Aleksandra Biedrzycka

Does reduced MHC diversity decrease viability of vertebrate populations

Abstract Loss of genetic variation may render populations more vulnerable to pathogens due to inbreeding depression and depletion of variation in genes responsible for immunity against parasites. Here we review the evidence for the significance of variation in genes of the Major Histocompatibility Complex (MHC) for conservation efforts. MHC molecules present pathogen-derived antigens to the effector cells of the immune system and thus trigger the adaptive immune response. Some MHC genes are the most variable functional genes in the vertebrate genome. Their variation is clearly of adaptive significance and there is considerable evidence that its maintenance is mainly due to balancing selection imposed by pathogens. However, while the evidence for selection shaping MHC variation on the historical timescale is compelling, a correlation between levels of MHC variation and variation at neutral loci is often observed, indicating that on a shorter timescale drift also substantially affects MHC, leading to depletion of MHC diversity. The evidence that the loss of MHC variation negatively affects population survival is so far equivocal and difficult to separate from effects of general inbreeding. Some species with depleted MHC variation seem to be particularly susceptible to infection, but other species thrive and expand following severe bottlenecks that have drastically limited their MHC variation. However, while the latter demonstrate that MHC variation is not always critical for population survival, these species may in fact represent rare examples of survival despite of the loss of MHC variation. There is clearly a compelling need for data that would disclose the possible consequences of MHC diversity for population viability. In particular, we need more data on the impact of MHC allelic richness on the abundance of parasites or prevalence of disease in populations, while controlling for the role of general inbreeding. Before such evidence accumulates, captive breeding programs and other conservation measures aimed at inbreeding avoidance should be favoured over those protecting only MHC variation, especially since inbreeding avoidance programs would usually conserve both types of genetic diversity simultaneously.

Population fragmentation and major histocompatibility complex variation in the spotted suslik, Spermophilus suslicus

The fragmentation of populations typically enhances depletion of genetic variation, but highly polymorphic major histocompatibility complex (MHC) genes are thought to be under balancing selection and therefore retain polymorphism despite population bottlenecks. In this study, we investigate MHC DRB (class II) exon 2 variation in 14 spotted suslik populations from two regions differing in their degree of habitat fragmentation and gene flow. We found 16 alleles that segregated in a sample of 248 individuals. The alleles were highly divergent and revealed the hallmark signs of positive selection acting on them in the past, showing a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen‐binding sites, which suggests that past selection was driven by pathogens. MHC diversity was significantly lower in fragmented western populations than in the eastern populations, characterized by significant gene flow. In contrast to neutral variation, amova did not reveal genetic differentiation between the two regions. This may indicate similar selective pressures shaping MHC variation in both regions until the recent past. However, MHC allelic richness within a population was correlated with that for microsatellites. FST outlier analyses have shown that population differentiation at DRB was neither higher nor lower than expected under neutrality. The results suggest that selection on MHC is not strong enough to counteract drift that results from recent fragmentation of spotted suslik populations.

The genetic structure of raccoon introduced in Central Europe reflects multiple invasion pathways

Invasions of non-native species are of great concern as they have a devastating impact on native biodiversity and can also affect the economy of a region. Multiple introductions in several locations of a new range greatly promote the success of non-native species. The raccoon (Procyon lotor) is an omnivore whose native distribution extends from southern Canada to Panama. It has been successfully introduced in many European countries. We examined the microsatellite and mitochondrial diversity of raccoon populations in Central Europe (Germany, Poland, and Czech Republic) in order to determine their introduction sources and pathways as well as the factors affecting genetic structure in this invasive species. We found low diversity of the mtDNA control region and moderate diversity of microsatellite markers. Raccoon showed three hierarchic levels of genetic structure which separate at different levels sampled from Czech Republic, Germany and raccoon inhabiting two different habitats in Poland. In Poland the raccoon population was established through migration from Germany to Czech Republic. Analysis of the intensity of migration between two different habitat types indicated source-sink dynamics in the Polish populations of raccoons. Our results confirm the high intensity of the raccoon invasion in Central Europe and point to specific measures needed as part of an effective management strategy.

Hybridization between native and introduced species of deer in Eastern Europe

Abstract A consequence of introduction of alien species can be hybridization with a closely related native species. Hybridization can have a large effect on the genetic structure and conservation status of native populations. Here, we present a study of hybridization and introgression between native red deer (Cervus elaphus) and introduced sika deer (C. nippon) from 5 regions in Poland, the Kaliningrad District (Russia), and Lithuania. With a set of microsatellite loci and a mitochondrial marker, we uncovered extensive hybridization in all regions despite different population dynamics and no reports of hybrid individuals. We propose that sika populations in Eastern Europe were established with individuals coming from at least 2 different localities in southern Japan and eastern China. Legislation designed to reduce threats posed by sika deer could help to prevent further hybridization.

Molecular characterization of putative Hepatozoon sp. from the sedge warbler (Acrocephalus schoenobaenus).

We characterized partial sequences of 18S rDNA from sedge warblers infected with a parasite described previously as Hepatozoon kabeeni. Prevalence was 47% in sampled birds.We detected 3 parasite haplotypes in 62 sequenced samples from infected animals. In phylogenetic analyses, 2 of the putative Hepatozoon haplotypes closely resembled Lankesterella minima and L. valsainensis. The third haplotype grouped in a wider clade composed of Caryospora and Eimeria. None of the haplotypes showed resemblance to sequences of Hepatozoon from reptiles and mammals. Molecular detection results were consistent with those from microscopy of stained blood smears, confirming that the primers indeed amplified the parasite sequences. Here we provide evidence that the avian Hepatozoon-like parasites are most likely Lankesterella, supporting the suggestion that the systematic position of avian Hepatozoon-like species needs to be revised.

Development of novel associations between MHC alleles and susceptibility to parasitic infections in an isolated population of an endangered mammal

The role of pathogens in dynamics of endangered species is not fully understood, and the effect of infection often interacts with other processes affecting those species, such as fragmentation and isolation or loss of genetic variation. Small, isolated populations are prone to losing functional alleles due to demographic processes and genetic drift, which may diminish their ability to resist infection if immune genes are affected. Demographic processes may also alter the selective pressure exerted by a parasite, as they influence the rate of parasite transmission between individuals. In the present paper we studied changes in parasite infection levels and genetic variability in an isolated population of spotted suslik (Spermophillus suslicus). Over a three-year period (approx. three generations), when the population size remained relatively stable, we observed a considerable increase in parasite prevalence and infection intensity, followed by the development of novel associations between MHC DRB alleles and parasite burden. Contrary to expectations, the change in MHC allele frequency over time was not consistent with the effect of the allele - for instance, Spsu-DRB*07, associated with higher intensity of infection with a nematode Capillaria sp., increased in frequency from 11.8 to 20.2%. Yet, we found no signatures of selection in the studied loci. Our results show that an isolated, stable population may experience a sudden increase in parasitic infections, resulting in a development of novel associations between MHC alleles and parasite susceptibility/resistance, even though no signatures of selection can be found.

AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data

AmpliSAS and AmpliHLA are web server tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de-novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human-specific version, it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Here we describe four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.

Blood parasites shape extreme major histocompatibility complex diversity in a migratory passerine

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.