Wolf habitat selection at the territory level : seasonal and interannual variation and influence on reproductive success

Habitat selection has been one of the main research topics in ecology for decades. Nevertheless, many aspects of habitat selection still need to be explored. In particular, previous studies have overlooked the importance of temporal variation in habitat selection and the value of including data on reproductive success in order to describe the best quality habitat for a species. We used data collected from radiocollared wolves in Yellowstone National Park (USA), between 1996 and 2008, to describe wolf habitat selection. In particular, we aimed to identify i) seasonal differences in wolf habitat selection, ii) factors influencing interannual variation in habitat selection, and iii) the effect of habitat selection on wolf reproductive success. We used probability density functions to describe wolf habitat use and habitat coverages to represent the habitat available to wolves. We used regression analysis to connect habitat use with habitat characteristics and habitat selection with reproductive success. Our most relevant result was discovering strong interannual variability in wolf habitat selection. This variability was in part explained by pack identity and differences in litter size and leadership of a pack between two years (summer) and in pack size and precipitation (winter). We also detected some seasonal differences. Wolves selected open habitats, intermediate elevations, intermediate distances from roads, and avoided steep slopes in late winter. They selected areas close to roads and avoided steep slopes in summer. In early winter, wolves selected wetlands, herbaceous and shrub vegetation types, and areas at intermediate elevation and distance from roads. Surprisingly, the habitat characteristics selected by wolves were not useful in predicting reproductive success. We hypothesize that interannual variability in wolf habitat selection may be too strong to detect effects on reproductive success. Moreover, prey availability and competitor pressure may also have an influence on wolf reproductive success, which we did not assess. This project demonstrated how important temporal variation is in shaping patterns of habitat selection. We still believe in the value of running long-term studies, but the effect of temporal variation should always be taken into account.

PHYLOGENETIC ANALYSES, GENE DOSAGE EFFECT AND SELECTION IN MEMBERS OF THE LATERAL BOUNDARY DOMAIN (LBD) GENES TRANSCRIPTION FACTOR FAMILY

Wood formation is an economically and environmentally important process and has played a significant role in the evolution of terrestrial plants. Despite its significance, the molecular underpinnings of the process are still poorly understood. We have previously shown that four Lateral Boundary Domain (LBD) transcription factors have important roles in the regulation of wood formation with two (LBD1 and LBD4) involved in secondary phloem and ray cell development and two (LBD15 and LBD18) in secondary xylem formation. Here, we used comparative phylogenetic analyses to test potential roles of the four LBD genes in the evolution of woodiness. We studied the copy number and variation in DNA and amino acid sequences of the four LBDs in a wide range of woody and herbaceous plant taxa with fully sequenced and annotated genomes. LBD1 showed the highest gene copy number across the studied species, and LBD1 gene copy number was strongly and significantly correlated with the level of ray seriation. The lianas, cucumber and grape, with multiseriate ray cells showed the highest gene copy number (12 and 11, respectively). Because lianas’ growth habit requires significant twisting and bending, the less lignified ray parenchyma cells likely facilitate stem flexibility and maintenance of xylem conductivity. We further demonstrate conservation of amino acids in the LBD18 protein sequences that are specific to woody taxa. Neutrality tests showed evidence for strong purifying selection on these gene regions across various orders, indicating adaptive convergent evolution of LBD18. Structural modeling demonstrates that the conserved amino acids have a significant impact on the tertiary protein structure and thus are likely of significant functional importance.

Selection of preadapted populations allowed Senecio inaequidens to invade Central Europe

Invasive species often evolve rapidly in response to the novel biotic and abiotic conditions in their introduced range. Such adaptive evolutionary changes might play an important role in the success of some invasive species. Here, we investigated whether introduced European populations of the South African ragwort Senecio inaequidens (Asteraceae) have genetically diverged from native populations. We carried out a greenhouse experiment where 12 South African and 11 European populations were for several months grown at two levels of nutrient availability, as well as in the presence or absence of a generalist insect herbivore. We found that, in contrast to a current hypothesis, plants from introduced populations had a significantly lower reproductive output, but higher allocation to root biomass, and they were more tolerant to insect herbivory. Moreover, introduced populations were less genetically variable, but displayed greater plasticity in response to fertilization. Finally, introduced populations were phenotypically most similar to a subset of native populations from mountainous regions in southern Africa. Taking into account the species' likely history of introduction, our data support the idea that the invasion success of Senecio inaequidens in Central Europe is based on selective introduction of specific preadapted and plastic genotypes rather than on adaptive evolution in the introduced range.

