Phylogeny and taxonomy of the genus Ilyodon Eigenmann, 1907 (Teleostei: Goodeidae), based on mitochondrial and nuclear DNA sequences

Taxonomy of the live‐bearing fish of the genus Ilyodon Eigenmann, 1907 (Goodeidae), in Mexico, is controversial, with morphology and mitochondrial genetic analyses in disagreement about the number of valid species. The present study accumulated a comprehensive DNA sequences dataset of 98 individuals of all Ilyodon species and mitochondrial and nuclear loci to reconstruct the evolutionary history of the genus. Phylogenetic inference produced five clades, one with two sub‐clades, and one clade including three recognized species. Genetic distances in mitochondrial genes (cytb: 0.5%–2.1%; coxI: 0.5%–1.1% and d‐loop: 2.3%–10.2%) were relatively high among main clades, while, as expected, nuclear genes showed low variation (0.0%–0.2%), with geographic concordance and few shared haplotypes among river basins. High genetic structure was observed among clades and within basins. Our genetic analyses, applying the priority principle, suggest the recognition only of Ilyodon whitei and Ilyodon furcidens, with I. cortesae relegated to an invalid species, the populations of which belong to I. whitei.     

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Background  

Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.     

Consequences of concurrent Ascaridia galli and Escherichia coli infections in chickens

   

Three experiments were carried out to examine the consequences of concurrent infections with Ascaridia galli and Escherichia coli in chickens raised for table egg production. Characteristic pathological lesions including airsacculitis, peritonitis and/or polyserositis were seen in all groups infected with E. coli. Furthermore, a trend for increased mortality rates was observed in groups infected with both organisms which, however, could not be confirmed statistically. The mean worm burden was significantly lower in combined infection groups compared to groups infected only with A. galli. It was also shown that combined infections of E. coli and A. galli had an added significant negative impact on weight gain.     

Phylogenetic diversity of stress signalling pathways in fungi

Background  

Microbes must sense environmental stresses, transduce these signals and mount protective responses to survive in hostile environments. In this study we have tested the hypothesis that fungal stress signalling pathways have evolved rapidly in a niche-specific fashion that is independent of phylogeny. To test this hypothesis we have compared the conservation of stress signalling molecules in diverse fungal species with their stress resistance. These fungi, which include ascomycetes, basidiomycetes and microsporidia, occupy highly divergent niches from saline environments to plant or mammalian hosts.     

Proliferative activity in the cerebellar external granular layer evaluated by bromodeoxyuridine labeling

We have optimised an indirect immunoperoxidase technique demonstrating bromodeoxyuridine (BrdU) incorporation into dividing cells for cerebellar tissue sections of four-day-old rats injected with this marker. This permits confident identification of granule-cell precursors engaged in DNA synthesis in the external granular layer of the developing cerebellum. Preservation of BrdU immunoreactivity is attained using methanol/acetic acid fixation and different pretreatments before immunostaining, while unlabeled nuclei can be recognized clearly after Feulgen or hematoxylin counterstaining. We established conditions to ensure satisfactory BrdU uptake without affecting cell-cycle progression during the postlabeling time period. The dose of BrdU employed provides saturation S-phase labeling from at least 1 h after BrdU delivery. Various kinetic parameters and phase durations have been determined in experiments involving a single injection or cumulative labeling sequences, and the cycle time was calculated based on two models of generative behavior: steady-state and exponential growth. The working hypothesis of steadystate kinetics can be adopted successfully if the existence of neuroblasts with different proliferation rates is taken into account.     

Interactions Among Flower-Size QTL of Mimulus guttatus Are Abundant but Highly Variable in Nature

