MHC class I typing in a songbird with numerous loci and high polymorphism using motif-specific PCR and DGGE

The major histocompatibility complex (MHC) has a central role in the specific immune defence of vertebrates. Exon 3 of MHC class I genes encodes the domain that binds and presents peptides from pathogens that trigger immune reactions. Here we develop a fast population screening method for detecting genetic variation in the MHC class I genes of birds. We found evidence of at least 15 exon 3 sequences in the investigated great reed warbler individual. The organisation of the great reed warbler MHC class I genes suggested that a locus-specific screening protocol is impractical due to the high similarity between alleles across loci, including the introns flanking exon 3. Therefore, we used motif-specific PCR to amplify two subsets of alleles (exon 3 sequences) that were separated with by DGGE. The motif-specific primers amplify a substantial proportion of the transcribed class I alleles (2-12 alleles per individual) from as many as six class I loci. Although not exhaustive, this gives a reliable estimate of the class I variation. The method is highly repeatable and more sensitive in detecting genetic variation than the RFLP method. The motif-specific primers also allow us to avoid screening pseudogenes. In our study population of great reed warblers, we found a high level of genetic variation in MHC class I, and no less than 234 DGGE genotypes were detected among 248 screened individuals.     

MHC-based patterns of social and extra-pair mate choice in the Seychelles warbler

The existence and nature of indirect genetic benefits to mate choice remain contentious. Major histocompatibility complex (MHC) genes, which play a vital role in determining pathogen resistance in vertebrates, may be the link between mate choice and the genetic inheritance of vigour in offspring. Studies have shown that MHC-dependent mate choice can occur in mammal and fish species, but little work has focused on the role of the MHC in birds. We tested for MHC-dependent mating patterns in the Seychelles warbler (Acrocephalus sechellensis). There was no influence of MHC class I exon 3 variation on the choice of social mate. However, females were more likely to obtain extra-pair paternity (EPP) when their social mate had low MHC diversity, and the MHC diversity of the extra-pair male was significantly higher than that of the cuckolded male. There was no evidence that females were mating disassortatively, or that they preferred males with an intermediate number of MHC bands. Overall, the results are consistent with the 'good genes' rather than the 'genetic compatibility' hypothesis. As female choice will result in offspring of higher MHC diversity, MHC-dependent EPP may provide indirect benefits in the Seychelles warbler if survival is positively linked to MHC diversity.     

Polymorphism and transcription of Mhc class I genes in a passerine bird, the great reed warbler

 The class I genes of the major histocompatibility complex (Mhc) are here investigated for the first time in a passerine bird. The great reed warbler is a rare species in Sweden with a few semi-isolated populations. Yet, we found extensive Mhc class I variation in the study population. The variable exon 3, corresponding to the α₂ domain, was amplified from genomic DNA with degenerated primers. Seven different genomic class I sequences were detected in a single individual. One of the sequences had a deletion leading to a shift in the reading frame, indicating that it was not a functional gene. A randomly selected clone was used as a probe for restriction fragment length polymorphism (RFLP) studies in combination with the restriction enzyme Pvu II. The RFLP pattern was complex with 21–25 RFLP fragments per individual and extensive variation. Forty-nine RFLP genotypes were detected in 55 tested individuals. To study the number of transcribed genes, we isolated 14 Mhc class I clones from a cDNA library from a single individual. We found eight different sequences of four different lengths (1.3–2.2 kilobases), suggesting there are at least four transcribed loci. The number of nonsynonymous substitutions (d _N ) in the peptide binding region of exon 3 were higher than the number of synonymous substitutions (d _S ), indicating balancing selection in this region. The number of transcribed genes and the numerous RFLP fragments found so far suggest that the great reed warbler does not have a "minimal essential Mhc" as has been suggested for the chicken. Received: 13 May 1998 / Revised: 18 August 1998     

