Seim I, .., Lenz TL, .., Sunyaev SR, Zhang G, Krogh A, Wang J, Gladyshev VN.
Genome analysis reveals insights into physiology and longevity of the Brandt’s bat Myotis brandtii. Nature Communications. 2013;4 :2212.
DOI linkAbstractBats account for one-fifth of mammalian species, are the only mammals with powered flight, and are among the few animals that echolocate. The insect-eating Brandt’s bat (Myotis brandtii) is the longest-lived bat species known to date (lifespan exceeds 40 years) and, at 4–8 g adult body weight, is the most extreme mammal with regard to disparity between body mass and longevity. Here we report sequencing and analysis of the Brandt’s bat genome and transcriptome, which suggest adaptations consistent with echolocation and hibernation, as well as altered metabolism, reproduction and visual function. Unique sequence changes in growth hormone and insulin-like growth factor 1 receptors are also observed. The data suggest that an altered growth hormone/insulin-like growth factor 1 axis, which may be common to other long-lived bat species, together with adaptations such as hibernation and low reproductive rate, contribute to the exceptional lifespan of the Brandt’s bat.
Lenz TL, Mueller B, Trillmich F, Wolf JBW.
Divergent allele advantage at MHC-DRB through direct and maternal genotypic effects and its consequences for allele pool composition and mating. Proceedings of the Royal Society: B. 2013;280 :20130714.
Publisher's VersionAbstractIt is still debated whether main individual fitness differences in naturalpopulations can be attributed to genome-wide effects or to particular lociof outstanding functional importance such as the major histocompatibilitycomplex (MHC). In a long-term monitoring project on Galápagos sea lions (Zalophus wollebaeki), we collected comprehensive fitness and mating datafor a total of 506 individuals. Controlling for genome-wide inbreeding, wefind strong associations between the MHC locus and nearly all fitnesstraits. The effect was mainly attributable to MHC sequence divergenceand could be decomposed into contributions of own and maternal genotypes.In consequence, the population seems to have evolved a pool ofhighly divergent alleles conveying near-optimal MHC divergence even byrandom mating. Our results demonstrate that a single locus can significantlycontribute to fitness in the wild and provide conclusive evidence for the‘divergent allele advantage’ hypothesis, a special form of balancing selectionwith interesting evolutionary implications.
Lenz TL, Eizaguirre C, Kalbe M, Milinski M.
Evaluating patterns of convergent evolution and trans-species polymorphism at MHC immunogenes in two sympatric stickleback species. Evolution. 2013;67 (8) :2400-2412.
Publisher's VersionAbstractThe immunologically important major histocompatibility complex (MHC) harbors some of the most polymorphic genes in vertebrates. These genes presumably evolve under parasite-mediated selection and frequently show inconsistent allelic genealogies, where some alleles are more similar between species than within species. This phenomenon is thought to arise either from convergent evolution under parallel selection or from the preservation of ancient allelic lineages beyond speciation events (trans-species polymorphism, TSP). Here we examine natural populations of two sympatric stickleback species (Gasterosteus aculeatus and Pungitius pungitius) to investigate the contribution of these two mechanisms to the evolution of inconsistent allelic genealogies at the MHC. Overlapping parasite taxa between the two host species in three different habitats suggest contemporary parallel selection on the MHC genes. Accordingly, we detected a lack of species-specific phylogenetic clustering in the immunologically relevant antigen-binding residues of the MHC IIB genes which contrasted with the rest of the coding and non-coding sequence. However, clustering was not habitat-specific and a codon-usage analysis revealed patterns of similarity by descent. In this light, common descent via TSP, in combination with intra-species gene conversion, rather than convergent evolution is the more strongly supported scenario for the inconsistent genealogy at the MHC.
Lenz TL, Eizaguirre C, Rotter B, Kalbe M, Milinski M.
Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis. Molecular Ecology. 2013;22 (3) :774–786.
WebsiteAbstractUnderstanding the extent of local adaptation in natural populations and the mechanisms that allow individuals to adapt to their native environment is a major avenue in molecular ecology research. Evidence for the frequent occurrence of diverging ecotypes in species that inhabit multiple ecological habitats is accumulating, but experimental approaches to understanding the biological pathways as well as the underlying genetic mechanisms are still rare. Parasites are invoked as one of the major selective forces driving evolution and are themselves dependent on the ecological conditions in a given habitat. Immunological adaptation to local parasite communities is therefore expected to be a key component of local adaptation in natural populations. Here we use next generation sequencing technology to compare the transcriptome-wide response of experimentally infected three-spined sticklebacks from a lake and a river population, which are known to evolve under selection by distinct parasite communities. By comparing overall gene expression levels as well as the activation of functional pathways in response to parasite exposure, we identified potential differences between the two stickleback populations at several levels. Our results suggest locally adapted patterns of gene regulation in response to parasite exposure, which may reflect different local optima in the trade-off between the benefits and the disadvantages of mounting an immune response due to quantitative differences of the local parasite communities.
Feulner PGD, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Mundry M, Samonte IE, Stoll M, Milinski M, et al. Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Molecular Ecology. 2013;22 (3) :635–649.
DOI linkAbstractSince the end of the Pleistocene, the three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to various freshwater habitats probably originating from ancestral marine populations. Standing genetic variation and the underlying genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Here, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of paired-end and mate-pair libraries, we detected a wide size range of genetic variation. Among the six individuals, we found more than 7% of the genome is polymorphic, consisting of 2 599 111 SNPs, 233 464 indels and structural variation (SV) (>50 bp) such as 1054 copy-number variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. Based on SNP diversity, we determined outlier regions concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such SV when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.