Annual rhythms that underlie phenology: biological time-keeping meets environmental change

Seasonal recurrence of biological processes (phenology) and its relationship to environmental change is recognized as being of key scientific and public concern, but its current study largely overlooks the extent to which phenology is based on biological time-keeping mechanisms. We highlight the relevance of physiological and neurobiological regulation for organisms’ responsiveness to environmental conditions. Focusing on avian and mammalian examples, we describe circannual rhythmicity of reproduction, migration and hibernation, and address responses of animals to photic and thermal conditions. Climate change and urbanization are used as urgent examples of anthropogenic influences that put biological timing systems under pressure. We furthermore propose that consideration of Homo sapiens as principally a ‘seasonal animal’ can inspire new perspectives for understanding medical and psychological problems.     

Latitudinal clines: an evolutionary view on biological rhythms

Properties of the circadian and annual timing systems are expected to vary systematically with latitude on the basis of different annual light and temperature patterns at higher latitudes, creating specific selection pressures. We review literature with respect to latitudinal clines in circadian phenotypes as well as in polymorphisms of circadian clock genes and their possible association with annual timing. The use of latitudinal (and altitudinal) clines in identifying selective forces acting on biological rhythms is discussed, and we evaluate how these studies can reveal novel molecular and physiological components of these rhythms.     

Molecular clocks: when times are a-changin'

The molecular clock has proved to be extremely valuable in placing timescales on evolutionary events that would otherwise be difficult to date. However, debate has arisen about the considerable disparities between molecular and palaeontological or archaeological dates, and about the remarkably high mutation rates inferred in pedigree studies. We argue that these debates can be largely resolved by reference to the "time dependency of molecular rates", a recent hypothesis positing that short-term mutation rates and long-term substitution rates are related by a monotonic decline from the former to the latter. Accordingly, the extrapolation of rates across different timescales will result in invalid date estimates. We examine the impact of this hypothesis with respect to various fields, including human evolution, animal domestication and conservation genetics. We conclude that many studies involving recent divergence events will need to be reconsidered.     

Hibernation: when good clocks go cold

Hibernating animals have been a successful model system for elucidating fundamental properties of many physiological systems. Over the past 50 years, a diverse literature has emerged on the role of the circadian system in control and expression of winter torpor in several orders of birds and mammals. This body of research has also provided insights to circadian function in non-hibernating species. The aim of this review is to examine how this work applies to questions of general interest to chronobiologists, such as temperature compensation, the 2-oscillator model of entrainment, and suprachiasmatic nucleus (SCN) function. Convergent lines of evidence suggest a role for the SCN in timing daily torpor and controlling several parameters of hibernation. In addition to its role as a circadian pacemaker, the SCN may serve a noncircadian function in hibernators related to maintenance of energy balance.     

Biological clocks in Arabidopsis thaliana

Biological rhythms are ubiquitous in eukaryotes, and the best understood of these occur with a period of approximately a day – circadian rhythms. Such rhythms persist even when the organism is placed under constant conditions, with a period that is close, but not exactly equal, to 24 h, and are driven by an endogenous timer – one of the many 'biological clocks'. In plants, research into circadian rhythms has been driven forward by genetic experiments using Arabidopsis . Higher plant genomes include a particularly large number of genes involved in metabolism, and circadian rhythms may well provide the necessary coordination for the control of these – for example, around the diurnal rhythm of photosynthesis – to suit changing developmental or environmental conditions. The endogenous timer must be flexible enough to support these requirements. Current research supports this notion most strongly for the input pathway, in which multiple photoreceptors have been shown to mediate light input to the clock. Both input and output components are now related to putative circadian oscillator mechanisms by sequence homology or by experimental observation. It appears that the pathways linking some domains of the basic clock model may be very short indeed, or the mechanisms of these domains may overlap. Components of the first plant circadian output pathway to be identified unequivocally will help to determine exactly how many output pathways control the various phases of overt rhythms in plants.     

