Investigating the evolution and development of biological complexity under the framework of epigenetics

Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore the link between complexity and adaptation. Although recently developed metrics allow for a unified framework, they omit developmental mechanisms. We argue that a better approach to the empirical study of complexity and its evolution includes developmental mechanisms. We then consider epigenetic mechanisms and their role in shaping developmental and evolutionary trajectories, as well as the development and organization of complexity. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Finally, we explore hybridization complexes and hybrid organisms as potential models for studying the association between epigenetics and complexity. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution.     

Forest complexity drives dung beetle assemblages along an edge-interior gradient in the southwest Amazon rainforest

1. The habitat heterogeneity hypothesis predicts that heterogeneous habitats may provide more niches and diverse ways of exploiting environmental resources, thereby allowing more species to coexist, persist and diversify. 2. We aimed to investigate how an edge-interior gradient related to forest complexity influences species composition, abundance and richness of dung beetles in the western Amazon rainforest. We expected dung beetle abundance and richness to increase along the forest edge-interior gradient, in accordance with the habitat heterogeneity hypothesis. We also expected strong changes in species composition driven by species turnover in the forest interior and nestedness along the forest edges. We sampled dung beetles using baited pitfall traps across an edge-interior gradient. We also assessed the variation in forest features along the edge-interior gradient to identify changes in forest complexity. 3. Both species richness and abundance of dung beetles increased along the forest edge-interior, following the gradient of forest complexity. The Sorensen dissimilarity of dung beetle assemblages was higher among sampling units placed near the forest edge, although neither turnover, nor nestedness was different between the extremes of the forest edge-interior gradient. There was a clear compositional change along the edge-interior gradient mostly driven by species turnover. Individual indicator value analysis revealed that species were strongly associated with the forest interior conditions. 4. The simplification of the Amazon rainforest near clearings causes compositional changes in dung beetle assemblages. These changes are characterised by species-poor and low-abundance assemblages and may impair dung beetle ecological functions and therefore forest recovery.     

Causal mediation analysis in nested case-control studies using conditional logistic regression

The paper proposes an approach to causal mediation analysis in nested case-control study designs, often incorporated with countermatching schemes using conditional likelihood, and we compare the method's performance to that of mediation analysis using the Cox model for the full cohort with a continuous or dichotomous mediator. Simulation studies are conducted to assess our proposed method and investigate the efficiency relative to the cohort. We illustrate the method using actual data from two studies of potential mediation of radiation risk conducted within the Adult Health Study cohort of atomic-bomb survivors. The performance becomes comparable to that based on the full cohort, illustrating the potential for valid mediation analysis based on the reduced data obtained through the nested case-control design.     

Dynamic prediction: A challenge for biostatisticians,but greatly needed by patients,physicians and the public

Prognosis is usually expressed in terms of the probability that a patient will or will not have experienced an event of interest t years after diagnosis of a disease. This quantity, however, is of little informative value for a patient who is still event-free after a number of years. Such a patient would be much more interested in the conditional probability of being event-free in the upcoming t years, given that he/she did not experience the event in the s years after diagnosis, called “conditional survival.” It is the simplest form of a dynamic prediction and can be dealt with using straightforward extensions of standard time-to-event analyses in clinical cohort studies. For a healthy individual, a related problem with further complications is the so-called “age-conditional probability of developing cancer” in the next t years. Here, the competing risk of dying from other diseases has to be taken into account. For both situations, the hazard function provides the central dynamic concept, which can be further extended in a natural way to build dynamic prediction models that incorporate both baseline and time-dependent characteristics. Such models are able to exploit the most current information accumulating over time in order to accurately predict the further course or development of a disease. In this article, the biostatistical challenges as well as the relevance and importance of dynamic prediction are illustrated using studies of multiple myeloma, a hematologic malignancy with a formerly rather poor prognosis which has improved over the last few years.     

‘Heritability’ of dispersal propensity in a patchy population

Although dispersal is often considered to be a plastic, condition-dependent trait with low heritability, growing evidence supports medium to high levels of dispersal heritability. Obtaining unbiased estimates of dispersal heritability in natural populations nevertheless remains crucial to understand the evolution of dispersal strategies and their population consequences. Here we show that dispersal propensity (i.e. the probability of dispersal between habitat patches) displays a significant heritability in the collared flycatcher Ficedula albicollis, as estimated by within-family resemblance when accounting for environmental factors. Offspring of dispersing mothers or fathers had a higher propensity to disperse to a new habitat patch themselves. The effect of parental dispersal status was additional to that of local habitat quality, as measured by local breeding population size and success, confirming previous results about condition-dependent dispersal in this population. The estimated levels of heritability varied between 0.30±0.07 and 0.47±0.10, depending on parent–offspring comparisons made and correcting for a significant assortative mating with respect to dispersal status. Siblings also displayed a significant resemblance in dispersal propensity. These results suggest that variation in between-patch natal dispersal in the collared flycatcher is partly genetically determined, and we discuss ways to quantify this genetic basis and its implications.     

