taxonomic and phytogeographic studies ofOenothera subsect.Oenothera in the eastern part of the Czech Republic (Moravia and Silesia) are presented. A new hybridogenous species,Oe. moravica Jehlík etRostański (=Oe. fallax × Oe. victorini), is described from S Moravia. Several taxa and hybrids are reported for the first time for the Czech Republic:Oe. victorini Gates etCatcheside (=Oe. rostanskii Jehlík),Oe. × wienii Renner exRostański,Oe. acutifolia × Oe. victorini. Other taxa are recorded from the eastern part of the Czech Republic for the first time:Oe. acutifolia Rostański,Oe. hoelscheri Renner exRostański,Oe. parviflora L.,Oe. subterminalis Gates. The taxonomy ofOe. pycnocarpa Atkinson etBartlett is discussed. A survey of species and hybrids ofOenothera subsect.Oenothera in the Czech Republic is added.     

How variable is delayed selfing in a fluctuating pollinator environment? A comparison between a delayed selfing and a pollinator-dependent Schizanthus species of the high Andes

Delayed selfing has been considered the best-of-both-worlds response to pollinator unpredictability because it can provide reproductive assurance without decreasing outcrossing potential. According to this hypothesis, selfing rates in delayed selfing species should be highly variable in fluctuating pollinator environments. To test this prediction, as well to explore the consequences of delayed selfing on genetic patterns, we compared two sister species that grow in the high Andes of Chile: Schizanthus grahamii that exhibits delayed selfing and Schizanthus hookeri, which is self-compatible but requires pollinators for seed set. We estimated genetic diversity within and among five populations of each species using six shared microsatellites. Our results indicated that selfing rates in S. grahamii (range 0.07–0.81) were significantly more variable than in S. hookeri (range 0–0.26). The highest levels of selfing were found in the populations of S. grahamii located at highest altitudes (r = 0.78) and at northern margin range, where pollinators are probably more scarce. These populations also showed the lowest allelic richness and heterozygosity values. Southern populations of S. grahamii had mixed mating, and showed heterozygosity and diversity values close to those detected for S. hookeri along all the sampled range. Selfing in this species results from geitonogamy, and did not covary with altitude. Schizanthus grahamii showed greater population differentiation than S. hookeri. Overall, our results indicated that selfing rates were widely variable in S. grahamii, with some populations predominantly selfing and others showing mixed mating. This pattern may be associated with the strong fluctuations in pollinator service that typically occur in the high Andes of Chile.     

The Use of High-Throughput DNA Sequencing in the Investigation of Antigenic Variation: Application to Neisseria Species

Antigenic variation occurs in a broad range of species. This process resembles gene conversion in that variant DNA is unidirectionally transferred from partial gene copies (or silent loci) into an expression locus. Previous studies of antigenic variation have involved the amplification and sequencing of individual genes from hundreds of colonies. Using the pilE gene from Neisseria gonorrhoeae we have demonstrated that it is possible to use PCR amplification, followed by high-throughput DNA sequencing and a novel assembly process, to detect individual antigenic variation events. The ability to detect these events was much greater than has previously been possible. In N. gonorrhoeae most silent loci contain multiple partial gene copies. Here we show that there is a bias towards using the copy at the 3′ end of the silent loci (copy 1) as the donor sequence. The pilE gene of N. gonorrhoeae and some strains of Neisseria meningitidis encode class I pilin, but strains of N. meningitidis from clonal complexes 8 and 11 encode a class II pilin. We have confirmed that the class II pili of meningococcal strain FAM18 (clonal complex 11) are non-variable, and this is also true for the class II pili of strain NMB from clonal complex 8. In addition when a gene encoding class I pilin was moved into the meningococcal strain NMB background there was no evidence of antigenic variation. Finally we investigated several members of the opa gene family of N. gonorrhoeae, where it has been suggested that limited variation occurs. Variation was detected in the opaK gene that is located close to pilE, but not at the opaJ gene located elsewhere on the genome. The approach described here promises to dramatically improve studies of the extent and nature of antigenic variation systems in a variety of species.     

Floral and mating system divergence in secondary sympatry: testing an alternative hypothesis to reinforcement in Clarkia

Background and Aims

Reproductive character displacement (RCD) is often an important signature of reinforcement when partially cross-compatible taxa meet in secondary sympatry. In this study, floral evolution is examined during the Holocene range expansion of Clarkia xantiana subsp. parviflora from eastern Pleistocene refugia to a western zone of sympatry with its sister taxon, subsp. xantiana. Floral divergence between the two taxa is greater in sympatry than allopatry. The goal was to test an alternative hypothesis to reinforcement – that floral divergence of sympatric genotypes is simply a by-product of adaptation to pollination environments that differ between the allopatric and sympatric portions of the subspecies'' range.

