How traits shape trees: new approaches for detecting character state‐dependent lineage diversification

Biologists have long sought to understand the processes underlying disparities in clade size across the tree of life and the extent to which such clade size differences can be attributed to the evolution of particular traits. The association of certain character states with species‐rich clades suggests that trait evolution can lead to increased diversification, but such a pattern could also arise due other processes, such as directional trait evolution. Recent advances in phylogenetic comparative methods have provided new statistical approaches for distinguishing between these intertwined and potentially confounded macroevolutionary processes. Here, we review the historical development of methods for detecting state‐dependent diversification and explore what new methods have revealed about classic examples of traits that affect diversification, including evolutionary dead ends, key innovations and geographic traits. Applications of these methods thus far collectively suggest that trait diversity commonly arises through the complex interplay between transition, speciation and extinction rates and that long hypothesized evolutionary dead ends and key innovations are instead often cases of directional trends in trait evolution.     

Glycoproteomics: Past, present and future

This invited paper reviews the study of protein glycosylation, commonly known as glycoproteomics, beginning with the origins of the subject area in the early 1970s shortly after mass spectrometry was first applied to protein sequencing. We go on to describe current analytical approaches to glycoproteomic analyses, with exemplar projects presented in the form of the complex story of human glycodelin and the characterisation of blood group H eptitopes on the O-glycans of gp273 from Unio elongatulus. Finally, we present an update on the latest progress in the field of automated and semi-automated interpretation and annotation of these data in the form of GlycoWorkBench, a powerful informatics tool that provides valuable assistance in unravelling the complexities of glycoproteomic studies.     

Assessing the causes of diversification slowdowns: temperature‐dependent and diversity‐dependent models receive equivalent support

Diversification rates vary over time, yet the factors driving these variations remain unclear. Temporal declines in speciation rates have often been interpreted as the effect of ecological limits, competition, and diversity dependence, emphasising the role of biotic factors. Abiotic factors, such as climate change, are also supposed to have affected diversification rates over geological time scales, yet direct tests of these presumed effects have mainly been limited to few clades well represented in the fossil record. If warmer climatic periods have sustained faster speciation, this could explain slowdowns in speciation during the Cenozoic climate cooling. Here, we apply state‐of‐the art diversity‐dependent and temperature‐dependent phylogenetic models of diversification to 218 tetrapod families, along with constant rate and time‐dependent models. We confirm the prevalence of diversification slowdowns, and find as much support for temperature‐dependent than diversity‐dependent models. These results call for a better integration of these two processes in studies of diversification dynamics.     

Past, present and future of ACE inhibitors

This satellite symposium was organised and sponsored by Servier. The aim of the symposium was to evaluate the past 30 years of experience with and the future of angiotensin-converting enzyme (ACE) inhibitors. The session was chaired by R. Ferrari (Ferrara, Italy) and M. Tendera (Katowice, Poland).     

Past, present and future of organic nutrients

Background

Slowing crop yield increases despite high fertiliser application rates, declining soil health and off-site pollution are testimony that many bioproduction systems require innovative nutrient supply strategies. One avenue is a greater contribution of organic compounds as nutrient sources for crops. That plants take up and metabolise organic molecules (‘organic nutrients’) has been discovered prior to more recent interest with scientific roots reaching far into the 19th century. Research on organic nutrients continued in the early decades of the 20th century, but after two world wars and yield increases achieved with mineral and synthetic fertilisers, a smooth continuation of the research was not to be expected, and we find major gaps in the transmission of methods and knowledge.

Scope

Addressing the antagonism of ‘organicists’ and ‘mineralists’ in plant nutrition, we illustrate how the focus of crop nutrition has shifted from organic to inorganic nutrients. We discuss reasons and provide evidence for a role of organic compounds as nutrients and signalling agents.

Conclusion

After decades of focussing on inorganic nutrients, perspectives have greatly widened again. As has occurred before in agricultural history, science has to validate agronomic practises. We argue that a framework that views plants as mixotrophs with an inherent ability to use organic nutrients, via direct uptake or aided by exoenzyme-mediated degradation, will transform nutrient management and crop breeding to complement inorganic and synthetic fertilisers with organic nutrients.     