Great reed warbler Acrocephalus arundinaceus and reed warbler Acrocephalus scirpaceus respond differently to cuckoo dummy at the nest

A cuckoo Cuculus canorus dummy was exposed at 24 nests of great reed warbler Acrocephalus arundinaceus (GRW) and 34 nests of reed warbler Acrocephalus scirpaceus (RW) during the egg-laying stage. The eight GRW pairs attacked the cuckoo directly, striking the dummy, but such a behaviour was not recorded in RWs. Also, other behavioural measures (closest distance from the model, duration of distress calls and number of excitement calls) indicated a lower level of defence by RWs compared to GRWs. In the study area, the parasitism rate was much lower in GRWs (1.7% of nests) than in RWs (11.3%). We suggest that one of the reasons for the lower level of cuckoo parasitism on GRWs is its stronger nest defence and hence higher risk of injury or even death for the cuckoo during egg dumping.     

Hybrid origin of Audubon's warbler

Several animal species have recently been shown to have hybrid origins, but no avian examples have been documented with molecular evidence. We investigate whether the Audubon’s warbler (Dendroica auduboni), one of four visually distinct species in the yellow‐rumped warbler complex, has originated through hybridization between two other species in this group, the myrtle warbler (D. coronata) and black‐fronted warbler (D. nigrifrons). Analysis of nuclear amplified fragment length polymorphism (AFLP) and sequence markers shows that Audubon’s warblers are genetically intermediate and carry a mixture of alleles otherwise found only in one or the other of their putative parental species. Audubon’s warblers also carry two deeply divergent mitochondrial DNA lineages, each shared with only one putative parental form. Broad clines between Audubon’s and black‐fronted warblers in AFLP markers call into question the validity of these two forms as full species; nevertheless, our results suggest that the Audubon’s warbler probably originated through hybridization between two long‐diverged species. It is likely that more cases of avian species of hybrid origin will be revealed by surveys of variation in nuclear DNA and other traits.     

Syllable sharing and changes in syllable repertoire size and composition within and between years in the great reed warbler, Acrocephalus arundinaceus

The syllable repertoire size of the great reed warbler (GRW) is known to underlay female preferences. However, its stability over a season—a key factor of this quality-related feature—has never been tested. Similarly, syllable repertoire composition, syllable sharing and its function in GRW have received little attention so far. GRW syllables fit into two categories: whistles and rattles. They differ in structure but nothing is known about their function. In the present study we analyze the above aspects of GRW vocalization. We found that syllable repertoire size and composition were stable within a season but significantly changed between years. Longitudinal analyses revealed that the changes in repertoire size were influenced more by the season than the age of individuals. The repertoire size correlated with harem size. Changes in repertoire size were significantly smaller than changes in composition, indicating varying seasonal usage of syllables present in the repertoires of individual birds. Syllable sharing was high and indifferent between neighbors and distant males. This pattern suggests that syllable sharing in GRW acts as a dialect. High levels of within- and between-season repertoire similarity among all recorded birds supported this view. Whistles were more shared and repeatable within and between seasons than rattles. We suppose that whistles may play an important role in determining a local dialect due to their lower changeability both between individuals and years. Within-season similarity of whistle repertoire to other males correlated with harem size, but similarity of rattle repertoire did not. This correlation may result from a female preference for philopatric males using the local dialect.     