Methods

Floral trait data from two common garden studies were used to examine floral divergence between sympatric and allopatric regions and among phylogeographically defined lineages. In natural populations of C. x. parviflora, the magnitude of pollen limitation and reproductive assurance were quantified across its west-to-east range. Potted sympatric and allopatric genotypes were also reciprocally translocated between geographical regions to distinguish between the effects of floral phenotype versus contrasting pollinator environments on reproductive ecology.

Key Results

Sympatric populations are considerably smaller flowered with reduced herkogamy. Pollen limitation and the reproductive assurance value of selfing are greater in sympatric than in allopatric populations. Most significantly, reciprocal translocation experiments showed these differences in reproductive ecology cannot be attributed to contrasting pollinator environments between the sympatric and allopatric regions, but instead reflect the effects of flower size on pollinator attraction.

Conclusions

Floral evolution occurred during the westward range expansion of parviflora, particularly in the zone of sympatry with xantiana. No evidence was found that strongly reduced flower size in sympatric parviflora (and RCD between parviflora and xantiana) is due to adaptation to limited pollinator availability. Rather, floral divergence appears to have been driven by other factors, such as interactions with congenerics in secondary sympatry.     

Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

The effect of MHC polymorphism on individual fitness variation in the wild remains equivocal; however, much evidence suggests that heterozygote advantage is a major determinant. To understand the contribution of MHC polymorphism to individual disease resistance or susceptibility in natural populations, we investigated two MHC class II B loci, DQB and DRB, in the New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened species which is unusually susceptible to death by bacterial infection at an early age; it has suffered three bacterial induced epizootics resulting in high mortality levels of young pups since 1997. The MHC DQB and DRB haplotypes of dead NZSL pups with known cause of death (bacteria, enteritis or trauma) were sequenced and reconstructed, compared to pups that survived beyond 2 months of age, and distinct MHC DRB allele frequency and genotype differences were identified. Two findings were striking: (i) one DRB allele was present only in dead pups, and (ii) one heterozygous DRB genotype, common in live pups, was absent from dead pups. These results are consistent with some functional relationship with these variants and suggest heterozygote advantage is operating at DRB. We found no association between heterozygosity and fitness at 17 microsatellite loci, indicating that general heterozygosity is not responsible for the effect on fitness detected here. This result may be a consequence of recurrent selection by multiple pathogen assault over recent years and highlights the importance of heterozygote advantage at MHC as a potential mechanism for fitness differences in wild populations.     

Immunogenetic Variation and Differential Pathogen Exposure in Free-Ranging Cheetahs across Namibian Farmlands

Background

Genes under selection provide ecologically important information useful for conservation issues. Major histocompatibility complex (MHC) class I and II genes are essential for the immune defence against pathogens from intracellular (e.g. viruses) and extracellular (e.g. helminths) origins, respectively. Serosurvey studies in Namibian cheetahs (Acinonyx juabuts) revealed higher exposure to viral pathogens in individuals from north-central than east-central regions. Here we examined whether the observed differences in exposure to viruses influence the patterns of genetic variation and differentiation at MHC loci in 88 free-ranging Namibian cheetahs.

Methodology/Principal Findings

Genetic variation at MHC I and II loci was assessed through single-stranded conformation polymorphism (SSCP) analysis and sequencing. While the overall allelic diversity did not differ, we observed a high genetic differentiation at MHC class I loci between cheetahs from north-central and east-central Namibia. No such differentiation in MHC class II and neutral markers were found.

Conclusions/Significance

Our results suggest that MHC class I variation mirrors the variation in selection pressure imposed by viruses in free-ranging cheetahs across Namibian farmland. This is of high significance for future management and conservation programs of this species.     

Nuclear Gene-Induced Plastome Mutations in OENOTHERA HOOKERI. I. Genetic Analysis

A nuclear gene mutation in Oenothera hookeri increases the frequency of variegated sectors. The gene is recessive; the variegation is cytoplasmically transmitted. Once variegation is induced, the mutant gene is not required for its continued expression. The induced sectors may differ one from another. The gene expresses unique patterns of penetrance and of maternal effect. The genetic data implicate the chloroplasts as the site for the expression of variegation. The chloroplasts of O. parviflora are also subject to the action of the nuclear gene. Possible mechanisms by which a gene might cause chloroplasts to mutate are discussed.     

