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Journal Cover Evolution Letters
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  This is an Open Access Journal Open Access journal
   ISSN (Online) 2056-3744
   Published by John Wiley and Sons Homepage  [1592 journals]
  • How should we interpret estimates of individual repeatability'

    • Authors: Alastair J. Wilson
      Abstract: Individual repeatability (R), defined as the proportion of observed variance attributable to among-individual differences, is a widely used summary statistic in evolutionarily motivated studies of morphology, life history, physiology and, especially, behaviour. Although statistical methods to estimate R are well known and widely available, there is a growing tendency for researchers to interpret R in ways that are subtly, but importantly, different. Some view R as a property of a dataset and a statistic to be interpreted agnostically with respect to mechanism. Others wish to isolate the contributions of ‘intrinsic’ and/or ‘permanent’ individual differences, and draw a distinction between true (intrinsic) and pseudo-repeatability arising from uncontrolled extrinsic effects. This latter view proposes a narrower, more mechanistic interpretation, than the traditional concept of repeatability, but perhaps one that allows stronger evolutionary inference as a consequence (provided analytical pitfalls are successfully avoided). Neither perspective is incorrect, but if we are to avoid confusion and fruitless debate, there is a need for researchers to recognise this dichotomy, and to ensure clarity in relation to how, and why, a particular estimate of R is appropriate in any case.
      PubDate: 2018-01-31T00:01:08.249987-05:
      DOI: 10.1002/evl3.40
       
  • Ancient genomic variation underlies repeated ecological adaptation in
           young stickleback populations

    • Authors: Thomas C. Nelson; William A. Cresko
      Abstract: Adaptation in the wild often involves standing genetic variation (SGV), which allows rapid responses to selection on ecological timescales. However, we still know little about how the evolutionary histories and genomic distributions of SGV influence local adaptation in natural populations. Here, we address this knowledge gap using the threespine stickleback fish (Gasterosteus aculeatus) as a model. We extend restriction site-associated DNA sequencing (RAD-seq) to produce phased haplotypes approaching 700 base pairs (bp) in length at each of over 50,000 loci across the stickleback genome. Parallel adaptation in two geographically isolated freshwater pond populations consistently involved fixation of haplotypes that are identical-by-descent. In these same genomic regions, sequence divergence between marine and freshwater stickleback, as measured by dXY, reaches tenfold higher than background levels and genomic variation is structured into distinct marine and freshwater haplogroups. By combining this dataset with a de novo genome assembly of a related species, the ninespine stickleback (Pungitius pungitius), we find that this habitat-associated divergent variation averages six million years old, nearly twice the genome-wide average. The genomic variation that is involved in recent and rapid local adaptation in stickleback has therefore been evolving throughout the 15-million-year history since the two species lineages split. This long history of genomic divergence has maintained large genomic regions of ancient ancestry that include multiple chromosomal inversions and extensive linked variation. These discoveries of ancient genetic variation spread broadly across the genome in stickleback demonstrate how selection on ecological timescales is a result of genome evolution over geological timescales, and vice versa.
      PubDate: 2018-01-26T00:01:04.563825-05:
      DOI: 10.1002/evl3.37
       
  • Genomic associations with bill length and disease reveal drift and
           selection across island bird populations

    • Authors: Claire Armstrong; David S. Richardson, Helen Hipperson, Gavin J. Horsburgh, Clemens Küpper, Lawrence Percival-Alwyn, Matt Clark, Terry Burke, Lewis G. Spurgin
      Abstract: Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterized genetic diversity and population structuring that supported previous inferences of a history of recent colonizations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands, and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in nonequilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.
      PubDate: 2018-01-26T00:01:03.080635-05:
      DOI: 10.1002/evl3.38
       
  • Sexual competition and the evolution of condition-dependent ageing

    • Authors: Amy K. Hooper; Jussi Lehtonen, Lisa E. Schwanz, Russell Bonduriansky
      Abstract: Increased individual resources (condition) can be correlated with either increased or decreased longevity. While variation in resource acquisition and allocation can account for some of this variation, the general conditions that select for either pattern remain unclear. Previous models suggest that nonlinearity of payoffs from investment in reproduction (e.g., male secondary sexual traits) can select for high-condition individuals that sacrifice longevity to increase reproductive opportunity. However, it remains unclear what mating systems or patterns of sexual competition might select for such life-history strategies. We used a model of condition-dependent investment to explore how expected payoffs from increased expression of secondary sexual traits affect optimal investment in lifespan. We find that nonlinearity of these payoffs results in a negative relationship between condition and lifespan under two general conditions: first, when there are accelerating marginal benefits from increasing investment; second, when individuals that invest minimally in secondary sexual trait expression can still achieve matings. In the second scenario, the negative relationship occurs due to selection on low-condition individuals to extend lifespan at the cost of secondary sexual trait expression. Our findings clarify the potential role of sexual selection in shaping patterns of condition-dependent ageing, and highlight the importance of considering the strategies of both low- and high-condition individuals when investigating patterns of condition-dependent ageing.
      PubDate: 2018-01-13T00:01:02.263306-05:
      DOI: 10.1002/evl3.36
       
  • Parallel evolution of gene expression between trophic specialists despite
           divergent genotypes and morphologies

    • Abstract: Parallel evolution of gene expression commonly underlies convergent niche specialization, but parallel changes in expression could also underlie divergent specialization. We investigated divergence in gene expression and whole‐genome genetic variation across three sympatric Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist and two derived specialists adapted to novel niches: a scale‐eating and a snail‐eating pupfish. We sampled total mRNA from all three species at two early developmental stages and compared gene expression with whole‐genome genetic differentiation among all three species in 42 resequenced genomes. Eighty percent of genes that were differentially expressed between snail‐eaters and generalists were up or down regulated in the same direction between scale‐eaters and generalists; however, there were no fixed variants shared between species underlying these parallel changes in expression. Genes showing parallel evolution of expression were enriched for effects on metabolic processes, whereas genes showing divergent expression were enriched for effects on cranial skeleton development and pigment biosynthesis, reflecting the most divergent phenotypes observed between specialist species. Our findings reveal that even divergent niche specialists may exhibit convergent adaptation to higher trophic levels through shared genetic pathways. This counterintuitive result suggests that parallel evolution in gene expression can accompany divergent ecological speciation during adaptive radiation.
       
  • Issue information

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  • Male‐biased gene expression resolves sexual conflict through the
           evolution of sex‐specific genetic architecture

    • Abstract: Many genes are subject to contradictory selection pressures in males and females, and balancing selection resulting from sexual conflict has the potential to substantially increase standing genetic diversity in populations and thereby act as an important force in adaptation. However, the underlying causes of sexual conflict, and the potential for resolution, remains hotly debated. Using transcriptome‐resequencing data from male and female guppies, we use a novel approach, combining patterns of genetic diversity and intersexual divergence in allele frequency, to distinguish the different scenarios that give rise to sexual conflict, and how this conflict may be resolved through regulatory evolution. We show that reproductive fitness is the main source of sexual conflict, and this is resolved via the evolution of male‐biased expression. Furthermore, resolution of sexual conflict produces significant differences in genetic architecture between males and females, which in turn lead to specific alleles influencing sex‐specific viability. Together, our findings suggest an important role for sexual conflict in shaping broad patterns of genome diversity, and show that regulatory evolution is a rapid and efficient route to the resolution of conflict.
       
 
 
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