Intestinal Tritrichomonas foetus infection in cats in Switzerland detected by in vitro cultivation and PCR

Tritrichomonas foetus, a parasite well known for its significance as venereally transmitted pathogen in cattle, has recently been identified as a cause of chronic large-bowel diarrhea in domestic cats in the US, UK, and, more recently, also in Norway. In a period of 3 months (October to December 2007), 45 cats of Switzerland suffering from chronic diarrhea were investigated for intestinal infections, including a search for trichomonads. A commercially available in vitro culture system was used to screen for infection, complemented with a PCR and subsequent amplicon sequencing to support speciation. The PCR is based upon amplification of a sequence derived from the internal transcribed spacer region 1 (ITS1) on the ribosomal RNA gene (rRNA) using primers designed to detect a broad range of genera and species belonging to the family of Trichomonadidae. The method was furthermore adapted to the uracil DNA glycosylase (UDG) system in order to prevent carry-over contamination and it included a recombinant internal control to track for inhibitory reactions. Eleven out of the 45 cats were culture-positive, as revealed by microscopic identification of trichomonadid organisms. One of the isolates was subjected to scanning electron microscopy and findings revealed the presence of three flagella, thus placing the isolate into the gender Tritrichomonas sp. PCR and subsequent amplicon sequencing were carried out with ten of the 11 isolates. A total homology with published T. foetus sequences was confirmed in all of the cases. T. foetus therefore appears to range among those organisms that can cause chronic diarrhea in cats in Switzerland.

Color and Scent: How Single Genes Influence Pollinator Attraction

A major function of angiosperm flowers is the recruitment of animal pollinators that serve to transfer pollen among conspecific plants. Distinct sets of floral characteristics, called pollination syndromes, are correlated with visitation by specific groups of pollinators. Switches among pollination syndromes have occurred in many plant families. Such switches must have involved coordinated changes in multiple traits and multiple genes. Two well-studied floral traits affecting pollinator attraction are petal color and scent production. We review current knowledge about the biosynthetic pathways for floral color and scent production and their interaction at the genetic and biochemical levels. A key question in the field concerns the genes that underlie natural variation in color and scent and how such genes affect pollinator preference, reproductive isolation, and ultimately speciation.

Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae

Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. The monophyly of representatives of the genus Gallibacterium was recognized by analysis of all housekeeping genes, while members of Mannheimia, Actinobacillus sensu stricto and the core group of Pasteurella sensu stricto formed monophyletic groups with two out of three housekeeping genes. Representatives of Mannheimia, Actinobacillus sensu stricto, [Haemophilus] ducreyi and [Pasteurella] trehalosi formed a monophyletic unit by analysis of all three housekeeping genes, which was in contrast to the 16S rRNA gene-derived phylogeny, where these taxa occurred at separate positions in the phylogenetic tree. Representatives of the Rodent, Avian and Aphrophilus-Haemophilus 16S rRNA gene groups were weakly supported by phylogenetic analysis of housekeeping genes. Phylogenies derived by comparison of the housekeeping genes diverged significantly from the 16S rRNA gene-derived phylogeny as evaluated by the likelihood ratio test. A low degree of congruence was also observed between the individual housekeeping gene-derived phylogenies. Estimates on speciation derived from 16S rRNA and housekeeping gene sequence comparisons resulted in quite different evolutionary scenarios for members of the Pasteurellaceae. The phylogeny based on the housekeeping genes supported observed host associations between Mannheimia, Actinobacillus sensu stricto and [Pasteurella] trehalosi and animals with paired hooves.

Short-term response of the Ca cycle of a montane forest in Ecuador to low experimental CaCl 2 additions