Major histocompatibility complex class II compatibility,but not class I,predicts mate choice in a bird with highly developed olfaction

Mate choice for major histocompatibility complex (MHC) compatibility has been found in several taxa, although rarely in birds. MHC is a crucial component in adaptive immunity and by choosing an MHC-dissimilar partner, heterozygosity and potentially broad pathogen resistance is maximized in the offspring. The MHC genotype influences odour cues and preferences in mammals and fish and hence olfactory-based mate choice can occur. We tested whether blue petrels, Halobaena caerulea, choose partners based on MHC compatibility. This bird is long-lived, monogamous and can discriminate between individual odours using olfaction, which makes it exceptionally well suited for this analysis. We screened MHC class I and II B alleles in blue petrels using 454-pyrosequencing and quantified the phylogenetic, functional and allele-sharing similarity between individuals. Partners were functionally more dissimilar at the MHC class II B loci than expected from random mating (p = 0.033), whereas there was no such difference at the MHC class I loci. Phylogenetic and non-sequence-based MHC allele-sharing measures detected no MHC dissimilarity between partners for either MHC class I or II B. Our study provides evidence of mate choice for MHC compatibility in a bird with a high dependency on odour cues, suggesting that MHC odour-mediated mate choice occurs in birds.     

High allozyme diversity and unidirectional linear migration patterns within a population of tetraploid Isoetes sinensis, a rare and endangered pteridophyte

Isoetes sinensis (Isoetaceae), an aquatic quillwort which occurs only in two fragmented sites of China as an allotetraploid, is critically endangered. Genetic variation among eight subpopulations of I. sinensis was examined in the Xin’an River (119°14′–15′E, 29°28′N) by using allozyme polymorphism. Eighteen loci of 10 enzyme systems were examined and used for the analysis of population genetic parameters. As expected for allotetraploids, fixed heterozygosity was found at four loci. A high level of genetic diversity was observed in the population, with mean number of alleles per loci of 1.8, and mean percentage of polymorphic loci of 55.6%, which were much higher than the average values in fern species. The genetic variation within each subpopulation was not positively correlated with its size, which may be explained by high gene flow (Nm = 2.57), clonal reproduction and fixed heterozygosity of allopolyploid. The I. sinensis population contained high clonal diversity (PD = 0.39, D = 0.95), indicating the successful seedling recruitment of the population. Significant positive relationship was detected between clonal diversity and the size of subpopulation. Partitioning the genetic diversity indicated that 91.1% of the genetic variation was within subpopulations and only 8.9% existed among subpopulations. The migration pattern of I. sinensis along the Xin’an River is best explained by a source–sink model, but with unidirectional gene flow among subpopulations underlined by hydrochoric force. The results were then discussed in relation to both in situ and ex situ conservation efforts of the population.     

Callose Deposition During Megagametogenesis in Two Species of Oenothera

Callose deposits are present both in degenerating megasporesof the heteropolar tetrad in Oenothera hookeri and in degeneratingembryo sacs of the homopolar developing tetrad in O biennis.They are partially continuous with the cell wall and partiallyenclosed in the degenerating cytoplasm and show electron opaquebands within a less electron opaque material Vesicles calledcallose grains are present in the degenerating cytoplasm ofthe embryo sac in O biennis These show an electron opaque fibnllaror granular core surrounded by a halo of low electron opacity Similarities in fine structure between callose deposits of femalegametophytes which follow the degenerating pathway of development,and callose plugs present in pollen tubes during their growth,are discussed. Oenothera, evening primrose, megagametogenesis, megasporogenesis, callose, ultrastructure     

Seedling traits, plasticity and local differentiation as strategies of invasive species of Impatiens in central Europe

Background and Aims

Invasiveness of some alien plants is associated with their traits, plastic responses to environmental conditions and interpopulation differentiation. To obtain insights into the role of these processes in contributing to variation in performance, we compared congeneric species of Impatiens (Balsaminaceae) with different origin and invasion status that occur in central Europe.

Methods

Native I. noli-tangere and three alien species (highly invasive I. glandulifera, less invasive I. parviflora and potentially invasive I. capensis) were studied and their responses to simulated canopy shading and different nutrient and moisture levels were determined in terms of survival and seedling traits.

Key Results and Conclusions

Impatiens glandulifera produced high biomass in all the treatments and the control, exhibiting the ‘Jack-and-master’ strategy that makes it a strong competitor from germination onwards. The results suggest that plasticity and differentiation occurred in all the species tested and that along the continuum from plasticity to differentiation, the species at the plasticity end is the better invader. The most invasive species I. glandulifera appears to be highly plastic, whereas the other two less invasive species, I. parviflora and I. capensis, exhibited lower plasticity but rather strong population differentiation. The invasive Impatiens species were taller and exhibited higher plasticity and differentiation than native I. noli-tangere. This suggests that even within one genus, the relative importance of the phenomena contributing to invasiveness appears to be species''specific.     

