Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

Sarah H Carl, Steven Russell
doi: http://dx.doi.org/10.1101/012872

Background: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known. Results: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species. Conclusion: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.

Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

Noah Ribeck, Richard E. Lenski
doi: http://dx.doi.org/10.1101/012807

Coexistence of multiple populations by frequency-dependent selection is common in nature, and it often arises even in well-mixed experiments with microbes. If ecology is to be incorporated into models of population genetics, then it is important to represent accurately the functional form of frequency-dependent interactions. However, measuring this functional form is problematic for traditional fitness assays, which assume a constant fitness difference between competitors over the course of an assay. Here, we present a theoretical framework for measuring the functional form of frequency-dependent fitness by accounting for changes in abundance and relative fitness during a competition assay. Using two examples of ecological coexistence that arose in a long-term evolution experiment with Escherichia coli, we illustrate accurate quantification of the functional form of frequency-dependent relative fitness. Using a Monod-type model of growth dynamics, we show that two ecotypes in a typical cross-feeding interaction—such as when one bacterial population uses a byproduct generated by another—yields relative fitness that is linear with relative frequency.

Maternal microRNAs in Drosophila eggs: selection against target sites in maternal protein-coding transcripts

Maternal microRNAs in Drosophila eggs: selection against target sites in maternal protein-coding transcripts

Antonio Marco
doi: http://dx.doi.org/10.1101/012757

In animals, before the zygotic genome is expressed, the egg already contains gene products deposited by the mother. These maternal products are crucial during the initial steps of development. In Drosophila melanogaster a large number of maternal products are found in the oocyte, some of which are indispensable. Many of these products are RNA molecules, such as gene transcripts and ribosomal RNAs. Recently, microRNAs – small RNA gene regulators – have been detected early during development and are important in these initial steps. The presence of some microRNAs in unfertilized eggs has been reported, but whether they have a functional impact in the egg or early embryo has not being explored. To characterize a maternal microRNA set, I have extracted and sequenced small RNAs from Drosophila unfertilized eggs. The unfertilized egg is rich in small RNAs, particularly in ribosomal RNAs, and contains multiple microRNA products. I further validated two of these microRNAs by qPCR and also showed that these are not present in eggs from mothers without Dicer-1 activity. Maternal microRNAs are often encoded within the intron of maternal genes, suggesting that many maternal microRNAs are the product of transcriptional hitch-hiking. Comparative genomics and population data suggest that maternally deposited transcripts tend to avoid target sites for maternally deposited microRNAs. A potential role of the maternal microRNA mir-9c in maternal-to-zygotic transition is also discussed. In conclusion, maternal microRNAs in Drosophila have a functional impact in maternal protein-coding transcripts.

Fitness costs in spatially structured environments

Fitness costs in spatially structured environments

Florence Debarre
doi: http://dx.doi.org/10.1101/012740

The clustering of individuals that results from limited dispersal is a double-edged sword: while it allows for local interactions to be mostly among related individuals, it also results in increased local competition. Here I show that, because they mitigate local competition, fitness costs such as reduced fecundity or reduced survival are less costly in spatially structured environments than in non spatial settings. I first present a simple demographic example to illustrate how spatial structure weakens selection against fitness costs. Then, I illustrate the importance of disentangling the evolution of a trait from the evolution of potential associated costs, using an example taken from a recent study investigating the effect of spatial structure on the evolution of host defence. In this example indeed, the differences between spatial and non-spatial selection gradients are entirely due to differences in the fitness costs, thereby undermining interpretations of the results made in terms of the trait only. This illustrates the need to consider fitness costs as proper traits in both theoretical and empirical studies.

Origin and cross-century dynamics of an avian hybrid zone

Origin and cross-century dynamics of an avian hybrid zone

Andrea Morales-Rozo, Elkin A. Tenorio, Matthew D. Carling, Carlos Daniel Cadena
doi: http://dx.doi.org/10.1101/012856

Background: Characterizations of the dynamics of hybrid zones in space and time can give insights about traits and processes important in population divergence and speciation. We characterized a hybrid zone between tanagers in the genus Ramphocelus (Aves, Thraupidae) located in southwestern Colombia. We tested whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using spatial analyses of molecular, morphological, and coloration data in combination with paleodistribution modeling. Results: Models of potential historical distributions based on climatic data and genetic signatures of demographic expansion suggested that the hybrid zone originated following secondary contact between populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Estimates of phenotypic cline parameters obtained using specimens collected over nearly a century revealed that, in recent decades, the zone has moved to the east and to higher elevations, and has become narrower. Genetic variation was not clearly structured along the hybrid zone, but comparisons between historical and contemporary specimens suggested that temporal changes in its genetic makeup may also have occurred. Conclusions: Our data suggest that the hybrid zone resulted from secondary contact between populations. The observed changes in the hybrid zone may be a result of sexual selection, asymmetric gene flow, or environmental change.

Reproductive workers show queen-like gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris

Reproductive workers show queen-like gene expression in an intermediately eusocial insect, the buff-tailed bumble bee Bombus terrestris.

Mark Christian Harrison, Robert L Hammond, Eamonn B Mallon
doi: http://dx.doi.org/10.1101/012500

Bumble bees represent a taxon with an intermediate level of eusociality within Hymenoptera. The clear division of reproduction between a single founding queen and the largely sterile workers is characteristic for highly eusocial species, whereas the morphological similarity between the bumble bee queen and the workers is typical for more primitively eusocial hymenopterans. Also, unlike other highly eusocial hymenopterans, division of labour among worker sub-castes is plastic and not predetermined by morphology or age. We conducted a differential expression analysis based on RNA-seq data from 11 combinations of developmental stage and caste to investigate how a single genome can produce the distinct castes of queens, workers and males in the buff-tailed bumble bee Bombus terrestris. Based on expression patterns, we found males to be the most distinct of all adult castes (2,411 transcripts differentially expressed compared to non-reproductive workers). However, only relatively few transcripts were differentially expressed between males and workers during development (larvae: 71, pupae: 162). This indicates the need for more distinct expression patterns to control behaviour and physiology in adults compared to those required to create different morphologies. Among the female castes, the expression of over ten times more transcripts differed signifcantly between reproductive workers and their non-reproductive sisters than when comparing reproductive workers to the mother queen. This suggests a strong shift towards a more queen-like behaviour and physiology when a worker becomes fertile. This is in contrast to findings for higher eusocial species, in which reproductive workers are more similar to non-reproductive workers than the queen.

An experimental test of the relationship between melanism and desiccation survival in insects

An experimental test of the relationship between melanism and desiccation survival in insects

Subhash Rajpurohit, Lisa Marie Peterson, Andrew Orr, Anthony J. Marlon, Allen G Gibbs
doi: http://dx.doi.org/10.1101/012369

We used experimental evolution to test the ?melanism-desiccation? hypothesis, which proposes that dark cuticle in several Drosophila species is an adaptation for increased desiccation tolerance. We selected for dark and light body pigmentation in replicated populations of D. melanogaster and assayed traits related to water balance. We also scored pigmentation and desiccation tolerance in populations selected for desiccation survival. Populations in both selection regimes showed large differences in the traits directly under selection. However, after over 40 generations of pigmentation selection, dark-selected populations were not more desiccation-tolerant than light-selected and control populations, nor did we find significant changes in carbohydrate amounts that could affect desiccation resistance. Body pigmentation of desiccation-selected populations did not differ from control populations after over 140 generations of selection. Our results do not support an important role for melanization in Drosophila water balance.