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 linkAbstract
Bats 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 VersionAbstract
It 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 VersionAbstract
The 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. WebsiteAbstract

Understanding 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 linkAbstract

Since 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.

Eizaguirre C *, Lenz TL *, Kalbe M, Milinski M. Divergent selection on locally adapted major histocompatibility complex immune genes experimentally proven in the field. Ecology Letters. 2012;15 :723-731. WebsiteAbstract

Although crucial for the understanding of adaptive evolution, genetically resolved examples of local adaptation are rare. To maximize survival and reproduction in their local environment, hosts should resist their local parasites and pathogens. The major histocompatibility complex (MHC) with its key function in parasite resistance represents an ideal candidate to investigate parasite-mediated local adaptation. Using replicated field mesocosms, stocked with second-generation lab-bred three-spined stickleback hybrids of a lake and a river population, we show local adaptation of MHC genotypes to population-specific parasites, independently of the genetic background. Increased allele divergence of lake MHC genotypes allows lake fish to fight the broad range of lake parasites, whereas more specific river genotypes confer selective advantages against the less diverse river parasites. Hybrids with local MHC genotype gained more body weight and thus higher fitness than those with foreign MHC in either habitat, suggesting the evolutionary significance of locally adapted MHC genotypes.

Eizaguirre C, Lenz TL, Kalbe M, Milinski M. Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations. Nature Communications. 2012;3 :621. Publisher's VersionAbstract

The genes of the major histocompatibility complex are the most polymorphic genes in vertebrates, with more than 1,000 alleles described in human populations. How this polymorphism is maintained, however, remains an evolutionary puzzle. Major histocompatibility complex genes have a crucial function in the adaptive immune system by presenting parasite-derived antigens to T lymphocytes. Because of this function, varying parasite-mediated selection has been proposed as a major evolutionary force for maintaining major histocompatibility complex polymorphism. A necessary prerequisite of such a balancing selection process is rapid major histocompatibility complex allele frequency shifts resulting from emerging selection by a specific parasite. Here we show in six experimental populations of sticklebacks, each exposed to one of two different parasites, that only those major histocompatibility complex alleles providing resistance to the respective specific parasite increased in frequency in the next host generation. This result demonstrates experimentally that varying parasite selection causes rapid adaptive evolutionary changes, thus facilitating the maintenance of major histocompatibility complex polymorphism.

Lenz TL. Uterine selection for immunocompetent offspring. Proceedings of the National Academy of Sciences of the United States of America. 2011;108 :E253. Publisher's VersionAbstract
Lenz TL. Computational prediction of MHC II-antigen binding supports divergent allele advantage and explains trans-species polymorphism. Evolution. 2011;65 :2380-2390. Publisher's VersionAbstract

The major histocompatibility complex (MHC), coding for antigen presenting molecules of the adaptive immune system, represents one of the most polymorphic regions in the vertebrate genome. The exceptional polymorphism, which is potentially maintained by balancing selection under host-parasite coevolution, comprises excessive sequence divergence among alleles as well as ancient allelic lineages that predate species divergence (trans-species polymorphism). Here, the mechanisms which are proposed to maintain such sequence divergence and ancient lineages are investigated. Established computational antigen-binding prediction algorithms, which are based on empirical databases, are employed to determine the overlap in bound antigens among individual MHC class IIB alleles. The results show that genetically more divergent allele pairs experience less overlap and thus present a broader range of potential antigens. These findings support the divergent allele advantage hypothesis and furthermore suggest an evolutionary advantage explaining the maintenance of divergent allelic lineages, i.e. trans-species polymorphism. In addressing a quantitative rather than qualitative aspect of MHC alleles, these insights highlight a new direction for future research on MHC evolution.

Samonte-Padilla IE, Eizaguirre C, Scharsack JP, Lenz TL, Milinski M. Induction of diploid gynogenesis in an evolutionary model organism, the three-spined stickleback (Gasterosteus aculeatus). BMC Developmental Biology. 2011;11 :55. WebsiteAbstract