Avian circannual clocks: adaptive significance and possible involvement of energy turnover in their proximate control

Endogenous circannual clocks are found in many long-lived organisms, but are best studied in mammal and bird species. Circannual clocks are synchronized with the environment by changes in photoperiod, light intensity and possibly temperature and seasonal rainfall patterns. Annual timing mechanisms are presumed to have important ultimate functions in seasonally regulating reproduction, moult, hibernation, migration, body weight and fat deposition/stores. Birds that live in habitats where environmental cues such as photoperiod are poor predictors of seasons (e.g. equatorial residents, migrants to equatorial/tropical latitudes) rely more on their endogenous clocks than birds living in environments that show a tight correlation between photoperiod and seasonal events. Such population-specific/interspecific variation in reliance on endogenous clocks may indicate that annual timing mechanisms are adaptive. However, despite the apparent adaptive importance of circannual clocks, (i) what specific adaptive value they have in the wild and (ii) how they function are still largely untested. Whereas circadian clocks are hypothesized to be generated by molecular feedback loops, it has been suggested that circannual clocks are either based upon (i) a de-multiplication ('counting') of circadian days, (ii) a sequence of interdependent physiological states, or (iii) one or more endogenous oscillators, similar to circadian rhythms. We tested the de-multiplication of days (i) versus endogenous regulation hypotheses (ii) and (iii) in captive male and female house sparrows (Passer domesticus). We assessed the period of reproductive (testicular and follicular) cycles in four groups of birds kept either under photoperiods of LD 12L:12D (period length: 24h), 13.5L:13.5D (27 h), 10.5L:10.5D (23 h) or 12D:8L:3D:1L (24-h skeleton photoperiod), respectively, for 15 months. Contrary to predictions from the de-multiplication hypothesis, individuals experiencing 27-h days did not differ (i.e. did not have longer) annual reproductive rhythms than individuals from the 21- or 24-h day groups. However, in line with predictions from endogenous regulation, birds in the skeleton group had significantly longer circannual period lengths than all other groups. Birds exposed to skeleton photoperiods experienced fewer light hours per year than all other groups (3285 versus 4380) and had a lower daily energy expenditure, as tested during one point of the annual cycle using respirometry. Although our results are tantalizing, they are still preliminary as birds were only studied over a period of 15 months. Nevertheless, the present data fail to support a 'counting of circadian days' and instead support hypotheses proposing whole-organism processes as the mechanistic basis for circannual rhythms. We propose a novel energy turnover hypothesis which predicts a dependence of the speed of the circannual clock on the overall energy expenditure of an organism.     

哺乳动物营养代谢的时间生物学研究进展

时间生物学主要是研究生物体内生理和行为的时间机制的学科,而这种机制主要是由生物钟调控的。研究表明,营养代谢的各个方面如葡萄糖转运、糖原异生、脂质合成及降解、氧化磷酸化等作用都受到生物钟核心转录机制的调控,并具有时间敏感性;相反,代谢信号也可以反馈调节生物钟系统,包括生物钟基因表达和行为活动。生物钟的紊乱会造成诸如心血管疾病、肥胖、糖尿病等多种疾病。本文从代谢与生物钟的相互关系、各类营养信号和营养素对生物钟的作用以及生物钟与营养代谢相关疾病的关系等多方面综述了哺乳动物营养代谢的时间生物学研究进展。     

Auxology: when auxin meets plant evo-devo

Auxin is implicated throughout plant growth and development. Although the effects of this plant hormone have been recognized for more than a century, it is only in the past two decades that light has been shed on the molecular mechanisms that regulate auxin homeostasis, signaling, transport, crosstalk with other hormonal pathways as well as its roles in plant development. These discoveries established a molecular framework to study the role of auxin in land plant evolution. Here, we review recent advances in auxin biology and their implications in both micro- and macro-evolution of plant morphology. By analogy to the term 'hoxology', which refers to the critical role of HOX genes in metazoan evolution, we propose to introduce the term 'auxology' to take into account the crucial role of auxin in plant evo-devo.     

