Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes

During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.

Linking Plant Functional Traits to Demography in a Fragmented Landscape

Habitat loss in highly deforested landscapes such as the Brazilian Atlantic Forest has been severely affecting the diversity and survival of palm species. As some species are more sensitive than others, trait responses to the environment, as well as environmental effects on fecundity, growth, and mortality rates, may affect species demography. Considering this context, we studied functional and demographic responses of three palm species (Astrocaryum aculeatissimum, Euterpe edulis, and Geonoma schottiana) to habitat loss in the Atlantic Forest in southeastern Brazil by measuring morpho-physiological traits related to plant growth and light acquisition for photosynthesis. We also tested the response of population fitness to fragment size. Plant survival and growth was subsequently monitored in 2006 and 2007, and population dynamics were summarized in pool matrices for large and small forest fragments in the monitoring periods comprehending one full year between 2005–2006 and 2006–2007. The asymptotic growth rate of populations (defined here as population fitness, λ) in five forest fragments was then calculated. Diameter of individuals of the demography plots (from year 2005 to 2007) was used to calculate the relative diameter growth rate. Later, in 2015, we measured a set of morpho-physiological functional traits in palms in the same plots used in the demographic studies. While A. aculeatissimum populations were stable in both monitoring periods in small and large fragments, E. edulis populations were predicted to decline due to intense predation by monkeys in the large fragment, but were stable in the smaller fragments, and G. schottiana populations were stable in the large fragments in both monitoring periods, but populations in the smaller fragments were predicted to decline in the second period, i.e., with lower fitness in these fragments. In addition, the functional traits analyzed showed that G. schottiana is a forest interior species associated with the shade/understory environment response. E. edulis was also affected by the size of the fragment, but due to a disruptive interaction with a predator and showed intermediate functional traits values. On the other hand, A. aculeatissimum thrived in areas with higher and lower incidence of light and was not demographically affected by forest remnant size. This suggests that E. edulis and A. aculeatissimum are habitat generalists. We concluded that differences in the ecophysiological performance of palms due to distinct morpho-physiological functional traits related to leaf economic spectrum, such as LDMC or specific leaf area (SLA) and to photosynthetic responses to light environment as electron transport rate (ETR) and saturation irradiance (Ik) were linked to the demographic variation observed in forest remnants of different size.

The stagnation paradox: the ever-improving but (more or less) stationary population fitness

Fisher's fundamental theorem states that natural selection improves mean fitness. Fitness, in turn, is often equated with population growth. This leads to an absurd prediction that life evolves to ever-faster growth rates, yet no one seriously claims generally slower population growth rates in the Triassic compared with the present day. I review here, using non-technical language, how fitness can improve yet stay constant (stagnation paradox), and why an unambiguous measure of population fitness does not exist. Subfields use different terminology for aspects of the paradox, referring to stasis, cryptic evolution or the difficulty of choosing an appropriate fitness measure; known resolutions likewise use diverse terms from environmental feedback to density dependence and ‘evolutionary environmental deterioration’. The paradox vanishes when these concepts are understood, and adaptation can lead to declining reproductive output of a population when individuals can improve their fitness by exploiting conspecifics. This is particularly readily observable when males participate in a zero-sum game over paternity and population output depends more strongly on female than male fitness. Even so, the jury is still out regarding the effect of sexual conflict on population fitness. Finally, life-history theory and genetic studies of microevolutionary change could pay more attention to each other.

Acceleration of Evolutionary Processes by Learning and Extended Fisher's Fundamental Theorem

Natural selection is general and powerful concept not only to explain evolutionary processes of biological organisms but also to design engineering systems such as genetic algorithms and particle filters.There is a surge of interest, both from biology and engineering, in considering natural selection of intellectual agents that can learn individually. Learning by individual agents of better behaviors for survival may accelerate the evolutionary processes by natural selection. We have accumulating pieces of evidence that organisms can transmit its information to the next generation via epigenetic states or memes. Also, such idea is important for engineering applications to improve the genetic algorithms and the particle filter. To accelerate the evolutionary process, an agent should change their strategy so that the population fitness increases the most. Equivalently, an agent should update the strategy towards a gradient (derivative) of the population fitness with respect to the strategy. However, it has not yet been clarified whether and how an agent can estimate the gradient and accelerate the evolutionary process. We also lack methodology to quantify the acceleration to understand and predict the impact of learning. In this paper, we address these problems. We show that an learning agent can accelerate the evolutionary process by proposing ancestral learning, which uses the information transmitted from the ancestor (ancestral information) via epigenetic states or memes. Numerical experiments show that ancestral learning actually accelerates the evolutionary process. We next show that the ancestral information is sufficient to estimate the gradient. In particular, learning can accelerate the evolutionary process without communications between agents. Finally, to quantify the acceleration, we extend the Fisher's fundamental theorem (FF-thm) for natural selection to ancestral learning. The conventional FF-thm relates the speed of evolution by natural selection to the variety of the individual fitness in the population. Our extended FF-thm relates the acceleration of the evolutionary process to the variety of individual fitness of the agent. By the theorem, we can quantitatively understand when and why learning is beneficial.

Hurricane-induced demographic changes in a non-human primate population

Major disturbance events can have large impacts on the demography and dynamics of animal populations. Hurricanes are one example of an extreme climatic event, predicted to increase in frequency due to climate change, and thus expected to be a considerable threat to population viability. However, little is understood about the underlying demographic mechanisms shaping population response following these extreme disturbances. Here, we analyse 45 years of the most comprehensive free-ranging non-human primate demographic dataset to determine the effects of major hurricanes on the variability and maintenance of long-term population fitness. For this, we use individual-level data to build matrix population models and perform perturbation analyses. Despite reductions in population growth rate mediated through reduced fertility, our study reveals a demographic buffering during hurricane years. As long as survival does not decrease, our study shows that hurricanes do not result in detrimental effects at the population level, demonstrating the unbalanced contribution of survival and fertility to population fitness in long-lived animal populations.