BACKGROUND: Rapid advances in genomics have provided nearly complete genome sequences for many different species. However, no matter how the sequencing technology has improved, natural genetic polymorphism complicates the production of high quality reference genomes. To address this problem, researchers have tried using artificial modes of genome manipulation such as gynogenesis for fast production of inbred lines.RESULTS: Here, we present the first successful induction of diploid gynogenesis in an evolutionary model system, the three-spined sticklebacks (Gasterosteus aculeatus), using a combination of UV-irradiation of the sperm and heat shock (HS) of the resulting embryo to inhibit the second meiotic division. Optimal UV irradiation of the sperm was established by exposing stickleback sperm to a UV- light source at various times. Heat shock parameters like temperature, duration, and time of initiation were tested by subjecting eggs fertilized with UV inactivated sperm 5, 10, 15, 20, 25, or 30 minutes post fertilization (mpf) to 30degreesC, 34degreesC, or 38degreesC for 2, 4, 6 or 8 minutes. Gynogen yield was highest when stickleback eggs were activated with 2 minutes UV-irradiated sperm and received HS 5 mpf at 34degreesC for 4 minutes.CONCLUSIONS: Diploid gynogenesis has been successfully performed in three-spined stickleback. This has been confirmed by microsatellite DNA analysis which revealed exclusively maternal inheritance in all gynogenetic fry tested. Ploidy verification by flow cytometry showed that gynogenetic embryos/larvae exhibiting abnormalities were haploids and those that developed normally were diploids, i.e., double haploids that can be raised until adult size.

Eizaguirre C, Lenz TL, Sommerfeld R, Harrod C, Kalbe M, Milinski M. Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes. Evolutionary Ecology. 2011;25 :605-622. Publisher's VersionAbstract

Ecological speciation has been the subject of intense research in evolutionary biology but the genetic basis of the actual mechanism driving reproductive isolation has rarely been identified. The extreme polymorphism of the major histocompatibility complex (MHC), probably maintained by parasite-mediated selection, has been proposed as a potential driver of population divergence. We performed an integrative field and experimental study using three-spined stickleback river and lake ecotypes. We characterized their parasite load and variation at MHC class II loci. Fish from lakes and rivers harbor contrasting parasite communities and populations possess different MHC allele pools that could be the result of a combined action of genetic drift and parasite-mediated selection. We show that individual MHC class II diversity varies among populations and is lower in river ecotypes. Our results suggest the action of homogenizing selection within habitat type and diverging selection between habitat types. Finally, reproductive isolation was suggested by experimental evidence: in a flow channel design females preferred assortatively the odor of their sympatric male. This demonstrates the role of olfactory cues in maintaining reproductive isolation between diverging fish ecotypes.

Eizaguirre C, Lenz TL. Major histocompatibility complex polymorphism: dynamics and consequences of parasite-mediated local adaptation in fishes. Journal of Fish Biology. 2010;77 :2023-2047. Publisher's VersionAbstract

Parasitism is a common form of life and represents a strong selective pressure for host organisms. In response to this evolutionary pressure, vertebrates have developed genetically coded defences such as the major histocompatibility complex (MHC). Mechanisms of parasite-mediated selection not only maintain outstanding polymorphism in these genes but have also been proposed to further promote host population divergence and ultimately speciation because it can drive evolution of local adaptation in which MHC genes play a crucial role. This review first highlights the dynamics and complexity of parasite-mediated selection in natural systems, which not only depends on dominating parasite strategies and on the taxonomic diversity of the parasite community but also includes the differences in parasite communities between habitats and niches, creating divergent selection on locally adapted populations. Then the different ways in which MHC genes potentially allow vertebrates to respond to these dynamics and to adapt locally are outlined. Finally, it is proposed that varying selection strength in time and space may lead to variation in the strength of precopulatory reproductive isolation which has evolved to maintain local adaptation.

Lenz TL, Wells K, Pfeiffer M, Sommer S. Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the Long-tailed giant rat (Leopoldamys sabanus). BMC Evolutionary Biology. 2009;9 :269. Publisher's VersionAbstract

BACKGROUND: Genes of the major histocompatibility complex (MHC) code for key functions in the adaptive immune response of vertebrates and most of them show exceptionally high polymorphism. This polymorphism has been associated with the selection by diverse and changing parasite communities. We analysed MHC class IIB diversity, gastrointestinal parasite load and body condition in the wild ranging tropical rat Leopoldamys sabanus (Thomas, 1887) under natural selection conditions in a highly variable rainforest environment in Borneo to explore the mechanisms that maintain these high levels of genetic polymorphism. RESULTS: Allelic diversity was determined via SSCP and sequencing, and parasite screening was done through non-invasive faecal egg count. The detected alleles showed expected high levels of polymorphism and balancing selection. Besides a clear advantage for more diverse MHC genotypes in terms of number of alleles, reflected in better body condition and resistance against helminth infection, our data also suggested a positive effect of MHC allele divergence within an individual on these parameters.CONCLUSION: In accordance with the heterozygote advantage hypothesis, this study provides evidence for an advantage of more diverse MHC genotypes. More specifically, the potential negative relation between individual allele divergence and number of parasite species is in line with the 'divergent allele advantage' hypothesis.