Restricted dispersal in a long-distance migrant bird with patchy distribution,the great reed warbler

In patchily distributed species dispersal connects local populations into metapopulations. Reliable quantifications of dispersal are therefore crucial to understanding the population dynamics and genetic structure of such metapopulation systems. The great reed warbler (Acrocephalus arundinaceus) inhabits eutrophic lakes and has a patchy breeding distribution. In this study we investigated the dispersal pattern of the great reed warbler based on an extensive capture-recapture effort covering a large census area (22,500 km²). At two adjacent breeding sites (10 km apart) in southern Central Sweden, the "main study area", we ringed the majority of adult and nestling great reed warblers between 1992 and 1999. In 1998 and 1999, we opportunistically searched for territorial males at the majority of the Swedish breeding sites, and were able to examine about 56% of all males in the region. Analyses of recaptured males demonstrated that philopatry predominated. Sixty-nine percent of the recruiting nestlings returned to breed in the main study area (their natal area), and 92% of the resighted adults were found at the same breeding locality in both study years. Breeding dispersal was significantly more restricted than natal dispersal. Additional data on natal and breeding dispersal within the main study area in 1992-1999 suggested that females were as philopatric as males. The overall high level of philopatry, with only occasional longer dispersal distances documented, yielded a root-mean-square dispersal distance of 33 km per generation. High philopatry, short dispersal distances and similar dispersal patterns of male and female great reed warblers contrast the findings among birds in general, but conform to data of species having patchy breeding habitat and isolated populations. Restricted dispersal suggests limited gene flow even among several Swedish populations, which is in line with some previous findings of the population ecology of the great reed warbler: (1) structured mtDNA lineages among European populations; (2) small-scale population differences in song patterns; and (3) low genetic variation and occurrence of inbreeding depression in our main study population.     

The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler

Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short‐ and long‐term persistence of populations and species. However, the relative spatio‐temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23‐year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool.     

MHC class I variation in a natural blue tit population (Cyanistes caeruleus)

The major histocompatibility complex (MHC) is central to the vertebrate immune system and its highly polymorphic genes are considered to influence several life-history traits of individuals. To characterize the MHC in a natural population of blue tits (Cyanistes caeruleus) we investigated the class I exon 3 diversity of more than 900 individuals. We designed two pairs of motif-specific primers that reliably amplify independent subsets of MHC alleles. Applying denaturing gradient gel electrophoresis (DGGE) we obtained 48 independently inherited units of unique band patterns (DGGE-haplogroups), which were validated in a segregation analysis within 105 families. In a second approach, we extensively sequenced 6 unrelated individuals to confirm that DGGE-haplogroup composition reflects individual allelic variation. The highest number of different DGGE-haplogroups in a single individual corresponded in 19 MHC exon 3 sequences, suggesting a minimum of 10 amplified MHC class I loci in the blue tit. In total, we identified 50 unique functional and 3 non-functional sequences. Functional sequences showed high levels of recombination and strong positive selection in the antigen binding region, whereas nucleotide diversity was comparatively low in the range of all passerine species. Finally, in a phylogenetic comparison of passerine MHC class I exon 3 sequences we discuss conflicting evolutionary signals possibly due to recent gene duplication, recombination events and concerted evolution. Our results indicate that the described method is suitable to effectively explore the MHC diversity and its ecological impacts in blue tits in future studies.     

In silico peptide-binding predictions of passerine MHC class I reveal similarities across distantly related species, suggesting convergence on the level of protein function

The major histocompatibility complex (MHC) genes are the most polymorphic genes found in the vertebrate genome, and they encode proteins that play an essential role in the adaptive immune response. Many songbirds (passerines) have been shown to have a large number of transcribed MHC class I genes compared to most mammals. To elucidate the reason for this large number of genes, we compared 14 MHC class I alleles (α1–α3 domains), from great reed warbler, house sparrow and tree sparrow, via phylogenetic analysis, homology modelling and in silico peptide-binding predictions to investigate their functional and genetic relationships. We found more pronounced clustering of the MHC class I allomorphs (allele specific proteins) in regards to their function (peptide-binding specificities) compared to their genetic relationships (amino acid sequences), indicating that the high number of alleles is of functional significance. The MHC class I allomorphs from house sparrow and tree sparrow, species that diverged 10 million years ago (MYA), had overlapping peptide-binding specificities, and these similarities across species were also confirmed in phylogenetic analyses based on amino acid sequences. Notably, there were also overlapping peptide-binding specificities in the allomorphs from house sparrow and great reed warbler, although these species diverged 30 MYA. This overlap was not found in a tree based on amino acid sequences. Our interpretation is that convergent evolution on the level of the protein function, possibly driven by selection from shared pathogens, has resulted in allomorphs with similar peptide-binding repertoires, although trans-species evolution in combination with gene conversion cannot be ruled out.     