Sampling-Design Effects on Properties of Species-Area Relationships - A Case Study from Estonian Dry Grassland Communities

Despite widespread use of species-area relationships (SARs), dispute remains over the most representative SAR model. Using data of small-scale SARs of Estonian dry grassland communities, we address three questions: (1) Which model describes these SARs best when known artifacts are excluded? (2) How do deviating sampling procedures (marginal instead of central position of the smaller plots in relation to the largest plot; single values instead of average values; randomly located subplots instead of nested subplots) influence the properties of the SARs? (3) Are those effects likely to bias the selection of the best model? Our general dataset consisted of 16 series of nested-plots (1 cm(2)-100 m(2), any-part system), each of which comprised five series of subplots located in the four corners and the centre of the 100-m(2) plot. Data for the three pairs of compared sampling designs were generated from this dataset by subsampling. Five function types (power, quadratic power, logarithmic, Michaelis-Menten, Lomolino) were fitted with non-linear regression. In some of the communities, we found extremely high species densities (including bryophytes and lichens), namely up to eight species in 1 cm(2) and up to 140 species in 100 m(2), which appear to be the highest documented values on these scales. For SARs constructed from nested-plot average-value data, the regular power function generally was the best model, closely followed by the quadratic power function, while the logarithmic and Michaelis-Menten functions performed poorly throughout. However, the relative fit of the latter two models increased significantly relative to the respective best model when the single-value or random-sampling method was applied, however, the power function normally remained far superior. These results confirm the hypothesis that both single-value and random-sampling approaches cause artifacts by increasing stochasticity in the data, which can lead to the selection of inappropriate models.

Support for the predictions of the pollinator-mediated stabilizing selection hypothesis

Aims Floral traits are frequency used in traditional plant systematics because Of their assumed constancy. One potential reason for the apparent constancy of flower size is that effective pollen transfer between flowers depends oil the accuracy of the physical fit between the flower and pollinator. Therefore, dowels are likely to he under stronger stabilizing selection for uniform size than vegetative plant parts. Moreover, as predicted by the pollinator-mediated stabilizing selection (PMSS) hypothesis, all accurate fit between flowers and their pollinators is likely to he more important for specialized pollination systems as found in many species with bilaterally symmetric (zygomorphic) flowers than for species, with radially symmetric (actinomorphic) flowers. Methods In a comparative study of 15 zygomorphic and 13 actinomorphic species ill Switzerland, we tested whether variation in flower size, among and within individuals, is smaller than variation ill leaf size and whether variation in flower size is smaller ill zygomorphic compared to actinomorphic species. Important findings Indeed, variation ill leaf length was significantly larger than variation in flower length and width. Within-individual variation ill flower and leaf sizes did not differ significantly between zygomorphic and actinomorphic species. In line with the predictions of the PMSS, among-individual variation ill flower length and flower width was significantly smaller for zygomorphic species than for actinomorphic species, while the two groups did not differ in leaf length variation. This suggests that plants with zygomorphic flowers have undergone stronger selection for uniform flowers than plants with actinomorphic flowers. This supports that the uniformity of flowers compared to vegetative structures within species, as already observed in traditional plant systematics, is, at least in part, a consequence of the requirement for effective pollination.

Divergent selection and phenotypic plasticity during incipient speciation in Lake Victoria cichlid fish

Divergent selection acting on several different traits that cause multidimensional shifts are supposed to promote speciation, but the outcome of this process is highly dependent on the balance between the strength of selection vs. gene flow. Here, we studied a pair of sister species of Lake Victoria cichlids at a location where they hybridize and tested the hypothesis that divergent selection acting on several traits can maintain phenotypic differentiation despite gene flow. To explore the possible role of selection we tested for correlations between phenotypes and environment and compared phenotypic divergence (P-ST) with that based on neutral markers (F-ST). We found indications for disruptive selection acting on male breeding colour and divergent selection acting on several morphological traits. By performing common garden experiments we also separated the environmental and heritable components of divergence and found evidence for phenotypic plasticity in some morphological traits contributing to species differences.