Arabidopsis epigenetics: when RNA meets chromatin

Recent work in plants and other eukaryotes has uncovered a major role for RNA interference in silent chromatin formation. The heritability of the silent state through multiple cell division cycles and, in some instances, through meiosis is assured by epigenetic marks. In plants, transposable elements and transgenes provide striking examples of the stable inheritance of repressed states, and are characterized by dense DNA methylation and heterochromatin histone modifications. Arabidopsis is a useful higher eukaryotes model with which to explore the crossroads between silent chromatin and RNA interference both during development and in the genome-wide control of repeat elements.     

Extracellular crosstalk: when GDNF meets N-CAM

N-CAM has now been identified as a receptor for glial cell line-derived neurotrophic factor (GDNF). This finding solves a long-standing question regarding RET-independent GDNF signaling, and reveals a novel pathway distinct from both GDNF-RET and N-CAM-N-CAM signaling. Functional assays of Schwann cell migration and axon growth of CNS neurons suggest physiological significance for this GDNF-N-CAM pathway.     

Circadian clocks and adaptation in Arabidopsis

Endogenous circadian rhythms are almost ubiquitous among organisms from cyanobacteria to mammals and regulate diverse physiological processes. It has been suggested that having an endogenous circadian system enables an organism to anticipate periodic environmental changes and adapt its physiological and developmental states accordingly, thus conferring a fitness advantage. However, it is hard to measure fitness directly and there is, to date, only limited evidence supporting the assumption that having a circadian system can increase fitness and therefore be adaptive. In this article, we report an evolutionary approach to examine the adaptive significance of a circadian system. By crossing Arabidopsis thaliana plants containing mutations that cause changes in circadian rhythms, we have created heterozygous 'Mother' (F1) plants with genetic variance for circadian rhythmicity. The segregating F2 offspring present a range of circadian rhythm periods. We have applied a selection to the F2 plants of short and long T-cycles under different competition strengths and found that the average phenotype of circadian period of the resulting F3 plants show a strong positive correlation with the T-cycle growth conditions for the competing F2 plants. Consistent with their circadian phenotypes, the frequency of long-period alleles was altered in the F3 plants. Our results show that F2 plants with endogenous rhythms that more closely match the environmental T-cycle are fitter, producing relatively more viable offspring in the F3 population. Thus, having a circadian clock that matches with the environment is adaptive in Arabidopsis.     

Evolution of time-keeping mechanisms: early emergence and adaptation to photoperiod

Virtually all species have developed cellular oscillations and mechanisms that synchronize these cellular oscillations to environmental cycles. Such environmental cycles in biotic (e.g. food availability and predation risk) or abiotic (e.g. temperature and light) factors may occur on a daily, annual or tidal time scale. Internal timing mechanisms may facilitate behavioural or physiological adaptation to such changes in environmental conditions. These timing mechanisms commonly involve an internal molecular oscillator (a 'clock') that is synchronized ('entrained') to the environmental cycle by receptor mechanisms responding to relevant environmental signals ('Zeitgeber', i.e. German for time-giver). To understand the evolution of such timing mechanisms, we have to understand the mechanisms leading to selective advantage. Although major advances have been made in our understanding of the physiological and molecular mechanisms driving internal cycles (proximate questions), studies identifying mechanisms of natural selection on clock systems (ultimate questions) are rather limited. Here, we discuss the selective advantage of a circadian system and how its adaptation to day length variation may have a functional role in optimizing seasonal timing. We discuss various cases where selective advantages of circadian timing mechanisms have been shown and cases where temporarily loss of circadian timing may cause selective advantage. We suggest an explanation for why a circadian timing system has emerged in primitive life forms like cyanobacteria and we evaluate a possible molecular mechanism that enabled these bacteria to adapt to seasonal variation in day length. We further discuss how the role of the circadian system in photoperiodic time measurement may explain differential selection pressures on circadian period when species are exposed to changing climatic conditions (e.g. global warming) or when they expand their geographical range to different latitudes or altitudes.