Adaptive divergence and the evolution of hybrid phenotypes in threespine stickleback

The fitness of hybrids is a critical determinant of gene flow between hybridizing populations. If hybrid phenotypes change predictably as parental populations become increasingly divergent, this could provide insight into general mechanisms linking ecological divergence with reproductive isolation. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to examine how phenotypic divergence between populations drives the evolution of dominance, phenotypic variation, and trait ‘mismatch’ in hybrids. We generated F1 and F2 hybrids between 12 freshwater populations—which ranged from highly planktivorous to highly benthic-feeding—and an anadromous population that is highly planktivorous and resembles the ancestral state of derived freshwater populations. We measured 16 phenotypic traits in hybrids and pure parental individuals raised under common conditions. We found that dominance varied markedly among traits. By contrast, dominance for a given trait was typically consistent among populations except for two traits where dominance was predicted by the phenotype of the freshwater parent. We find that multivariate phenotypic variation is greater in hybrids between more divergent parents. Finally, we demonstrate that the extent to which parental traits are ‘mismatched’ in both F1 and F2 hybrids increases with the phenotypic distance between the parent populations. Critically, this relationship was clearer in F1 hybrids than in F2s—largely due to traits having different dominance coefficients and F1s having relatively little phenotypic variation. Our results demonstrate that some aspects of hybrid phenotypes evolve predictably as parental populations diverge. We also find evidence for a possible general mechanistic link between ecological divergence and reproductive isolation—that more divergent parent populations tend to produce hybrids with novel and potentially deleterious multivariate phenotypes.

Temporal encoding of bacterial identity and traits in growth dynamics

In biology, it is often critical to determine the identity of an organism and phenotypic traits of interest. Whole-genome sequencing can be useful for this but has limited power for trait prediction. However, we can take advantage of the inherent information content of phenotypes to bypass these limitations. We demonstrate, in clinical and environmental bacterial isolates, that growth dynamics in standardized conditions can differentiate between genotypes, even among strains from the same species. We find that for pairs of isolates, there is little correlation between genetic distance, according to phylogenetic analysis, and phenotypic distance, as determined by growth dynamics. This absence of correlation underscores the challenge in using genomics to infer phenotypes and vice versa. Bypassing this complexity, we show that growth dynamics alone can robustly predict antibiotic responses. These findings are a foundation for a method to identify traits not easily traced to a genetic mechanism.

Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets

When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favoured over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala . We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and whether the likelihood of QTL sharing is related to QTL effect size. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more frequently than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.

On the Runtime Analysis of the Clearing Diversity-Preserving Mechanism

Clearing is a niching method inspired by the principle of assigning the available resources among a niche to a single individual. The clearing procedure supplies these resources only to the best individual of each niche: the winner. So far, its analysis has been focused on experimental approaches that have shown that clearing is a powerful diversity-preserving mechanism. Using rigorous runtime analysis to explain how and why it is a powerful method, we prove that a mutation-based evolutionary algorithm with a large enough population size, and a phenotypic distance function always succeeds in optimising all functions of unitation for small niches in polynomial time, while a genotypic distance function requires exponential time. Finally, we prove that with phenotypic and genotypic distances, clearing is able to find both optima for [Formula: see text] and several general classes of bimodal functions in polynomial expected time. We use empirical analysis to highlight some of the characteristics that makes it a useful mechanism and to support the theoretical results.

Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets

ABSTRACTWhen the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favored over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and the likelihood that sharing QTL is related to phenotypic effect sizes. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.

Friendship across species borders: factors that facilitate and constrain heterospecific sociality

Our understanding of animal sociality is based almost entirely on single-species sociality. Heterospecific sociality, although documented in numerous taxa and contexts, remains at the margins of sociality research and is rarely investigated in conjunction with single-species sociality. This could be because heterospecific and single-species sociality are thought to be based on fundamentally different mechanisms. However, our literature survey shows that heterospecific sociality based on mechanisms similar to single-species sociality is reported from many taxa, contexts and for various benefits. Therefore, we propose a conceptual framework to understand conspecific versus heterospecific social partner choice. Previous attempts, which are all in the context of social information, model partner choice as a trade-off between information benefit and competition cost, along a single phenotypic distance axis. Our framework of partner choice considers both direct grouping benefits and information benefits, allows heterospecific and conspecific partners to differ in degree and qualitatively, and uses a multi-dimensional trait space analysis of costs (competition and activity matching) and benefits (relevance of partner and quality of partner). We conclude that social partner choice is best-viewed as a continuum: some social benefits are obtainable only from conspecifics, some only from dissimilar heterospecifics, while many are potentially obtainable from conspecifics and heterospecifics. This article is part of the theme issue ‘Collective movement ecology'.