Genetic Variation in Hawaiian Drosophila. IV. Allozymic Similarity between D. SILVESTRIS and D. HETERONEURA from the Island of Hawaii

The species are endemic to the newest island in the archipelago and are broadly sympatric. They are easily distinguished morphologically in both sexes. Using standard electrophoretic procedures, we have examined 25 loci encoding for structural proteins from 539 silvestris and 325 heteroneura collected at three widely-separated localities where the two species are sympatric. Pairwise comparisons within and between the species show the following coefficients of genetic identity (Nei''s I): within silvestris, 0.961 ± 0.01; within heteroneura, 0.949 ± 0.02; between silvestris and heteroneura, 0.939 ± 0.01. Neither the differences within nor between the species are significant. There are no fixed allelic differences either within or between the species. At the three areas of sympatry, the species show gene frequency differences (P < 0.05) at 9, 11 and 13 loci respectively. This is not much different from the variation within either one of the species across the three localities. The two species have similar heterozygosity ( H) levels (silvestris, 0.083; heteroneura, 0.089) and percent of polymorphic loci (both 0.37). It is suggested that despite their morphological divergence, these species are much more newly formed than classical sibling species. Significant allozymic differences may not have had time to accumulate.     

Drivers of natural spread of invasive <Emphasis Type="Italic">Impatiens parviflora</Emphasis> differ between life-cycle stages

Impatiens parviflora is one of the most widely spread invasive species in central Europe, yet the factors affecting its spread are still subject to discussion. The aim of this study was to determine which factors affect the spread of I. parviflora. This was achieved by observing the natural spread of the species on 15 permanent transects, in six different habitats, found within the Czech Republic from 2012 to 2016. The transects were divided into 321 plots, whilst data on environmental conditions, as well as of the spread of I. parviflora and its performance, were collected in each plot. The results showed that individual stages of the I. parviflora life-cycle were affected by individual environmental conditions to different extents. The most important factor preventing seedling emergence and establishment was a high cover of herb layer. It did not, however, affect survival of older plants. Thus, I. parviflora can grow in sites with dense cover of herb layer in case the cover formed after I. parviflora seedlings established. Juvenile mortality was the highest in sites with low nutrient levels and low soil moisture. Canopy openness had a negative effect on I. parviflora performance. Impatiens parviflora performed better in neutral soils, in comparison to acidic soils. Oak-hornbeam forests were the most suitable habitat for I. parviflora, followed by acidophilous oak and mixed coniferous forests. However, I. parviflora was able to penetrate into even species-rich habitats, such as thermophilous oak forests, as well as steppe grasslands on rocks. This makes it a potential threat to biodiversity. Only heathlands found on former pastures proved to be unsuitable for I. parviflora, as these remained uninvaded until the end of the study.     

Cytogeography and genome size variation in the Claytonia perfoliata (Portulacaceae) polyploid complex

Background and Aims

Genome duplication is a central process in plant evolution and contributes to patterns of variation in genome size within and among lineages. Studies that combine cytogeography with genome size measurements contribute to our basic knowledge of cytotype distributions and their associations with variation in genome size.

Methods

Ploidy and genome size were assessed with direct chromosome counts and flow cytometry for 78 populations within the Claytonia perfoliata complex, comprised of three diploid taxa with numerous polyploids that range to the decaploid level. The relationship between genome size and temperature and precipitation was investigated within and across cytotypes to test for associations between environmental factors and nuclear DNA content.

Key Results

A euploid series (n = 6) of diploids to octoploids was documented through chromosome counts, and decaploids were suggested by flow cytometry. Increased variation in genome size among populations was found at higher ploidy levels, potentially associated with differential contributions of diploid parental genomes, variation in rates of genomic loss or gain, or undetected hybridization. Several accessions were detected with atypical genome sizes, including a diploid population of C. parviflora ssp. grandiflora with an 18 % smaller genome than typical, and hexaploids of C. perfoliata and C. parviflora with genomes 30 % larger than typical. There was a slight but significant association of larger genome sizes with colder winter temperature across the C. perfoliata complex as a whole, and a strong association between lower winter temperatures and large genome size for tetraploid C. parviflora.

Conclusions

The C. perfoliata complex is characterized by polyploids ranging from tetraploid to decaploid, with large magnitude variation in genome size at higher ploidy levels, associated in part with environmental variation in temperature.     

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species'' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species'' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.     

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens

DNA sequence variation within human leukocyte antigen (HLA) genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC) makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals) and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918) with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes.