Thermal time – concepts and utility

Wheat was among the last of the major crops to be transformed (in 1992), and transformation is still difficult, with a lower efficiency than that for maize and rice. However, the recent development of Agrobacterium‐based systems is set to improve the precision of the process, while new methods of selection, removal of unnecessary DNA sequences, gene targeting and in vivo mutagenesis will make the process cleaner and more acceptable to regulatory authorities and consumers. Our current work is focussed on using transformation to understand and manipulate aspects of grain processing quality, notably dough strength and texture for milling. However, it is clear that a major priority for future work will be to improve nutritional quality, including vitamin and mineral contents for the developing world and starch digestibility and dietary fibre content and composition for developed countries.     

Pitch the niche – taking responsibility for the concepts we use in ecology and species distribution modelling

In a discussion it is often easier to staunchly reject or offer resolute support for an idea. This third paper on the niche concept aims to develop a balanced argument by exploring general principles for determining an appropriate level for pitching the niche concept that will guide better use and less abuse of niche concepts. To do this we first have to accept that niche concepts are not necessarily essential for ecology. Rather than to improve niche concepts, our aim should then be to pitch the niche in terms of ecology. This aim helps us develop an ‘ultimate goal of the niche’ by which we can evaluate the concepts we use. For species distribution modelling, there has been a focus on the niche as an equilibrium outcome that perhaps has less relevance for disequilibrium situations (e.g. climate change projections). As is the case for much of ecology, more causal explanations of species' distributions use alternative terminologies and less frequently use the word ‘niche’. We suggest that niche concepts that are better aligned with the rest of ecology could arise from taking more responsibility for our own implementations, and by explaining our models with terms other than niche. A general, holistic niche concept promotes this view and promotes practical thinking about what we are modelling and how we interpret those models, which in turn should help inspire and support innovative modelling approaches in species distribution modelling.     

Quantifying island isolation – insights from global patterns of insular plant species richness

Isolation is a driving factor of species richness and other island community attributes. Most empirical studies have investigated the effect of isolation measured as distance to the nearest continent. Here we expanded this perspective by comparing the explanatory power of seventeen isolation metrics in sixty‐eight variations for vascular plant species richness on 453 islands worldwide. Our objectives were to identify ecologically meaningful metrics and to quantify their relative importance for species richness in a globally representative data set. We considered the distances to the nearest mainland and to other islands, stepping stone distances, the area of surrounding landmasses, prevailing wind and ocean currents and climatic similarity between source and target areas. These factors are closely linked to colonization and maintenance of plant species richness on islands. We tested the metrics in spatial multi‐predictor models accounting for area, climate, topography and island geology. Besides area, isolation was the second most important factor determining species richness on the studied islands. A model including the proportion of surrounding land area as the isolation metric had the highest predictive power, explaining 86.1% of the variation. Distances to large islands, stepping stone distances and distances to climatically similar landmasses performed slightly better than distance to the nearest mainland. The effect of isolation was weaker for large islands suggesting that speciation counteracts the negative effect of isolation on immigration on large islands. Continental islands were less affected by isolation than oceanic islands. Our results suggest that a variety of immigration mechanisms influence plant species richness on islands and we show that this can be detected at macro‐scales. Although the distance to the nearest mainland is an adequate and easy‐to‐calculate measure of isolation, accounting for stepping stones, large islands as source landmasses, climatic similarity and the area of surrounding landmasses increases the explanatory power of isolation for species richness.     

SESAM – a new framework integrating macroecological and species distribution models for predicting spatio‐temporal patterns of species assemblages

Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S‐SDM) starts with constituent species to approximate the properties of assemblages. Here, we propose to unify the two approaches in a single ‘spatially explicit species assemblage modelling’ (SESAM) framework. This framework uses relevant designations of initial species source pools for modelling, macroecological variables, and ecological assembly rules to constrain predictions of the richness and composition of species assemblages obtained by stacking predictions of individual species distributions. We believe that such a framework could prove useful in many theoretical and applied disciplines of ecology and evolution, both for improving our basic understanding of species assembly across spatio‐temporal scales and for anticipating expected consequences of local, regional or global environmental changes. In this paper, we propose such a framework and call for further developments and testing across a broad range of community types in a variety of environments.     

