High variability in a mating type linked region in the dry rot fungus Serpula lacrymans caused by frequency-dependent selection?

<p>Abstract</p> <p>Background</p> <p>The mating type loci that govern the mating process in fungi are thought to be influenced by negative frequency-dependent selection due to rare allele advantage. In this study we used a mating type linked DNA marker as a proxy to indirectly study the allelic richness and geographic distribution of mating types of one mating type locus (MAT A) in worldwide populations of the dry rot fungus <it>Serpula lacrymans</it>. This fungus, which causes serious destruction to wooden constructions in temperate regions worldwide, has recently expanded its geographic range with a concomitant genetic bottleneck.</p> <p>Results</p> <p>High allelic richness and molecular variation was detected in the mating type linked marker as compared to other presumably neutral markers. Comparable amounts of genetic variation appeared in the mating type linked marker in populations from nature and buildings, which contrast the pattern observed with neutral genetic markers where natural populations were far more variable. Some geographic structuring of the allelic variation in the mating type linked marker appeared, but far less than that observed with neutral markers. In founder populations of <it>S. lacrymans</it>, alleles co-occurring in heterokaryotic individuals were more divergent than expected by chance, which agrees with the expectation for populations where few mating alleles exists. The analyzed DNA marker displays trans-species polymorphism wherein some alleles from the closely related species <it>S. himantoides </it>are more similar to those of <it>S. lacrymans </it>than other alleles from <it>S. himantoides</it>.</p> <p>Conclusions</p> <p>Our results support the idea that strong negative frequency-dependent selection maintains high levels of genetic variation in MAT-linked genomic regions, even in recently bottlenecked populations of <it>S. lacrymans</it>.</p

Selection in parental species predicts hybrid evolution

AbstractWhile hybridization is recognized as important in evolution, its contribution to adaptation and diversification remains poorly understood. Using genomically diverged island populations of the homoploid hybrid Italian sparrow, we test predictions for phenotypic trait values and evolvability based on patterns of parental species divergence in four plumage color traits. We find associations between parental divergence and trait evolution in Italian sparrows. Fixed major QTL in species differences lead to hybrids with higher trait variation, and hence evolvability, than the parent species. Back and crown plumage show no correlation between current within-parent variability and among-parent differentiation. For these traits, Italian sparrow phenotypes are biased towards axes of high parental differentiation and show greater phenotypic novelty along axes of low current parental evolvability, as predicted when major QTL are involved in species differences. Crown color has consistently evolved back towards one parent, while back color varies among islands. We also find significant among-population diversification within the Italian sparrow. Hence, hybridization of the same parent species can generate different phenotypes. In conclusion, we find support for parental phenotypic divergence patterns reflecting divergence mechanisms, and hence such patterns can be useful in predicting how hybridization alters the potential to evolve and adapt.</jats:p

Temporal differences in food abundance promote coexistence between two congeneric passerines

Many related species share the same environment and utilize similar resources. This is surprising because based on the principle of competitive exclusion one would predict that the superior competitor would drive the other species to extinction; coexistence is only predicted if interspecific competition is weaker than intraspecific competition. Interspecific competition is frequently reduced by differential resource use, resulting in habitat segregation. In this paper, we use the closely related collared and pied flycatcher to assess the potential of habitat differences to affect interspecific competition through a different mechanism, namely by generating temporal differences in availability of similar food resources between the two species. We found that the tree species composition of the breeding territories of the two species differed, mainly by a higher abundance of coniferous species around nest-boxes occupied by pied flycatchers. The temporal availability of caterpillars was measured using frass traps under four deciduous and two coniferous tree species. Deciduous tree species showed an early and narrow peak in abundance, which contrasted with the steady increase in caterpillar abundance in the coniferous tree species through the season. We subsequently calculated the predicted total caterpillar biomass available in each flycatcher territory. This differed between the species, with biomass decreasing more slowly in pied flycatcher territories. Caterpillar biomass is strongly correlated with the reproductive success of collared flycatchers, but much less so with pied flycatchers. However, caterpillar availability can only partly explain the differences in seasonal decline of reproductive success between the two species; we discuss additional factors that may contribute to this species difference. Overall, our results are consistent with the suggestion that minor habitat differences between these two species may contribute to promoting their coexistence