Heritability of dispersal in the great reed warbler

Dispersal is commonly considered to be a condition‐dependent behaviour with no or low heritability. Here, we show that dispersal in the great reed warbler (Acrocephalus arundinaceus) has a high heritability. Analyses of capture–recapture data of male great reed warblers gathered from the species’ whole Swedish breeding range revealed a remarkable offspring–parent resemblance in dispersal behaviour (philopatry vs. inter‐population dispersal). Also, the degree of dispersal differed between cohorts, which shows that dispersal was partly conditionally dependent. The offspring to mid‐parent estimate of heritability was 0.50. In a previous study of the same data set of male offspring, we did not detect associations between dispersal and several relevant environmental, parental and offspring condition factors. Thus, our results indicate that variation in dispersal partly has a genetic basis in great reed warblers.     

Why Does the Frequency of Nest Parasitism by the Cuckoo Differ Considerably Between Two Populations of Warblers Living in the Same Habitat?

The rate of nest parasitism is a product of two interacting phenomena: host selection by cuckoos and defence by hosts. In our study area the rate of nest parasitism by cuckoos is significantly lower in the great reed warbler (GRW; Acrocephalus arundinaceus) than in the reed warbler (RW; A. scirpaceus), even though they breed in the same habitat and their reproductive biology is similar. We hypothesized that the difference in the proportion of parasitized nests may reflect a narrow selection of host by cuckoos (they prefer RW nests) or/and the relatively better alien egg discrimination in the GRW. In the egg discrimination experiment the GRW rejected the higher proportion of alien eggs than the RW. However, in both species the discriminative ability considerably varied in time, both within the day and within the breeding cycle. A logistic regression model suggests that the GRW would be a frequent host if only nest parasites could exploit the period of its lowest sensitivity to alien eggs. We conclude that the relatively low rate of nest parasitism in the GRW may reflect both its good discriminative ability and the low number of cuckoos that are specialized in dumping eggs to nests of this warbler. The adaptation of cuckoos to the particular host species may involve not only production of mimetic eggs, but also adjusting activity to temporal changes in sensitivity to alien eggs in the host.     

Evolutionary history suggests rapid differentiation in the yellow-throated warbler Dendroica dominica

Molecular tools are reshaping many traditional paradigms concerning the timeframe of avian diversification in North America. Phylogeographic studies have become essential for guiding the emerging paradigms. However, the current pool of such studies tends not to be evenly dispersed across the landscape, which limits the generality of inferences. The southeastern United States is one region where the tempo and mode of recent avian diversification is poorly understood. One phylogeographic break in particular, the Tombigbee River discontinuity, divides eastern and western phylogroups in Alabama, and, though it is known to have influenced the phylogeographic patterns of some fish and reptiles, its role in promoting recent avian diversification is not well understood. Eastern and western morphological subspecies of the yellow-throated warbler Dendroica dominica divide along the phylogeographic break created by the Tombigbee River discontinuity suggesting that this bird was also affected by this vicariance. To determine whether the phylogeographic patterns of the yellow-throated warbler are consistent with this biogeographic barrier, I analyzed mitochondrial control region sequences of 109 yellow-throated warblers from across the species' range and, from a subset of these samples, sequences from a sex-linked nuclear gene. Considerable variation was uncovered, but most of this variation was found within rather than among populations or subspecies. A shallow phylogenetic tree, star-like haplotype network, and unimodal mismatch distribution all suggested a recent expansion. Coalescent modeling indicated that modern populations are derived from a single common ancestral population and that differences among subspecies in morphology, ecology, and migratory pathways are the result of recent and rapid evolution, possibly driven by selection.     