The tropical montane forests of the E Andean cordillera in Ecuador receive episodic Sahara-dust inputs particularly increasing Ca deposition. We added CaCl2 to isolate the effect of Ca deposition by Sahara dust to tropical montane forest from the simultaneously occurring pH effect. We examined components of the Ca cycle at four control plots and four plots with added Ca (2 × 5 kg ha–1 Ca annually as CaCl2) in a random arrangement. Between August 2007 and December 2009 (four applications of Ca), we determined Ca concentrations and fluxes in litter leachate, mineral soil solution (0.15 and 0.30 m depths), throughfall, and fine litterfall and Al concentrations and speciation in soil solutions. After 1 y of Ca addition, we assessed fine-root biomass, leaf area, and tree growth. Only < 3% of the applied Ca leached below the acid organic layer (pH 3.5–4.8). The added CaCl2 did not change electrical conductivity in the root zone after 2 y. In the second year of fertilization, Ca retention in the canopy of the Ca treatment tended to decrease relative to the control. After 2 y, 21% of the applied Ca was recycled to soil with throughfall and litterfall. One year after the first Ca addition, fine-root biomass had decreased significantly. Decreasing fine-root biomass might be attributed to a direct or an indirect beneficial effect of Ca on the soil decomposer community. Because of almost complete association of Al with dissolved organic matter and high free Ca2+ : Al3+ activity ratios in solution of all plots, Al toxicity was unlikely. We conclude that the added Ca was retained in the system and had beneficial effects on some plants.

Metabolic divergence between sibling species of cichlids Pundamilia nyererei and Pundamilia pundamilia

This study compared Pundamilia nyererei and Pundamilia pundamilia males in routine metabolic rate (RR ) and in the metabolic costs males pay during territorial interactions (active metabolic rate, RA ). Pundamilia nyererei and P. pundamilia males housed in social isolation did not differ in RR . In contrast to expectation, however, P. nyererei males used less oxygen than P. pundamilia males, for a given mass and level of agonistic activity. This increased metabolic efficiency may be an adaptation to limit the metabolic cost that P. nyererei males pay for their higher rate of aggressiveness compared to P. pundamilia males. Thus, the divergence between the species in agonistic behaviour is correlated with metabolic differentiation. Such concerted divergence in physiology and behaviour might be widespread in the dramatically diverse cichlid radiations in East African lakes and may be an important factor in the remarkably rapid speciation of these fishes. The results did not support the hypothesis that higher metabolic rates caused a physiological cost to P. nyererei males that would offset their dominance advantage.

Repeated and predictable patterns of ecotypic differentiation during a biological invasion: lake-stream divergence in parapatric Swiss stickleback

The relative importance of ecological selection and geographical isolation in promoting and constraining genetic and phenotypic differentiation among populations is not always obvious. Interacting with divergent selection, restricted opportunity for gene flow may in some cases be as much a cause as a consequence of adaptation, with the latter being a hallmark of ecologi- cal speciation. Ecological speciation is well studied in parts of the native range of the three-spined stickleback. Here, we study this process in a recently invaded part of its range. Switzerland was colonized within the past 140 years from at least three different colonization events involving differ- ent stickleback lineages. They now occupy diverse habitats, ranging from small streams to the pelagic zone of large lakes. We use replicated systems of parapatric lake and stream populations, some of which trace their origins to different invasive lineages, to ask (i) whether phenotypic divergence occurred among populations inhabiting distinct habitats, (ii) whether trajec- tories of phenotypic divergence follow predictable parallel patterns and (iii) whether gene flow constrains divergent adaptation or vice versa. We find consistent phenotypic divergence between populations occupying distinct habitats. This involves parallel evolution in several traits with known eco- logical relevance in independent evolutionary lineages. Adaptive divergence supersedes homogenizing gene flow even at a small spatial scale. We find evidence that adaptive phenotypic divergence places constraints on gene flow over and above that imposed by geographical distance, signalling the early onset of ecological speciation.

Experimental evidence for trait utility of gill raker number in adaptive radiation of a north temperate fish

North temperate fish in post-glacial lakes are textbook examples for rapid parallel adaptive radiation into multiple trophic specialists within individual lakes. Speciation repeatedly proceeded along the benthic – limnetic habitat axis, and benthic – limnetic sister species diverge in the number of gill rakers. Yet, the utility of different numbers of gill rakers for consuming benthic vs. limnetic food has only very rarely been experimentally demonstrated. We bred and raised families of a benthic – limnetic species pair of whitefish under common garden conditions to test whether these species (i) show heritable differentiation in feeding efficiency on zooplankton, and (ii) whether varia- tion in feeding efficiency is predicted by variation in gill raker numbers. We used zooplankton of three different size classes to investigate prey size dependency of divergence in feeding efficiency and to investigate the effect strength of variation in the number of gill rakers. Our results show strong interspecific differences in feeding efficiency. These differences are largest when fish were tested with the smallest zooplankton. Importantly, feeding efficiency is significantly positively correlated with the number of gill rakers when using small zooplankton, also when species identity is statistically controlled for. Our results support the hypothesis that a larger number of gill rakers are of adaptive significance for feeding on zooplankton and pro- vide one of the first experimental demonstrations of trait utility of gill raker number when fish feed on zooplankton. These results are consistent with the suggested importance of divergent selection driven feeding adaptation during adaptive radiation of fish in post-glacial lakes.