Ring species – Do they exist in birds?

According to current theory, the splitting of a single species into two is best observed by a ring of intergrading populations which occupy a ring-shaped distribution area and whose terminal populations not only meet but overlap and co-occur without or with only little hybridization. The three most discussed examples in birds are revisited here. The great tit complex (Parus major s. l.) turned out to be an assemblage of four subspecies groups forming a secondary ring of population. The herring gull/lesser black-backed gull complex (Larus argentatus s. l.) forms a circumpolar circle of intergrading populations, but lacks the crucial cornerstone, the geographical overlap. The greenish warbler complex (Phylloscopus trochiloides s. l.) is close to the ideal ring species, but the ring is not complete and the Siberian zone of overlap needs further clarification and characterisation.     

Distributional shifts – not geographic isolation – as a probable driver of montane species divergence

As biodiversity hotspots, montane regions have been a focus of research to understand the divergence process. Like their oceanic counterparts, the diversity of the ‘sky islands’ might be ascribed to geographic isolation of mountaintops. However, because the sky islands, and especially those in northern latitudes, are subject to extreme climatic events such as the glacial cycles that drove both altitudinal and geographical shifts in species’ distributions, the dynamic colonization process is also a possible factor driving divergence. Here we test these two hypotheses (i.e. isolation versus colonization) in a flightless montane grasshopper, Melanoplus oregonensis, which is a member of a diverse group that radiated across the Rocky Mountains of North America. Using approximate Bayesian computation (ABC) and spatially explicit simulations that account for spatial heterogeneity and temporal shifts in species distributions, we show that a colonization model of the sky islands from refugial populations provides a significantly better fit to the empirical genetic data than a model of the geographic isolation among sky islands. Moreover, support for the colonization model holds irrespective of whether the movement of individuals was modeled as a diffusion process or was informed by differences in habitat suitabilities across the landscape. With validation analyses to confirm the models provide a good fit to the data, as well as general power and quality analyses, the research not only adds to a growing body of work on the complex dynamics underlying montane biodiversity, but it also provides much needed evaluation of competing hypotheses based on explicit models of the divergence process, as opposed to inferences about diversification drivers from species diversity patterns.     

Lack of sex‐specific movement patterns in an alien species at its invasion front – consequences for invasion speed

Efficient targeting of actions to reduce the spread of invasive alien species relies on understanding the spatial, temporal, and individual variation of movement, in particular related to dispersal. Such patterns may differ between individuals at the invasion front compared to individuals in established and dense populations due to differences in environmental and ecological conditions such as abundance of conspecifics or sex‐specific dispersal affecting the encounter rate of potential mates. We assessed seasonal and diurnal variation in movement pattern (step length and turning angle) of adult male and female raccoon dog at their invasion front in northern Sweden using data from Global Positioning System (GPS)‐marked adult individuals and assessed whether male and female raccoon dog differed in their movement behavior. There were few consistent sex differences in movement. The rate of dispersal was rather similar over the months, suggesting that both male and female raccoon dog disperse during most of the year, but with higher speed during spring and summer. There were diurnal movement patterns in both sexes with more directional and faster movement during the dark hours. However, the short summer nights may limit such movement patterns, and long‐distance displacement was best explained by fine‐scale movement patterns from 18:00 to 05:00, rather than by movement patterns only from twilight and night. Simulation of dispersing raccoon dogs suggested a higher frequency of male–female encounters that were further away from the source population for the empirical data compared to a scenario with sex differences in movement pattern. The lack of sex differences in movement pattern at the invasion front results in an increased likelihood for reproductive events far from the source population. Animals outside the source population should be considered potential reproducing individuals, and a high effort to capture such individuals is needed throughout the year to prevent further spread.     

Phylogeography of western Palaearctic reptiles – Spatial and temporal speciation patterns

A phylogeographic analysis of eight species complexes of European reptiles was performed using different molecular methods. While mitochondrial genes (mainly cytochrome b sequences) enabled conclusions about phylogeography and differentiation, additional application of bisexually inherited markers provided information about speciation stages. As species with similar distribution patterns in southern and Central Europe were selected, matching phylogeographic patterns are useful for drawing general conclusions:

(1) The species complexes are in different stages of speciation. In some cases, cryptic species were detected.