Past,present, and future research in bipolar lichen‐forming fungi and their photobionts

Compared to other organisms, such as vascular plants or mosses, lichen‐forming fungi have a high number of species occurring in both northern and southern hemispheres but are largely absent from intermediate, tropical latitudes. For instance, ca. 160 Antarctic species also occur in polar areas or mountainous temperate regions of the northern hemisphere. Early interpretations of this particular distribution pattern were made in terms of vicariance or long‐distance dispersal. However, it was not until the emergence of phylogenetics and the possibility of dating past diversification and colonization events that these initial hypotheses started to be evaluated. The premise of a relatively recent colonization of the southern hemisphere by boreal lichens through long‐distance dispersal has gained support in recent studies based on either the comparison of genetic affinities (i.e., tree topology) or more robust, statistical migratory models. Still, the scarcity of such studies and a concern that taxonomic concepts for bipolar lichens are often too broad preclude the generation of sound explanations on the mechanisms and origin of such fascinating disjunct distributions. This review provides an up‐to‐date overview of bipolar distributions in lichen‐forming fungi and their photobionts. Evidence provided by recent, molecular‐based studies as well as data on the type of lichen reproduction, dispersal ability, photobiont identity and availability, and habitat preferences are brought together to discuss how and when these distributions originated and their genetic footprints. Ideas for future prospects and research are also discussed.     

Branching patterns in phylogenies cannot distinguish diversity‐dependent diversification from time‐dependent diversification

One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.     

Past, present and future experiments on muscle

Since the basic outline of the sliding filament mechanism became apparent some 45 years ago, the principal challenge, an experimental one, has been to produce definitive evidence about the detailed molecular mechanisms by which myosin cross-bridges produce force and movement in a muscle. More recently, similar questions could be posed about other molecular motors, in non-muscle cells. This problem proved unexpectedly difficult to solve, in part because of the technical difficulty of obtaining the structural and mechanical information required about rapid events within macromolecules, especially in a working system, and this triggered many remarkable technical developments. There is now very strong evidence for a large change in shape of the myosin heads during ATP hydrolysis, consistent with a lever-arm mechanism. Whether this does indeed provide the driving force for contraction and movement--and, if so, exactly how--and whether some other processes could also play a significant role, is discussed in the light of the experimental and theoretical findings presented at this meeting, and other recent and long-term evidence.     

Fungal pathogenesis: Past,present and future

Over the last 20 years a record number of fungal and fungal-like diseases have jeopardized wild species the world over, causing several of the most severe population declines and extinctions ever witnessed (Fisher et al. 2012). Such events include the devastating impact of Batrachochytrium dendrobatidis on amphibian populations and the extinction of bat populations as a result of Geomyces destructans infection. This commentary focusses on two human-infecting fungal pathogens causing much scientific interest, that is, Cryptococcus gattii and Trichophyton rubrum. It summarises recent research findings into their pathogenic evolution and adaptive strategies and highlights key gaps in our knowledge. Finally, the prose attempts to fuse such data with the work of Casadevall, exploiting his theories to predict the future of fungal pathogenesis, that is, where pathogenesis refers to the mechanism that results in disease (Casadevall 2012).     

Serum ferritin: Past,present and future

Background

Serum ferritin was discovered in the 1930s, and was developed as a clinical test in the 1970s. Many diseases are associated with iron overload or iron deficiency. Serum ferritin is widely used in diagnosing and monitoring these diseases.

Scope of review

In this chapter, we discuss the role of serum ferritin in physiological and pathological processes and its use as a clinical tool.

Major conclusions

Although many aspects of the fundamental biology of serum ferritin remain surprisingly unclear, a growing number of roles have been attributed to extracellular ferritin, including newly described roles in iron delivery, angiogenesis, inflammation, immunity, signaling and cancer.

General significance

Serum ferritin remains a clinically useful tool. Further studies on the biology of this protein may provide new biological insights.