Sexual dimorphism dominates divergent host plant use in stick insect trophic morphology

Background: Clear examples of ecological speciation exist, often involving divergence in trophic morphology. However, substantial variation also exists in how far the ecological speciation process proceeds, potentially linked to the number of ecological axes, traits, or genes subject to divergent selection. In addition, recent studies highlight how differentiation might occur between the sexes, rather than between populations. We examine variation in trophic morphology in two host-plant ecotypes of walking-stick insects (Timema cristinae), known to have diverged in morphological traits related to crypsis and predator avoidance, and to have reached an intermediate point in the ecological speciation process. Here we test how host plant use, sex, and rearing environment affect variation in trophic morphology in this species using traditional multivariate, novel kernel density based and Bayesian morphometric analyses. Results: Contrary to expectations, we find limited host-associated divergence in mandible shape. Instead, the main predictor of shape variation is sex, with secondary roles of population of origin and rearing environment. Conclusion: Our results show that trophic morphology does not strongly contribute to host-adapted ecotype divergence in T. cristinae and that traits can respond to complex selection regimes by diverging along different intraspecific lines, thereby impeding progress toward speciation.

Relaxed trait covariance in interspecific cichlid hybrids predicts morphological diversity in adaptive radiations

The process of adaptive radiation involves multiple events of speciation in short succession, associated with ecological diversification. Understanding this process requires identifying the origins of heritable phenotypic variation that allows adaptive radiation to progress. Hybridization is one source of genetic and morphological variation that may spur adaptive radiation. We experimentally explored the potential role of hybridization in facilitating the onset of adaptive radiation. We generated first- and second-generation hybrids of four species of African cichlid fish, extant relatives of the putative ancestors of the adaptive radiations of Lakes Victoria and Malawi. We com- pared patterns in hybrid morphological variation with the variation in the lake radiations. We show that significant fractions of the interspecific mor- phological variation and the major trajectories in morphospace that charac- terize whole radiations can be generated in second-generation hybrids. Furthermore, we show that covariation between traits is relaxed in second- generation hybrids, which may facilitate adaptive diversification. These results support the idea that hybridization can provide the heritable pheno- typic diversity necessary to initiate adaptive radiation.

A test of genetic association among male nuptial coloration, female mating preference, and male aggression bias within a polymorphic population of cichlid fish

Both inter- and intrasexual selection have been implicated in the origin and maintenance of species-rich taxa with diverse sexual traits. Simultaneous disruptive selection by female mate choice and male-male competition can, in theory, lead to speciation without geographical isolation if both act on the same male trait. Female mate choice can generate discontinuities in gene flow, while male-male competition can generate negative frequency-dependent selection stabilizing the male trait polymorphism. Speciation may be facilitated when mating preference and/or aggression bias are physically linked to the trait they operate on. We tested for genetic associations among female mating preference, male aggression bias and male coloration in the Lake Victoria cichlid Pundamilia. We crossed females from a phenotypically variable population with males from both extreme ends of the phenotype distribution in the same population (blue or red). Male offspring of a red sire were significantly redder than males of a blue sire, indicating that intra-population variation in male coloration is heritable. We tested mating preferences of female offspring and aggression biases of male offspring using binary choice tests. There was no evidence for associations at the family level between female mating preferences and coloration of sires, but dam identity had a significant effect on female mate preference. Sons of the red sire directed significantly more aggression to red than blue males, whereas sons of the blue sire did not show any bias. There was a positive correlation among individuals between male aggression bias and body coloration, possibly due to pleiotropy or physical linkage, which could facilitate the maintenance of color polymorphism.