The frequency and character of interactions among genes influencing complex traits remain unknown. Our ignorance is most acute for segregating variation within natural populations, the epistasis most relevant for quantitative trait evolution. Here, we report a comprehensive survey of interactions among a defined set of flower-size QTL: loci polymorphic within a single natural population of yellow monkeyflower (Mimulus guttatus). We find that epistasis is typical. Observed phenotypes routinely differ from those predicted on the basis of direct allelic affects in the isogenic background, although the direction of deviations is highly variable. Across QTL pairs, there are significantly positive and negative interactions for every trait. Across traits, specific locus pairs routinely exhibit both positive and negative interactions. There was a tendency for negative epistasis to accompany positive direct effects and vice versa for the trait of corolla width, which may be due, at least in part, to the fact that QTL were identified from their direct effects on this trait.EPISTASIS contributes significantly to intrapopulation variation in floral morphology, development time, and male fitness components of Mimulus guttatus (Kelly 2005). The aggregate effect of interactions among QTL substantially alters the resemblance of relatives and phenotypic response to inbreeding. However, previous experiments did not identify the specific character of interactions between QTL. For example, it is not clear whether interactions change the rank order of QTL genotypes. If the direction of allelic effect changes with genetic background, so-called “sign epistasis” (Weinreich et al. 2005), the same selection pressure may favor different alleles in different genomic contexts, e.g., different subpopulations of a species (De Brito et al. 2005). When the trait is fitness, these kinds of interactions naturally generate peaks and valleys in genotypic fitness landscapes (Wright 1932; Burch and Chao 2000).Sign epistasis can involve a reversal of allelic effect at one or both loci of an interacting pair. Poelwijk et al. (2007) define the double reversal as “reciprocal sign epistasis” and contrast sign epistasis generally to “magnitude epistasis” where the magnitude but not the direction of allelic effects changes with genetic background. Magnitude epistasis includes synergistic interactions (alleles have greater effect in combination than individually) and less-than-additive or diminishing returns interactions (alleles have lesser effect in combination) (see Crow and Kimura 1970). Alternatively, one can classify interactions as positive or negative (Phillips et al. 2000)—positive if the observed phenotype of an allelic combination exceeds that predicted from direct effects at each locus, and negative if the phenotype of the combination is less than the additive prediction. Unfortunately, there is no simple logical mapping from the magnitude/sign epistasis classification to the positive/negative classification, nor to epistasis in the classical sense (Bateson 1909), wherein one locus masks the effect of another. The taxonomy of epistasis is further complicated by dominance (Routman and Cheverud 1997), higher-order interactions (Templeton 2000), and environmental dependencies (Brock et al. 2010).Molecular genetic studies provide clear examples of sign epistasis. Here, the interacting polymorphisms are often within the same gene. For example, the stability of RNA secondary structures requires matching of nucleotides at different positions. Whether a particular nucleotide change increases or reduces stability depends entirely on the identity of the nucleotide at its paired site (Chen et al. 1999). With “compensatory evolution” (Moore et al. 2000), a mutation that is neutral or detrimental in the original genetic background becomes advantageous by compensating for some other mutation that has recently fixed or at least become prevalent within the population. Mutations conferring antibiotic resistance often have deleterious side effects that reduce bacterial fitness in the absence of the drug. These side effects are attenuated by secondary mutations that are often detrimental in the original genotype (Levin et al. 1997; Schrag et al. 1997).Despite the progress in research on microbes (Weinreich et al. 2005; Elena et al. 2010), we currently know little about the prevalence or nature of epistasis for quantitative traits (Carlborg and Haley 2004) and particularly its impact on standing (segregating) variation within natural populations. Eshed and Zamir (1996) found extensive epistasis among QTL in Lycopersicon (tomato), but interactions primarily influenced the magnitude of single-locus effects and not their direction. In contrast, Kroymann and Mitchell-Olds (2005) documented a case of QTL effect reversal in Arabidopsis thaliana. The high allele for biomass accumulation in the Ler-0 accession becomes the low allele when introgressed into another line (the Col-0 accession). Patterns of gene sequence variation suggest that this polymorphism is maintained by balancing selection. In Avena barbata, two loci with negligible average effects exhibit sign epistasis for fitness in a cross between mesic and xeric genotypes (Latta et al. 2010).Even with these examples, it is difficult to evaluate the quantitative frequency of epistasis or regularities in its nature from the current literature. In part, this is because discovery of QTL×QTL interactions is typically idiosyncratic. In a segregating mapping population such as F₂’s or recombinant inbred lines, there is limited replication of particular multi-locus genotypes. As a consequence, it is difficult to accurately estimate the mean phenotype of any particular multi-locus genotype. Also, there are an enormous number of pairwise tests in a full simultaneous scan, which leads to very stringent significance levels (see box 2 of Carlborg and Haley 2004). Thus, while genomic scans have successfully identified interactions (e.g., Li et al. 1997; Cheverud 2000; Montooth et al. 2003), it is hard to know if the many nonsignificant interactions are due to absence of effect or absence of power.Our intention in this study was to conduct a comprehensive survey of interactions among a specific set of monkeyflower QTL. These loci are polymorphic within a single contiguous natural population. We first mapped flower-size QTL within nearly isogenic lines (NILs). Measurements on the NILs isolate the “direct effect” of each QTL, i.e., how the polymorphism affects phenotype in a single uniform genetic background. We then intercrossed the various single-QTL NILs in all combinations to generate the four double homozygotes for each pair of QTL: aabb, AAbb, aaBB, and AABB. This design allows high replication of each multi-locus genotype and hence reasonable power to detect even moderate epistasis (e.g., Moyle and Nakazato 2009). Applying this methodology, we find that epistasis is more the rule than the exception, although the form of interaction is highly variable among QTL pairs.