Generation of conditional null alleles for APP and APLP2

Proteolytical cleavage of the β‐amyloid precursor protein (APP) generates β‐amyloid, which is deposited in the brains of patients suffering from Alzheimer's disease (AD). Despite the well‐established key role of APP for AD pathogenesis, the physiological function of APP and its close homologues APLP1 and APLP2 remains poorly understood. Previously, we generated APP^–/– mice that proved viable, whereas APP^–/–APLP2^–/– mice and triple knockouts died shortly after birth, likely due to deficits of neuromuscular synaptic transmission. Here, we generated conditional knockout alleles for both APP and APLP2 in which the promoter and exon1 were flanked by loxP sites. No differences in expression were detectable between wt and floxed alleles, whereas null alleles were obtained upon crossing with Cre‐transgenic deleter mice. These mice will now allow for tissue and time‐point controlled knockout of both genes. genesis 48:200–206, 2010. © 2010 Wiley‐Liss, Inc.     

Natural enemy diversity and biological control: Making sense of the context-dependency

Numerous studies have demonstrated that diverse predator assemblages can be more effective at controlling prey populations. Yet, other studies have shown no effect of predator diversity on prey mortality, or even negative effects (for example due to intraguild predation or interference). Much research emphasis has been placed on the traits of predators that maximise functional complementarity. However, comparatively less attention has been paid to the traits of the prey or habitat that may maximise predator diversity effects, even though there must be a variety of prey niches available to be partitioned in order for niche complementarity to occur. Following this logic, we review six hypotheses for when diverse enemy assemblages should be most effective: when 1) prey communities are diverse; 2) prey have complex life cycles; 3) prey are patchily distributed in space or time; 4) studies are conducted at larger spatial and temporal scales; 5) plant structures are complex; 6) prey are abundant. Many of these hypotheses lack direct tests, particularly in agricultural systems, but we find little or no direct or indirect support for hypotheses 1, 4, 5 and 6. However, previous work does provide some support for hypotheses 2 and 3. We discuss methods to test these hypotheses directly, and suggest that natural enemy diversity may only benefit the biological control of arthropods in heterogeneous systems.     

Oceanic thermal structure mediates dive sequences in a foraging seabird

1. Changes in marine ecosystems are easier to detect in upper‐level predators, like seabirds, which integrate trophic interactions throughout the food web.
2. Here, we examined whether diving parameters and complexity in the temporal organization of diving behavior of little penguins (Eudyptula minor) are influenced by sea surface temperature (SST), water stratification, and wind speed—three oceanographic features influencing prey abundance and distribution in the water column.
3. Using fractal time series analysis, we found that foraging complexity, expressed as the degree of long‐range correlations or memory in the dive series, was associated with SST and water stratification throughout the breeding season, but not with wind speed. Little penguins foraging in warmer/more‐stratified waters exhibited greater determinism (memory) in foraging sequences, likely as a response to prey aggregations near the thermocline. They also showed higher foraging efficiency, performed more dives and dove to shallower depths than those foraging in colder/less‐stratified waters.
4. Reductions in the long‐term memory of dive sequences, or in other words increases in behavioral stochasticity, may suggest different strategies concerning the exploration–exploitation trade‐off under contrasting environmental conditions.

     

Effects of cover and predator size on survival and development of Ranautricularia tadpoles

Size-limited predation is an important process during the development of many aquatic species, and mortality rates of early larval stages and small individuals can be particularly high. Structurally complex habitats can mediate predator-prey interactions and provide a potentially important mechanism for decreasing predation pressure on larvae. To determine whether structurally complex habitats mediate predation on tadpoles of the southern leopard frog (Ranautricularia), we designed a factorial experiment, crossing two levels of cover with three predator treatments (none, small, or large Trameacarolina naiads). Predator size had a larger effect on tadpole performance (survival, mass and age at metamorphosis) than did cover level, largely because small predators were ineffective. Within the large-predator treatment, however, tadpole survival was higher (78%) under high than under low cover (46%), suggesting that increased cover decreased predator foraging efficiency allowing more larvae to reach a size refuge. This study demonstrates that habitat structural complexity can play an important role in mediating predator-prey interactions, even when tadpoles start out at a size disadvantage relative to predators. Consideration of habitat structural complexity in future research should provide a more complete understanding of the role of size relationships in predator-prey systems. Received: 3 January 1997 / Accepted: 10 October 1997