Lenz TL, Eizaguirre C, Scharsack JP, Kalbe M, Milinski M. Disentangling the role of MHC-dependent ‘good genes’ and ‘compatible genes’ in mate choice decisions of three-spined sticklebacks under semi natural conditions. Journal of Fish Biology. 2009;75 :2122 - 2142. Publisher's VersionAbstract

To investigate and disentangle the role of major histocompatibility complex (MHC)-based 'good genes' and 'compatible genes' in mate choice, three-spined sticklebacks Gasterosteus aculeatus with specific MHC IIB genotypes were allowed to reproduce in an outdoor enclosure system. Here, fish were protected from predators but encountered their natural parasites. Mate choice for an intermediate genetic distance between parental MHC genotypes was observed, which would result in intermediate diversity in the offspring, but no mate choice based on good genes was found under the current semi-natural conditions. Investigation of immunological variables revealed that the less-specific innate immune system was more active in individuals with a genetically more divergent MHC allele repertoire. This suggests the need to compensate for an MHC-diminished T-cell repertoire and potentially explains the observed mate choice for intermediate MHC genetic distance. The present findings support a general pattern of mate choice for intermediate MHC diversity (i.e. compatible genes). In addition, the potentially dynamic role of MHC good genes in mate choice under different parasite pressures is discussed in the light of present and previous results.

Lenz TL, Eizaguirre C, Becker S, Reusch TBH. RSCA genotyping of MHC for high-throughput evolutionary studies in the model organism three-spined stickleback Gasterosteus aculeatus. BMC Evolutionary Biology. 2009;9 :57. Publisher's VersionAbstract

BACKGROUND: In all jawed vertebrates, highly polymorphic genes of the major histocompatibility complex (MHC) encode antigen presenting molecules that play a key role in the adaptive immune response. Their polymorphism is composed of multiple copies of recently duplicated genes, each possessing many alleles within populations, as well as high nucleotide divergence between alleles of the same species. Experimental evidence is accumulating that MHC polymorphism is a result of balancing selection by parasites and pathogens. In order to describe MHC diversity and analyse the underlying mechanisms that maintain it, a reliable genotyping technique is required that is suitable for such highly variable genes. RESULTS: We present a genotyping protocol that uses Reference Strand-mediated Conformation Analysis (RSCA), optimised for recently duplicated MHC class IIB genes that are typical for many fish and bird species, including the three-spined stickleback, Gasterosteus aculeatus. In addition we use a comprehensive plasmid library of MHC class IIB alleles to determine the nucleotide sequence of alleles represented by RSCA allele peaks. Verification of the RSCA typing by cloning and sequencing demonstrates high congruency between both methods and provides new insight into the polymorphism of classical stickleback MHC genes. Analysis of the plasmid library additionally reveals the high resolution and reproducibility of the RSCA technique. CONCLUSION: This new RSCA genotyping protocol offers a fast, but sensitive and reliable way to determine the MHC allele repertoire of three-spined sticklebacks. It therefore provides a valuable tool to employ this highly polymorphic and adaptive marker in future high-throughput studies of host-parasite co-evolution and ecological speciation in this emerging model organism.

Eizaguirre C, Yeates S, Lenz TL, Kalbe M, Milinski M. MHC-based mate choice combines good genes and maintenance of MHC polymorphism. Molecular Ecology. 2009;18 :3316 - 3329. Publisher's VersionAbstract

Polymorphic genes of the major histocompatibility complex (MHC) are regarded as essential genes for individual fitness under conditions of natural and sexual selection. To test this hypothesis, we investigated the ultimate individual fitness trait — that of reproductive success. We used three-spined sticklebacks (Gasterosteus aculeatus) in seminatural enclosures, located in natural breeding areas where the experimental fish had been caught. During their reproductive period, fish were exposed continuously to their natural sympatric parasites. By genotyping almost 4000 eggs with nine microsatellites, we determined parenthood and inferred female mating decision. We found that with reference to their own MHC profile, female sticklebacks preferred to mate with males sharing an intermediate MHC diversity. In addition, males with a specific MHC haplotype were bigger and better at fighting a common parasite (Gyrodactylus sp.). This translated directly into Darwinian fitness since fish harbouring this specific MHC haplotype were more likely to be chosen and had a higher reproductive output. We conclude that females also based their mating decision on a specific MHC haplotype conferring resistance against a common parasite. This identifies and supports 'good genes'. We argue that such an interaction between host and parasite driving assortative mating is not only a prerequisite for negative frequency-dependent selection — a potential mechanism to explain the maintenance of MHC polymorphism, but also potentially speciation.

