High major histocompatibility complex class I polymorphism despite bottlenecks in wild and domesticated populations of the zebra finch ()

Background Two subspecies of zebra finch, Taeniopygia guttata castanotis and T. g. guttata are native to Australia and the Lesser Sunda Islands, respectively. The Australian subspecies has been domesticated and is now an important model system for research. Both the Lesser Sundan subspecies and domesticated Australian zebra finches have undergone population bottlenecks in their history, and previous analyses using neutral markers have reported reduced neutral genetic diversity in these populations. Here we characterize patterns of variation in the third exon of the highly variable major histocompatibility complex (MHC) class I α chain. As a benchmark for neutral divergence, we also report the first mitochondrial NADH dehydrogenase 2 (ND2) sequences in this important model system. Results Despite natural and human-mediated population bottlenecks, we find that high MHC class I polymorphism persists across all populations. As expected, we find higher levels of nucleotide diversity in the MHC locus relative to neutral loci, and strong evidence of positive selection acting on important residues forming the peptide-binding region (PBR). Clear population differentiation of MHC allele frequencies is also evident, and this may be due to adaptation to new habitats and associated pathogens and/or genetic drift. Whereas the MHC Class I locus shows broad haplotype sharing across populations, ND2 is the first locus surveyed to date to show reciprocal monophyly of the two subspecies. Conclusions Despite genetic bottlenecks and genetic drift, all surveyed zebra finch populations have maintained high MHC Class I diversity. The diversity at the MHC Class I locus in the Lesser Sundan subspecies contrasts sharply with the lack of diversity in previously examined neutral loci, and may thus be a result of selection acting to maintain polymorphism. Given uncertainty in historical population demography, however, it is difficult to rule out neutral processes in maintaining the observed diversity. The surveyed populations also differ in MHC Class I allele frequencies, and future studies are needed to assess whether these changes result in functional immune differences

State-dependent capital and income breeding : a novel approach to evaluating individual strategies with stable isotopes

Background: Species-specific strategies for financing the costs of reproduction are well understood, forming a continuum ranging from high to low reliance on stored nutrients. Animals relying mostly on stored reserves are termed 'capital breeders', whereas 'income breeders' rely mostly on concurrent intake when financing the costs of reproduction. The role and adaptive value of individual variation in these strategies remain elusive. Life-history theory posits that capital breeding should be favoured when offspring reproductive value peaks, typically occurring early in the season, and that current income should increasingly be used with progressing season. Because resource limitation may hamper flexible resource allocation, a corollary prediction is that only good-condition individuals may show the expected seasonal shift in resource use. To test this prediction, we examined stable isotopes (delta C-13 and delta N-15) in blood and lipid-free egg yolk of breeding eider females (Somateria mollissima) from the Baltic Sea to assess the role of individual variation in the use of proteins from local diet vs. stored reserves. Results: We show for the first time that individuals from a single population differ in their utilization of stored reserves and concurrent intake to finance the costs of reproduction. Consistent with our prediction, heavy females predominantly used stored reserves for producing egg yolks early in the season, increasingly relying on local feeding with later onset of breeding, whereas light females showed no seasonal change in allocation strategy. Conclusions: Stable isotope profiling at the individual level is a powerful tool for monitoring relative changes in investment strategies through time, showing promise as an early warning indicator of ecological change in food webs.Peer reviewe

Gradients of seasonality and mortality risk cause rapid shifts in body size of determinate growers

<p>The dataset for the manuscript "Gradients of seasonality and mortality risk cause rapid shifts in body size of determinate growers". The dataset is packed in ZIP archive 'seasonality_size_clines.zip' and contain the results of the dynamic optimization model. Each file in the archive contains data (stored as Matlab workspaces).</p

Gradients of seasonality and mortality risk cause rapid shifts in body size of determinate growers

The dataset for the manuscript "Gradients of seasonality and mortality risk cause rapid shifts in body size of determinate growers". The dataset is packed in ZIP archive 'seasonality_size_clines.zip' and contain the results of the dynamic optimization model. Each file in the archive contains data (stored as Matlab workspaces)

Red queen processes drive positive selection on major histocompatibility complex (MHC) genes

Major Histocompatibility Complex (MHC) genes code for proteins involved in the incitation of the adaptive immune response in vertebrates, which is achieved through binding oligopeptides (antigens) of pathogenic origin. Across vertebrate species, substitutions of amino acids at sites responsible for the specificity of antigen binding (ABS) are positively selected. This is attributed to pathogen-driven balancing selection, which is also thought to maintain the high polymorphism of MHC genes, and to cause the sharing of allelic lineages between species. However, the nature of this selection remains controversial. We used individual-based computer simulations to investigate the roles of two phenomena capable of maintaining MHC polymorphism: heterozygote advantage and host-pathogen arms race (Red Queen process). Our simulations revealed that levels of MHC polymorphism were high and driven mostly by the Red Queen process at a high pathogen mutation rate, but were low and driven mostly by heterozygote advantage when the pathogen mutation rate was low. We found that novel mutations at ABSs are strongly favored by the Red Queen process, but not by heterozygote advantage, regardless of the pathogen mutation rate. However, while the strong advantage of novel alleles increased the allele turnover rate, under a high pathogen mutation rate, allelic lineages persisted for a comparable length of time under Red Queen and under heterozygote advantage. Thus, when pathogens evolve quickly, the Red Queen is capable of explaining both positive selection and long coalescence times, but the tension between the novel allele advantage and persistence of alleles deserves further investigation

An alternative route of bacterial infection associated with a novel resistance locus in the Daphnia-Pasteuria host-parasite system

To understand the mechanisms of antagonistic coevolution, it is crucial to identify the genetics of parasite resistance. In the Daphnia magna-Pasteuria ramosa host-parasite system, the most important step of the infection process is the one in which P. ramosa spores attach to the host's foregut. A matching-allele model (MAM) describes the host-parasite genetic interactions underlying attachment success. Here we describe a new P. ramosa genotype, P15, which, unlike previously studied genotypes, attaches to the host's hindgut, not to its foregut. Host resistance to P15 attachment shows great diversity across natural populations. In contrast to P. ramosa genotypes that use foregut attachment, P15 shows some quantitative variation in attachment success and does not always lead to successful infections, suggesting that hindgut attachment represents a less-efficient infection mechanism than foregut attachment. Using a Quantitative Trait Locus (QTL) approach, we detect two significant QTLs in the host genome: one that co-localizes with the previously described D. magna PR locus of resistance to foregut attachment, and a second, major QTL located in an unlinked genomic region. We find no evidence of epistasis. Fine mapping reveals a genomic region, the D locus, of ~13 kb. The discovery of a second P. ramosa attachment site and of a novel host-resistance locus increases the complexity of this system, with implications for both for the coevolutionary dynamics (e.g., Red Queen and the role of recombination), and for the evolution and epidemiology of the infection process