Resolution of conflict between parental genomes in a hybrid species

AbstractThe development of reproductive barriers against parent species is crucial during hybrid speciation, and post-zygotic isolation can be important in this process. Genetic incompatibilities that normally isolate the parent species can become sorted in hybrids to form reproductive barriers towards either parent. However, the extent to which this sorting process is systematically biased and therefore predictable in which loci are involved and which alleles are favored is largely unknown. Theoretically, reduced fitness in hybrids due to the mixing of differentiated genomes can be resolved through rapid evolution towards allelic combinations ancestral to lineage-splitting of the parent species, as these alleles have successfully coexisted in the past. However, for each locus, this effect may be influenced by its chromosomal location, function, and interactions with other loci. We use the Italian sparrow, a homoploid hybrid species that has developed post-zygotic barriers against its parent species, to investigate this prediction. We show significant bias towards fixation of the ancestral allele among 57 nuclear intragenic SNPs, particularly those with a mitochondrial function whose ancestral allele came from the same parent species as the mitochondria. Consistent with increased pleiotropy leading to stronger fitness effects, genes with more protein-protein interactions were more biased in favor of the ancestral allele. Furthermore, the number of protein-protein interactions was especially low among candidate incompatibilities still segregating within Italian sparrows, suggesting that low pleiotropy allows steep intraspecific clines in allele frequencies to form. Finally, we report evidence for pervasive epistatic interactions within one Italian sparrow population, particularly involving loci isolating the two parent species but not hybrid and parent. However there was a lack of classic incompatibilities and no admixture linkage disequilibrium. This suggests that parental genome admixture can continue to constrain evolution and prevent genome stabilization long after incompatibilities have been purged.</jats:p

Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species

Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse") at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows

Inferring the demographic history of European <it>Ficedula</it> flycatcher populations

<p>Abstract</p> <p>Background</p> <p>Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher.</p> <p>Results</p> <p>We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations.</p> <p>Conclusions</p> <p>Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.</p

A new upper jurassic ophthalmosaurid ichthyosaur from the Slottsmøya Member, Agardhfjellet Formation of central Spitsbergen

Abundant new ichthyosaur material has recently been documented in the Slottsmøya Member of the Agardhfjellet Formation from the Svalbard archipelago of Norway. Here we describe a partial skeleton of a new taxon, Janusaurus lundi, that includes much of the skull and representative portions of the postcranium. The new taxon is diagnosed by a suite of cranial character states including a very gracile stapedial shaft, the presence of a dorsal process on the prearticular and autapomorphic postcranial features such as the presence of an interclavicular trough and a conspicuous anterodorsal process of the ilium. The peculiar morphology of the ilia indicates a previously unrecognized degree of morphological variation in the pelvic girdle of ophthalmosaurids. We also present a large species level phylogenetic analysis of ophthalmosaurids including new and undescribed ichthyosaur material from the Upper Jurassic of Svalbard. Our results recover all Svalbard taxa in a single unresolved polytomy nested within Ophthalmosaurinae, which considerably increases the taxonomic composition of this clade. The paleobiogeographical implications of this result suggest the presence of a single clade of Boreal ophthalmosaurid ichthyosaurs that existed during the latest Jurassic, a pattern also reflected in the high degree of endemicity among some Boreal invertebrates, particularly ammonoids. Recent and ongoing descriptions of marine reptiles from the Slottsmøya Member Lagerstätte provide important new data to test hypotheses of marine amniote faunal turnover at the Jurassic-Cretaceous boundary. This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication

Data from: Inferring the demographic history of European Ficedula flycatcher populations

Background: Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results: We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of < 1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions: Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account

Hybridization and genome evolution II: Mechanisms of species divergence and their effects on evolution in hybrids

Recent genomic studies have highlighted the importance of hybridization and gene exchange in evolution. We ask what factors cause variation in the impact of hybridization, through adaptation in hybrids and the likelihood of hybrid speciation. During speciation, traits that diverge due to both divergent and stabilizing selection can contribute to the buildup of reproductive isolation. Divergent directional selection in parent taxa should lead to intermediate phenotypes in hybrids, whereas stabilizing selection can also produce extreme, transgressive phenotypes when hybridization occurs. By examining existing theory and empirical data, we discuss how these effects, combined with differences between modes of divergence in the chromosomal distribution of incompatibilities, affect adaptation and speciation in hybrid populations. The result is a clear and testable set of predictions that can be used to examine hybrid adaptation and speciation. Stabilizing selection in parents increases transgression in hybrids, increasing the possibility for novel adaptation. Divergent directional selection causes intermediate hybrid phenotypes and increases their ability to evolve along the direction of parental differentiation. Stabilizing selection biases incompatibilities towards autosomes, leading to reduced sexual correlations in trait values and reduced pleiotropy in hybrids, and hence increased freedom in the direction of evolution. Directional selection causes a bias towards sex-linked incompatibilities, with the opposite consequences. Divergence by directional selection leads to greater dominance effects than stabilizing selection, with major but variable impacts on hybrid evolution [Current Zoology 59 (5): 675-685, 2013]