Associations between malaria and MHC genes in a migratory songbird

Malaria parasites are a widespread and species-rich group infecting many wild populations of mammals, birds and reptiles. Studies on humans have demonstrated that genetic factors play a key role in the susceptibility and outcome of malaria infections. Until the present study, it has not been examined whether genetic variation in hosts is important for the outcome of malaria infections in natural avian populations. We investigated associations between major histocompatibility complex (MHC) genes and prevalence of three different avian malaria parasites (Haemoproteus payevskyi (GRW1), Plasmodium sp. (GRW2) and Plasmodium sp. (GRW4)) in a long-term study of great reed warblers Acrocephalus arundinaceus. We hypothesized that the MHC genes could either give full protection against a malaria infection, or confer protection against lethal malaria and direct the infection towards being milder. We found a positive association between numbers of MHC class I alleles (a measure of level of heterozygosity) and prevalence of the GRW2 parasite, suggesting the latter scenario. There was also a positive association between a specific MHC allele (B4b), previously shown to be under frequency-dependent selection in the study population, and prevalence of GRW2. These associations suggest that individuals carrying either a large number of MHC alleles or a specific MHC allele are protected against lethal malaria infections.     

Molecular Characterization of the Major Histocompatibility Complex Class Ia Gene in the Black-Spotted Frog, Pelophylax nigromaculata

The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. We improved rapid amplification of cDNA ends to obtain the whole coding sequence of the MHC class Ia gene of the black-spotted frog (Pelophylax nigromaculata), the most common amphibian in China. We also used genome walking to characterize the partial introns adjacent to exon 3 of the MHC Ia gene. Based on the sequences obtained, we designed locus-specific primers to investigate the molecular polymorphisms of this species in southeast China. The MHC class Ia gene showed a high level of genetic diversity, indicating that this species retains a relatively high potential for survival, despite a population decline among frog species in general and many other amphibians.     

Discovery of a breeding area of the enigmatic large‐billed reed warbler Acrocephalus orinus

The present study reports the discovery of the hitherto unknown breeding grounds of the large‐billed reed warbler Acrocephalus orinus in the Badakhshan region of Tajikistan. A total of eight adult individuals were caught at three riverine woodland sites and breeding was confirmed at one locality. The identity of the birds was confirmed on the basis of partial sequences of the cytochrome b gene. Even among individuals sampled at the same locality, genetic diversity was surprisingly high. This was interpreted as the result of secondary contact between previously isolated or fragmented populations. The breeding range of the large‐billed reed warbler is likely small and the species’ habitat is under intense pressure from the collection of firewood and fodder. Consequently, the large‐billed reed warbler remains of considerable conservation concern.     

Misleading correlations: The case of the Canada warbler and spruce budworm

In a recently published article Sleep et al. ( 2009 ) suggested that 30-yr declines in Canada warbler (1975–2005) based on Breeding Bird Survey (BBS) data could be attributed to 30-yr declines in spruce budworm through a series of analyses based principally on correlations. We demonstrate that the relationship does not hold when a longer-term data set (1968–2008) is used for the analysis. Sleep et al. ( 2009 ) also demonstrated a positive relationship between correlations of Canada warbler abundance and time and spruce budworm defoliation and time using provincial data sets. We examined the underlying BBS data and found that there were insufficient observations of Canada warbler in the western provinces (Alberta and Manitoba) to support the conclusion because most Canada warbler observations occurred far (>100 km) from any budworm defoliation. As well, we used a density-dependent stochastic population growth model as proposed by Sleep et al. ( 2009 ) and found only 2 significant relationships (Nova Scotia, Alberta) between Canada warbler population growth rate and budworm defoliation at the provincial scale. We conclude that little analytical evidence exists to support the idea that Canada warbler decline is a function of spruce budworm decline. © 2011 The Wildlife Society.     