Genetic Distance between Species Predicts Novel Trait Expression in Their Hybrids

Interspecific hybridization can generate transgressive hybrid phenotypes with extreme trait values exceeding the combined range of the parental species. Such variation can enlarge the working surface for natural selection, and may facilitate the evolution of novel adaptations where ecological opportunity exists. The number of quantitative trait loci fixed for different alleles in different species should increase with time since speciation. If transgression is caused by complementary gene action or epistasis, hybrids between more distant species should be more likely to display transgressive phenotypes. To test this prediction we collected data on transgression frequency from the literature, estimated genetic distances between the hybridizing species from gene sequences, and calculated the relationship between the two using phylogenetically controlled methods. We also tested if parental phenotypic divergence affected the occurrence of transgression. We found a highly significant positive correlation between transgression frequency and genetic distance in eudicot plants explaining 43% of the variance in transgression frequency. In total, 36% of the measured traits were transgressive. The predicted effect of time since speciation on transgressive segregation was unconfounded by the potentially conflicting effects of phenotypic differentiation between species. Our analysis demonstrates that the potential impact hybridization may have on phenotypic evolution is predictable from the genetic distance between species.

Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish

Background: Transgressive segregation describes the occurrence of novel phenotypes in hybrids with extreme trait values not observed in either parental species. A previously experimentally untested prediction is that the amount of transgression increases with the genetic distance between hybridizing species. This follows from QTL studies suggesting that transgression is most commonly due to complementary gene action or epistasis, which become more frequent at larger genetic distances. This is because the number of QTLs fixed for alleles with opposing signs in different species should increase with time since speciation provided that speciation is not driven by disruptive selection. We measured the amount of transgression occurring in hybrids of cichlid fish bred from species pairs with gradually increasing genetic distances and varying phenotypic similarity. Transgression in multi-trait shape phenotypes was quantified using landmark-based geometric morphometric methods. Results: We found that genetic distance explained 52% and 78% of the variation in transgression frequency in F1 and F2 hybrids, respectively. Confirming theoretical predictions, transgression when measured in F2 hybrids, increased linearly with genetic distance between hybridizing species. Phenotypic similarity of species on the other hand was not related to the amount of transgression. Conclusion: The commonness and ease with which novel phenotypes are produced in cichlid hybrids between unrelated species has important implications for the interaction of hybridization with adaptation and speciation. Hybridization may generate new genotypes with adaptive potential that did not reside as standing genetic variation in either parental population, potentially enhancing a population's responsiveness to selection. Our results make it conceivable that hybridization contributed to the rapid rates of phenotypic evolution in the large and rapid adaptive radiations of haplochromine cichlids.

Richness of Lichen Species, Especially of Threatened Ones, Is Promoted by Management Methods Furthering Stand Continuity

Lichens are a key component of forest biodiversity. However, a comprehensive study analyzing lichen species richness in relation to several management types, extending over different regions and forest stages and including information on site conditions is missing for temperate European forests. In three German regions (Schwäbische Alb, Hainich-Dün, Schorfheide-Chorin), the so-called Biodiversity Exploratories, we studied lichen species richness in 631 forest plots of 400 m2 comprising different management types (unmanaged, selection cutting, deciduous and coniferous age-class forests resulting from clear cutting or shelterwood logging), various stand ages, and site conditions, typical for large parts of temperate Europe. We analyzed how lichen species richness responds to management and habitat variables (standing biomass, cover of deadwood, cover of rocks). We found strong regional differences with highest lichen species richness in the Schwäbische Alb, probably driven by regional differences in former air pollution, and in precipitation and habitat variables. Overall, unmanaged forests harbored 22% more threatened lichen species than managed age-class forests. In general, total, corticolous, and threatened lichen species richness did not differ among management types of deciduous forests. However, in the Schwäbische-Alb region, deciduous forests had 61% more lichen species than coniferous forests and they had 279% more threatened and 76% more corticolous lichen species. Old deciduous age classes were richer in corticolous lichen species than young ones, while old coniferous age-classes were poorer than young ones. Overall, our findings highlight the importance of stand continuity for conservation. To increase total and threatened lichen species richness we suggest (1) conserving unmanaged forests, (2) promoting silvicultural methods assuring stand continuity, (3) conserving old trees in managed forests, (4) promoting stands of native deciduous tree species instead of coniferous plantations, and (5) increasing the amount of deadwood in forests.