Eizaguirre C, Lenz TL, Traulsen A, Milinski M. Speciation accelerated and stabilized by pleiotropic major histocompatibility complex immunogenes. Ecology Letters. 2009;12 :5-12. Publisher's VersionAbstract

Speciation and the maintenance of recently diverged species has been subject of intense research in evolutionary biology for decades. Although the concept of ecological speciation has been accepted, its mechanisms and genetic bases are still under investigation. Here, we present a mechanism for speciation that is orchestrated and strengthened by parasite communities acting on polymorphic genes of the immune system. In vertebrates, these genes have a pleiotropic role with regard to parasite resistance and mate choice. In contrasting niches, parasite communities differ and thus the pools of alleles of the adapted major histocompatibility complex (MHC) also differ between niches. Mate choice for the best-adapted MHC genotype will favour local adaptations and will accelerate separation of both populations: thus immune genes act as pleiotropic speciation genes 2013'magic traits'. This mechanism should operate not only in sympatric populations but also under allopatry or parapatry. Each individual has a small subset of the many MHC alleles present in the population. If all individuals could have all MHC alleles from the pool, MHC-based adaptation is neither necessary nor possible. However, the typically small optimal individual number of MHC loci thus enables MHC-based speciation. Furthermore, we propose a new mechanism selecting against species hybrids. Hybrids are expected to have super-optimal individual MHC diversity and should therefore suffer more from parasites in all habitats.

Urbach D, Bittner D, Lenz TL, Bernet D, Wahli T, Wedekind C. Sperm velocity in an Alpine whitefish: effects of age, size, condition, fluctuating asymmetry and gonad abnormalities. Journal of Fish Biology. 2007;71 :672-683. Publisher's VersionAbstract

The relationship between sperm velocity and individual age, size, body condition and fluctuating asymmetry was investigated in Alpine whitefish Coregonus fatioi. The fish analysed belonged to one among several sympatric whitefish populations of Lake Thun, Switzerland, which are characterized by a high prevalence of gonad alterations. Therefore, sperm velocity data were also tested for a link between gonad deformation and sperm swimming speed. Sperm velocity was significantly lower in larger-grown individuals and in individuals of higher body condition. As expected, sperm velocity was higher in males with higher levels of fluctuating asymmetry, but it did not significantly vary with male age. Moreover, variation in sperm velocity was found to be significantly higher in individuals showing some types of gonad alterations but it did not significantly correlate with the presence of other types of alterations.

Lenz TL, Jacob A, Wedekind C. Manipulating sex ratio to increase population growth: the example of the Lesser Kestrel. Animal Conservation. 2007;10 :236-244. Publisher's VersionAbstract

Small or decreasing populations call for emergency actions like, for example, captive breeding programs. Such programs aim at rapidly increasing population sizes in order to reduce the loss of genetic variability and to avoid possible Allee effects. The Lesser Kestrel Falco naumanni is one of the species that is currently supported in several captive breeding programs at various locations. Here, we model the demographic and genetic consequences of potential management strategies that are based on offspring sex ratio manipulation. Increased population growth could be achieved by manipulating female conditions and/or male attractiveness in the captive breeders and consequently shifting the offspring sex ratio towards more female offspring, which are then used for reintroduction. Fragmenting populations into wild-breeding and captive-breeding demes and manipulating population sex ratio both immediately increase the inbreeding coefficient in the next generation (i.e. decrease Ne) but may, in the long term, reduce the loss of genetic variability if population growth is restricted by the number of females. We use the Lesser Kestrel and the wealth of information that is available on this species to predict the long-term consequences of various kinds of sex-ratio manipulation. We find that, in our example and possibly in many other cases, a sex-ratio manipulation that seems realistic could have a beneficial effect on the captive breeding program. However, the possible long-term costs and benefits of such measures need to be carefully optimized.