Extremely high MHC class I variation in a population of a long-distance migrant,the Scarlet Rosefinch (<Emphasis Type="Italic">Carpodacus erythrinus</Emphasis>)

Although the number of studies focusing on the major histocompatibility complex (MHC) in non-model vertebrates is increasing, results are often contradictory, and the structure of MHC is still poorly understood in wild species. Here, we describe the structure and diversity of exon 3 of MHC class I in a passerine bird, the Scarlet Rosefinch (Carpodacus erythrinus). Using capillary electrophoresis single-strand conformation polymorphism, we identified 82 different MHC class I variants in one Rosefinch population nesting at one site in the Czech Republic. Thus far, this is the highest intra-populational MHC class I variation observed in birds. We have not found support for ‘minimal essential’ MHC in this species since individuals exhibited between three and nine different exon 3 sequences, indicating that there may be at least five amplified MHC class I genes. By cloning, we obtained and analysed 29 exon sequences and found that all of them could be translated into potentially functional proteins. We also show that strong positive selection appears to be acting mainly, but not only, on previously described antigen-binding sites in MHC class I genes. Furthermore, our results indicate that recombination has played an important role in generating genetic diversity of these genes in the Scarlet Rosefinch; we discuss the significance of this extremely high genetic diversity in light of the life history traits of this species, such as long-distance migration. The sequence data described in this paper are accessible in GenBank data library under accession numbers FJ392762–FJ392790.     

Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla)

We characterized the pattern and magnitude of phylogeographical variation among breeding populations of a long-distance migratory bird, the Wilson's warbler (Wilsonia pusilla), and used this information to assess the utility of mtDNA markers for assaying demographic connectivity between breeding and overwintering regions. We found a complex pattern of population differentiation in mitochondrial DNA (mtDNA) variation among populations across the breeding range. Individuals from eastern North America were differentiated from western individuals and the eastern haplotypes formed a distinct, well-supported cluster. The more diverse western group contained haplotype clusters with significant geographical structuring, but there was also broad mixing of haplotype groups such that no haplotype groups were population specific and the predominance of rare haplotypes limited the utility of frequency-based assignment techniques. Nonetheless, the existence of geographically diagnosable eastern vs. western haplotypes enabled us to characterize the distribution of these two groups across 14 overwintering locations. Western haplotypes were present at much higher frequencies than eastern haplotypes at most overwintering sites. Application of this mtDNA-based method of linking breeding and overwintering populations on a finer geographical scale was precluded by the absence of population-specific markers and by insufficient haplotype sorting among western breeding populations. Our results suggest that because migratory species such as the Wilson's warbler likely experienced extensive gene flow among regional breeding populations, molecular markers will have the greatest utility for characterizing breeding-overwintering connectivity at a broad geographical scale.     

Parentage assignment and extra-group paternity in a cooperative breeder: the Seychelles warbler (Acrocephalus sechellensis)

We describe the development and initial application of a semiautomated parentage testing system in the Seychelles warbler (Acrocephalus sechellensis). This system used fluorescently labelled primers for 14 polymorphic microsatellite loci in two multiplex loading groups to genotype efficiently over 96% of the warbler population on Cousin island. When used in conjunction with the program CERVUS, this system provided sufficient power to assign maternity and paternity within the Seychelles warbler, despite the complications associated with its cooperative breeding system and a relatively low level of genetic variation. Parentage analyses showed that subordinate 'helper' females as well as the dominant 'primary' females laid eggs in communal nests, indicating that the Seychelles warbler has an intermediate level of female reproductive skew, in between the alternative extremes of helper-at-the-nest and joint nesting systems. Forty-four per cent of helpers bred successfully, accounting for 15% of all offspring. Forty per cent of young resulted from extra-group paternity.