High plant species richness indicates management-related disturbances rather than the conservation status of forests

There is a wealth of smaller-scale studies on the effects of forest management on plant diversity. However, studies comparing plant species diversity in forests with different management types and intensity, extending over different regions and forest stages, and including detailed information on site conditions are missing. We studied vascular plants on 1500 20 m × 20 m forest plots in three regions of Germany (Schwäbische Alb, Hainich-Dün, Schorfheide-Chorin). In all regions, our study plots comprised different management types (unmanaged, selection cutting, deciduous and coniferous age-class forests, which resulted from clear cutting or shelterwood logging), various stand ages, site conditions, and levels of management-related disturbances. We analyzed how overall richness and richness of different plant functional groups (trees, shrubs, herbs, herbaceous species typically growing in forests and herbaceous light-demanding species) responded to the different management types. On average, plant species richness was 13% higher in age-class than in unmanaged forests, and did not differ between deciduous age-class and selection forests. In age-class forests of the Schwäbische Alb and Hainich-Dün, coniferous stands had higher species richness than deciduous stands. Among age-class forests, older stands with large quantities of standing biomass were slightly poorer in shrub and light-demanding herb species than younger stands. Among deciduous forests, the richness of herbaceous forest species was generally lower in unmanaged than in managed forests, and it was even 20% lower in unmanaged than in selection forests in Hainich-Dün. Overall, these findings show that disturbances by management generally increase plant species richness. This suggests that total plant species richness is not suited as an indicator for the conservation status of forests, but rather indicates disturbances.

Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish

Background: Speciation reversal: the erosion of species differentiation via an increase in introgressive hybridization due to the weakening of previously divergent selection regimes, is thought to be an important, yet poorly understood, driver of biodiversity loss. Our study system, the Alpine whitefish (Coregonus spp.) species complex is a classic example of a recent postglacial adaptive radiation: forming an array of endemic lake flocks, with the independent origination of similar ecotypes among flocks. However, many of the lakes of the Alpine radiation have been seriously impacted by anthropogenic nutrient enrichment, resulting in a collapse in neutral genetic and phenotypic differentiation within the most polluted lakes. Here we investigate the effects of eutrophication on the selective forces that have shaped this radiation, using population genomics. We studied eight sympatric species assemblages belonging to five independent parallel adaptive radiations, and one species pair in secondary contact. We used AFLP markers, and applied FST outlier (BAYESCAN, DFDIST) and logistic regression analyses (MATSAM), to identify candidate regions for disruptive selection in the genome and their associations with adaptive traits within each lake flock. The number of outlier and adaptive trait associated loci identified per lake were then regressed against two variables (historical phosphorus concentration and contemporary oxygen concentration) representing the strength of eutrophication. Results: Whilst we identify disruptive selection candidate regions in all lake flocks, we find similar trends, across analysis methods, towards fewer disruptive selection candidate regions and fewer adaptive trait/candidate loci associations in the more polluted lakes. Conclusions: Weakened disruptive selection and a concomitant breakdown in reproductive isolating mechanisms in more polluted lakes has lead to increased gene flow between coexisting Alpine whitefish species. We hypothesize that the resulting higher rates of interspecific recombination reduce either the number or extent of genomic islands of divergence surrounding loci evolving under disruptive natural selection. This produces the negative trend seen in the number of selection candidate loci recovered during genome scans of whitefish species flocks, with increasing levels of anthropogenic eutrophication: as the likelihood decreases that AFLP restriction sites will fall within regions of heightened genomic divergence and therefore be classified as FST outlier loci. This study explores for the first time the potential effects of human-mediated relaxation of disruptive selection on heterogeneous genomic divergence between coexisting species.