(2) Highest genetic diversity occurs in southern Europe, the Near East and the Caucasus, regions corresponding with glacial refuges in the Iberian, Apennine and Balkan Peninsulas as well as in Turkey and the Caucasus. Often, several microrefugia must have existed in close neighbourhood. Additional microrefugia were located in southern France and in the Carpathian Basin.

(3) North Africa and the Middle East did not serve as glacial refuges for Central or northern European lineages and are typically inhabited by independent clades.

(4) Evidence for multiple range retractions and expansions, which were postulated for the times of Pleistocene climatic oscillations, could be found in the Balkans, but in Central Europe their traces have been wiped out by the last glacial. Only the Holocene invasion has left imprints in the genomes from this area.

(5) Central and northern Europe were recolonized from Balkan and Pontic refugia in the Holocene.

(6) Groups from the Iberian and Apennine Peninsulas rarely conquered other regions. This limitation can be attributed to the barrier function of the Pyrenees and the Alps.

Agents of change – concepts in Mycobacterium tuberculosis Ser/Thr/Tyr phosphosignalling

The flow of information from the outside to the inside of bacterial cells is largely directed by protein kinases. In addition to histidine/aspartate phosphorelays of two‐component response regulators, recent work in Mycobacterium tuberculosis (Mtb) reinforces the idea that phosphorylation on serine (Ser), threonine (Thr) and tyrosine (Tyr) is central to bacterial physiology and pathogenesis, and that the corresponding phosphosystems are highly similar to those in eukaryotes. In this way, eukaryotes are a useful guide to understanding Ser/Thr/Tyr phosphorylation (O‐phosphorylation) in prokaryotes such as Mtb. However, as novel functions and components of bacterial O‐phosphorylation are identified, distinct differences between pro‐ and eukaryotic phosphosignalling systems become apparent. The emerging picture of O‐phosphorylation in Mtb is complicated, goes beyond the eukaryotic paradigms, and shows the limitations of viewing bacterial phosphosignalling within the confines of the ‘eukaryotic‐like’ model. Here, we summarize recent findings about Ser/Thr and the recently discovered Tyr phosphorylation pathways in Mtb, highlight the similarities and differences between eukaryotic and prokaryotic O‐phosphorylation, and pose additional questions about signalling components, pathway organization, and ultimately, the cellular roles of O‐phosphorylation in Mtb physiology and pathogenesis.     

Ossification patterns in the tetrapod limb – conservation and divergence from morphogenetic events

Two different patterns of the condensation and chondrification of the limbs of tetrapods are known from extensive studies on their early skeletal development. These are on the one hand postaxial dominance in the sequential formation of skeletal elements in amniotes and anurans, and on the other, preaxial dominance in urodeles. The present study investigates the relative sequence of ossification in the fore‐ and hindlimbs of selected tetrapod taxa based on a literature survey in comparison to the patterns of early skeletal development, i.e. mesenchymal condensation and chondrification, representing essential steps in the late stages of tetrapod limb development. This reveals the degree of conservation and divergence of the ossification sequence from early morphogenetic events in the tetrapod limb skeleton. A step‐by‐step recapitulation of condensation and chondrification during the ossification of limbs can clearly be refuted. However, some of the deeper aspects of early skeletal patterning in the limbs, i.e. the general direction of development and sequence of digit formation are conserved, particularly in anamniotes. Amniotes show a weaker coupling of the ossification sequence in the limb skeleton with earlier condensation and chondrification events. The stronger correlation between the sequence of condensation/chondrification and ossification in the limbs of anamniotes may represent a plesiomorphic trait of tetrapods. The pattern of limb ossification across tetrapods also shows that some trends in the sequence of ossification of their limb skeleton are shared by major clades possibly representing phylogenetic signals. This review furthermore concerns the ossification sequence of the limbs of the Palaeozoic temnospondyl amphibian Apateon sp. For the first time this is described in detail and its patterns are compared with those observed in extant taxa. Apateon sp. shares preaxial dominance in limb development with extant salamanders and the specific order of ossification events in the fore‐ and hindlimb of this fossil dissorophoid is almost identical to that of some modern urodeles.