Female preference for male color is necessary and sufficient for assortative mating in 2 cichlid sister species

A critical step for speciation in the face of gene flow is the origination of reproductive isolation. The evolution of assortative mating greatly facilitates this process. Assortative mating can be mediated by one or multiple cues across an array of sensory modalities. We here explore possible cues that may underlie female mate choice in a sympatric species pair of cichlid fish from Lake Victoria, Pundamilia pundamilia and Pundamilia nyererei. Previous studies identified species-specific female preferences for male coloration, but effects of other cues could not be ruled out. Therefore, we assessed female choice in a series of experiments in which we manipulated visual (color) and chemical cues. We show that the visibility of differences in nuptial hue (i.e., either blue or red) between males of the 2 species is necessary and sufficient for assortative mating by female mate choice. Such assortment mediated by a single cue may evolve relatively quickly, but could make reproductive isolation vulnerable to environmental changes. These findings confirm the important role of female mate choice for male nuptial hue in promoting the explosive speciation of African haplochromine cichlids.

Cichlid species-area relationships are shaped by adaptive radiations that scale with area

A positive relationship between species richness and island size is thought to emerge from an equilibrium between immigration and extinction rates, but the influence of species diversification on the form of this relationship is poorly understood. Here, we show that within-lake adaptive radiation strongly modifies the species-area relationship for African cichlid fishes. The total number of species derived from in situ speciation increases with lake size, resulting in faunas orders of magnitude higher in species richness than faunas assembled by immigration alone. Multivariate models provide evidence for added influence of lake depth on the species-area relationship. Diversity of clades representing within-lake radiations show responses to lake area, depth and energy consistent with limitation by these factors, suggesting that ecological factors influence the species richness of radiating clades within these ecosystems. Together, these processes produce lake fish faunas with highly variable composition, but with diversities that are well predicted by environmental variables.

Genomics and the origin of species

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics

Diversity versus disparity and the role of ecological opportunity in a continental bird radiation

Aim The Neotropical parrots (Arini) are an unusually diverse group which colonized South America in the Oligocene. The newly invaded Neotropics may have functioned as an underused adaptive zone and provided novel ecological opportunities that facilitated diversification. Alternatively, diversification may have been driven by ecological changes caused by Andean uplift and/or climate change from the Miocene onwards. Our aim was to find out whether Arini diversified in a classical adaptive radiation after their colonization of South America, or whether their diversification occurred later and was influenced by more recent environmental change. Location Neotropics. Methods We generated a time-calibrated phylogeny of more than 80% of all Arini species in order to analyse lineage diversification. This chronogram was also used as the basis for the reconstruction of morphological evolution within Arini using a multivariate ratio analysis of three size measurements. Results We found a concentration of size evolution and partitioning of size niches in the early history of Arini consistent with the process of adaptive radia- tion, but there were no signs of an early burst of speciation or a decrease in speci- ation rates through time. Although we detected no overall temporal shifts in diversification rates, we discovered two young, unexpectedly species-rich clades. Main conclusions Arini show signs of an early adaptive radiation, but we found no evidence of the slowdown in speciation rate generally considered a feature of island or lake radiations. Historical processes and environmental change from the Miocene onwards may have kept diversification rates roughly constant ever since the colonization of the Neotropics. Thus, Arini may not yet have reached equilibrium diversity. The lack of diversity-dependent speciation might be a general feature of adaptive radiations on a continental scale, and diversification processes on continents might therefore not be as ecologically limited as in isolated lakes or on oceanic islands.

MODELING REACTIVE GAS UPTAKE, TRANSPORT, AND TRANSFORMATION IN AGGREGATED SOILS

Gas diffusion research in soils covers, to a large extent, the transport behavior of practically insoluble gases. We extend the mathematical description of gas transport to include reactive gaseous components that hydrolyze in water such as SO2 and CO2. The path between the free atmosphere and the microporous niches is modeled by assuming penetration through gas-filled macropores, air-water phase transfer, and diffusion and speciation in the liquid phase. For hydrolyzable gases, the rate of mass transfer into and the total absorption capacity of the soil solution may be high. Both the capacity and the transfer rate are influenced by the soil-solution pH; for high pH, they become extremely high for SO2. The soil absorption of such gases is also influenced by soil structure. Well-aerated, near-neutral soils are a potentially important sink for SO2.