Phenotypic Dissimilarities among Inbreds of Maize (Zea Mays L.)

For development of single cross hybrids in maize, developed inbreds must be evaluated for the determination of highly heterotic inbred combination (HIC). One of the best methodologies for determination of heterotic inbred combination can be multivariate analysis (MVA) or scales of phenotypic distance or dissimilarities or cluster diagram. For it, inbred must be observed for useful trait measurements. Accordingly, an experimental evaluation was conducted including promising 55 inbred lines of winter maize planting on Sep 3, 2015 at National Maize Research Program Rampur, Chitwan Nepal (NMRP/NARC). The distant inbred lines were determined through MVA. Single plot research technique was done where each inbred line was provided with 2 rows of 20 plants each. Data were taken for fifteen traits. By the use of MINITAB software, the data was analysed. Graphics of principle component analysis (PCA) cluster diagram (CD or dendogram) were constructed and phenotypic dissimilarities are examined.The distant inbreds RML-8, RML-88, RML-13, RML-103, RML-89, RML-102, RML-11, RML-17, RML-83,RML-98,RML-85,RML-86,RML-94 and RML-28 could be crossed with RML-75,RML-6,RML-68,RML-36 and RML-32 which could be used as tester inbred for heterotic hybrid combination. Similarly, RML-98, RML-85, RML-86, RML-94 and RML-28 could be crossed with RML-24, RML-96 and RML-99. Though distant inbred, RML-104 had less ASI but it wasn’t feasible to use for crossing due to higher anthesis tasseling interval.Int J Appl Sci Biotechnol, Vol 4(3): 359-364

Detecting Patterns of Trait Evolution

This chapter examines a variety of methods for detecting the patterns of evolution of a certain trait. It first considers common metrics for evaluating phylogenetic signal and compares fit of alternative evolutionary models. When trait data deviates significantly from assumptions of Brownian motion (BM), the phylogenetic distances separating taxa on a time-calibrated tree might not accurately capture phenotypic distance between species. If we are able to identify the correct model of trait evolution, we can transform the branch lengths on the phylogenetic tree to match. Nevertheless, we might still favor using the untransformed tree because complex evolutionary models might not generalize across traits. The chapter also reviews alternative models of trait evolution, including a model of constrained evolution, multirate and multioptima models, speciational models, and white noise model. Finally, it looks at some of the common models for reconstructing ancestral states for discrete and continuous data.

Antagonistic coevolution between quantitative and Mendelian traits

Coevolution is relentlessly creating and maintaining biodiversity and therefore has been a central topic in evolutionary biology. Previous theoretical studies have mostly considered coevolution between genetically symmetric traits (i.e. coevolution between two continuous quantitative traits or two discrete Mendelian traits). However, recent empirical evidence indicates that coevolution can occur between genetically asymmetric traits (e.g. between quantitative and Mendelian traits). We examine consequences of antagonistic coevolution mediated by a quantitative predator trait and a Mendelian prey trait, such that predation is more intense with decreased phenotypic distance between their traits (phenotype matching). This antagonistic coevolution produces a complex pattern of bifurcations with bistability (initial state dependence) in a two-dimensional model for trait coevolution. Furthermore, with eco-evolutionary dynamics (so that the trait evolution affects predator–prey population dynamics), we find that coevolution can cause rich dynamics including anti-phase cycles, in-phase cycles, chaotic dynamics and deterministic predator extinction. Predator extinction is more likely to occur when the prey trait exhibits complete dominance rather than semidominance and when the predator trait evolves very rapidly. Our study illustrates how recognizing the genetic architectures of interacting ecological traits can be essential for understanding the population and evolutionary dynamics of coevolving species.