The concept of homoiology and its potential application in palaeontological phylogenetics

The neglected concept of homoiology is discussed in the context of palaeontological phylogenetic methods. Homoiology is the case of homoplasy where a parallel or convergent phenotypic development is actually due to shared ancestry, whether a common inherited genetic mechanism or simply a shared initial phenotype. A number of parallelisms/convergences in vertebrate and linguistic evolution are discussed to illustrate the concept of homoiology. It is proposed that parallelisms/convergences, although probably not useful in initial tree inference from morphological data, must not be simply written off as phylogenetically uninformative, but can actually be potentially used to provide additional support values for clades and to help to choose between equally parsimonious or likely trees. An R function is provided to calculate two measures for a given tree and matrix: (a) the potential support for clades based on potential homoiologies; and (b) the fit of the tree to all states given the concept of homoiology. The relationship between homoiology and constraints and to underlying mechanisms is also discussed.

The Divisive Gene

Despite its grip on the scientific culture of affluent societies, the reign of the gene as the supposed "secret of life" is coming to an end. The more we learn about natural systems the clearer it becomes that genes are only one class of factors influencing phenotypic development and evolution.Click here to purchase a PDF version of this article at the Monthly Review website.

Habitat- and season-specific temperatures affect phenotypic development of hatchling lizards

Embryonic environments influence phenotypic development, but relatively few experiments have explored the effects of natural environmental variation. We incubated eggs of the lizard Anolis sagrei under conditions that mimicked natural spatial and temporal thermal variation to determine their effects on offspring morphology and performance. Incubation temperatures mimicked two microhabitats (open, shade) at two different times of the incubation season (April, July). Egg survival, incubation duration and offspring size were influenced by interactions between habitat- and season-specific nest temperatures, and locomotor performance was influenced primarily by temporal factors. These findings highlight the importance of spatial and temporal environmental variation in generating variation in fitness-related phenotypes.

The evolution of sensitive periods in a model of incremental development

Sensitive periods, in which experience shapes phenotypic development to a larger extent than other periods, are widespread in nature. Despite a recent focus on neural–physiological explanation, few formal models have examined the evolutionary selection pressures that result in developmental mechanisms that produce sensitive periods. Here, we present such a model. We model development as a specialization process during which individuals incrementally adapt to local environmental conditions, while receiving a constant stream of cost-free, imperfect cues to the environmental state. We compute optimal developmental programmes across a range of ecological conditions and use these programmes to simulate developmental trajectories and obtain distributions of mature phenotypes. We highlight four main results. First, matching the empirical record, sensitive periods often result from experience or from a combination of age and experience, but rarely from age alone. Second, individual differences in sensitive periods emerge as a result of stochasticity in cues: individuals who obtain more consistent cue sets lose their plasticity at faster rates. Third, in some cases, experience shapes phenotypes only at a later life stage (lagged effects). Fourth, individuals might perseverate along developmental trajectories despite accumulating evidence suggesting the alternate trajectory is more likely to match the ecology.

Hormones and phenotypic plasticity: Implications for the evolution of integrated adaptive phenotypes

It is generally accepted that taxa exhibit genetic variation in phenotypic plasticity, but many questions remain unanswered about how divergent plastic responses evolve under dissimilar ecological conditions. Hormones are signaling molecules that act as proximate mediators of phenotype expression by regulating a variety of cellular, physiological, and behavioral responses. Hormones not only change cellular and physiological states but also influence gene expression directly or indirectly, thereby linking environmental conditions to phenotypic development. Studying how hormonal pathways respond to environmental variation and how those responses differ between individuals, populations, and species can expand our understanding of the evolution of phenotypic plasticity. Here, we explore the ways that the study of hormone signaling is providing new insights into the underlying proximate bases for individual, population or species variation in plasticity. Using several studies as exemplars, we examine how a ‘norm of reaction’ approach can be used in investigations of hormone-mediated plasticity to inform the following: 1) how environmental cues affect the component hormones, receptors and enzymes that comprise any endocrine signaling pathway, 2) how genetic and epigenetic variation in endocrine-associated genes can generate variation in plasticity among these diverse components, and 3) how phenotypes mediated by the same hormone can be coupled and decoupled via independent plastic responses of signaling components across target tissues. Future studies that apply approaches such as reaction norms and network modeling to questions concerning how hormones link environmental stimuli to ecologically-relevant phenotypic responses should help unravel how phenotypic plasticity evolves.