Frequency-Dependent Selection Predicts Patterns of Radiations and Biodiversity

Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking pre-existing niches, whereas constant rates have been attributed to non-adaptive processes such as sexual selection and mutation. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the temporal trend in the speciation rate can also be explained by frequency-dependent selection. We construct a frequency-dependent and DNA sequence-based model of speciation. We compare our model to empirical diversity patterns observed for cichlid fish and Darwin's finches, two classic systems for which speciation rates and richness data exist. Negative frequency-dependent selection predicts well both the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin's finches, in which speciation rates are constant and diversity is lower, speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity may be driven by incipient species abundance with frequency-dependent selection. Our results demonstrate that genetic-distance-based speciation and frequency-dependent selection are sufficient to explain the high diversity observed in natural systems and, importantly, predict decay through time in speciation rate in the absence of pre-existing niches.

Inheritance of female mating preference in a sympatric sibling species pair of Lake Victoria cichlids: implications for speciation

Female mate choice has often been proposed to play an important role in cases of rapid speciation, in particular in the explosively evolved haplochromine cichlid species flocks of the Great Lakes of East Africa. Little, if anything, is known in cichlid radiations about the heritability of female mating preferences. Entirely sympatric distribution, large ecological overlap and conspicuous differences in male nuptial coloration, and female preferences for these, make the sister species Pundamilia pundamilia and P. nyererei from Lake Victoria an ideally suited species pair to test assumptions on the genetics of mating preferences made in models of sympatric speciation. Female mate choice is necessary and sufficient to maintain reproductive isolation between these species, and it is perhaps not unlikely therefore, that female mate choice has been important during speciation. A prerequisite for this, which had remained untested in African cichlid fish, is that variation in female mating preferences is heritable. We investigated mating preferences of females of these sister species and their hybrids to test this assumption of most sympatric speciation models, and to further test the assumption of some models of sympatric speciation by sexual selection that female preference is a single-gene trait. We find that the differences in female mating preferences between the sister species are heritable, possibly with quite high heritabilities, and that few but probably more than one genetic loci contribute to this behavioural speciation trait with no apparent dominance. We discuss these results in the light of speciation models and the debate about the explosive radiation of cichlid fishes in Lake Victoria.

Adaptive Molecular Evolution in the Opsin Genes of Rapidly Speciating Cichlid Species

Cichlid fish inhabit a diverse range of environments that vary in the spectral content of light available for vision. These differences should result in adaptive selective pressure on the genes involved in visual sensitivity, the opsin genes. This study examines the evidence for differential adaptive molecular evolution in East African cichlid opsin genes due to gross differences in environmental light conditions. First, we characterize the selective regime experienced by cichlid opsin genes using a likelihood ratio test format, comparing likelihood models with different constraints on the relative rates of amino acid substitution, across sites. Second, we compare turbid and clear lineages to determine if there is evidence of differences in relative rates of substitution. Third, we present evidence of functional diversification and its relationship to the photic environment among cichlid opsin genes. We report statistical evidence of positive selection in all cichlid opsin genes, except short wavelength–sensitive 1 and short wavelength–sensitive 2b. In all genes predicted to be under positive selection, except short wavelength–sensitive 2a, we find differences in selective pressure between turbid and clear lineages. Potential spectral tuning sites are variable among all cichlid opsin genes; however, patterns of substitution consistent with photic environment–driven evolution of opsin genes are observed only for short wavelength–sensitive 1 opsin genes. This study identifies a number of promising candidate-tuning sites for future study by site-directed mutagenesis. This work also begins to demonstrate the molecular evolutionary dynamics of cichlid visual sensitivity and its relationship to the photic environment.

Intraspecific sexual selection on a speciation trait, male coloration, in the Lake Victoria cichlid Pundamilia nyererei

The haplochromine cichlids of Lake Victoria constitute a classical example of explosive speciation. Extensive intra– and interspecific variation in male nuptial coloration and female mating preferences, in the absence of postzygotic isolation between species, has inspired the hypothesis that sexual selection has been a driving force in the origin of this species flock. This hypothesis rests on the premise that the phenotypic traits that underlie behavioural reproductive isolation between sister species diverged under sexual selection within a species. We test this premise in a Lake Victoria cichlid, by using laboratory experiments and field observations. We report that a male colour trait, which has previously been shown to be important for behavioural reproductive isolation between this species and a close relative, is under directional sexual selection by female mate choice within this species. This is consistent with the hypothesis that female choice has driven the divergence in male coloration between the two species. We also find that male territoriality is vital for male reproductive success and that multiple mating by females is common.