The annual cycle of a trans-equatorial Eurasian-African passerine migrant: different spatio-temporal strategies for autumn and spring migration

The small size of the billions of migrating songbirds commuting between temperate breeding sites and the tropics has long prevented the study of the largest part of their annual cycle outside the breeding grounds. Using light-level loggers (geolocators), we recorded the entire annual migratory cycle of the red-backed shrike Lanius collurio, a trans-equatorial Eurasian-African passerine migrant. We tested differences between autumn and spring migration for nine individuals. Duration of migration between breeding and winter sites was significantly longer in autumn (average 96 days) when compared with spring (63 days). This difference was explained by much longer staging periods during autumn (71 days) than spring (9 days). Between staging periods, the birds travelled faster during autumn (356 km d(-1)) than during spring (233 km d(-1)). All birds made a protracted stop (53 days) in Sahelian sub-Sahara on southbound migration. The birds performed a distinct loop migration (22 000 km) where spring distance, including a detour across the Arabian Peninsula, exceeded the autumn distance by 22 per cent. Geographical scatter between routes was particularly narrow in spring, with navigational convergence towards the crossing point from Africa to the Arabian Peninsula. Temporal variation between individuals was relatively constant, while different individuals tended to be consistently early or late at different departure/arrival occasions during the annual cycle. These results demonstrate the existence of fundamentally different spatio-temporal migration strategies used by the birds during autumn and spring migration, and that songbirds may rely on distinct staging areas for completion of their annual cycle, suggesting more sophisticated endogenous control mechanisms than merely clock-and-compass guidance among terrestrial solitary migrants. After a century with metal-ringing, year-round tracking of long-distance migratory songbirds promises further insights into bird migration.     

Why Do Phage Play Dice?

Phage lambda is among the simplest organisms that make a developmental decision. An infected bacterium goes either into the lytic state, where the phage particles rapidly replicate and eventually lyse the cell, or into a lysogenic state, where the phage goes dormant and replicates along with the cell. Experimental observations by P. Kourilsky are consistent with a single phage infection deterministically choosing lysis and double infection resulting in a stochastic choice. We argue that the phage are playing a “game” of minimizing the chance of extinction and that the shift from determinism to stochasticity is due to a shift from a single-player to a multiplayer game. Crucial to the argument is the clonal identity of the phage.Organisms typically use information from the environment to suitably modify their behavior. Some of these can be considered “strategic” decisions for maximizing the chances of success of the population. For example, many organisms are able to adjust their reproductive strategies according to environmental conditions. A typical signal that often triggers changes in the reproductive strategy is population density (1, 6). Temperate bacteriophages are among the simplest organisms that are able to sense population density and choose their reproductive strategy accordingly. In general, temperate phage choose to stay dormant and replicate along with the host (lysogeny) rather than making many virions and killing the host (lysis) when larger numbers of phage attack a bacterial population (4, 7, 10). Phage lambda''s choice between lysis and lysogeny has become a paradigm for developmental decisions (12). For this lysis-lysogeny decision, we use game theory to understand under what conditions different strategies might be optimal. In particular, we focus on the determinism versus the stochasticity of the strategy. We show that deterministic strategies are best when the phage has minimal information and must consider itself as the only “player” in the game. In contrast, having multiple identical players can make a stochastic strategy the best.We consider the phage to be playing a game whose purpose is to minimize the chance of extinction. For single-player games of this kind, where the player has several options but limited information, the optimal strategies are typically deterministic (13). And it is indeed the case that the lysis-lysogeny decision is often deterministic. This statement is somewhat at odds with the general perception that stochasticity plays an important role in the decision, a view initiated by reference 2, which invoked stochasticity to explain Kourilsky''s measurements (7) of the frequency of lysogenization in lambda. However, our analysis of Kourilsky''s data (7, 8) (Fig. ​(Fig.1;1; see also Materials and Methods) shows that (i) when a single phage infects a bacterium (i.e., when the multiplicity of infection [MOI] is 1), it invariably goes lytic and (ii) when the MOI is 2, the decision is stochastic, with a slight preference toward lysogeny (this preference increases as the MOI increases).Open in a separate windowFIG. 1.Red circles show the fraction of bacteria that entered lysogeny as a function of the API (overall phage/bacterium ratio) in Kourilsky''s experiments (7, 8, 9). Solid lines are theoretical estimates using different functions for Q(m), which is the probability of going lytic as a function of the MOI (m) (see Materials and Methods). As shown by the red curve, the best fits ± estimated 95% intervals (Table ​(Table1)1) for Q(m) are 0.004 ± 0.001, 0.70 ± 0.04, and 0.99 ± 0.08 for m values of 1, 2, and 3, respectively. Even a small amount of stochasticity in the decision for an MOI of 1 is inconsistent with the data: for the orange curve the Q(m) values are 0.05, 0.70, and 0.99 for m values of 1, 2, and 3, respectively.The stochasticity in the strategy for an MOI of 2 refers to the fact that seemingly identical infection events lead to different developmental paths. This inhomogeneity in the decision could reflect either true randomness (for example, due to the stochasticity of individual molecular events) or inhomogeneity across different infected cells (for example, the cell size could affect the decision [14]).The determinism in the phage decision for an MOI of 1 fits the game-theoretic expectation, as we will show, but then, the conundrum is this: why is the decision stochastic for an MOI of 2? In this paper, we argue that the shift from determinism at an MOI of 1 to stochasticity at an MOI of 2 is analogous to the shift from deterministic to stochastic strategies in single-player versus multiplayer games.     

Predicting Habitat Utilization and Extent of Ecosystem Disturbance by an Increasing Herbivore Population

Herbivory can lead to shifts in ecosystem state or changes in ecosystem functioning, and recovery from herbivory is particularly slow in disturbance-sensitive ecosystems such as arctic tundra. Herbivore impacts on ecosystems are variable in space and time due to population fluctuations and selective utilization of habitats; thus there is a need to accurately predict herbivore impacts at the landscape scale. The habitat utilization and extent of disturbance caused by increasing populations of pink-footed geese (Anser brachyrhynchus) foraging in the high arctic tundra of Svalbard were assessed using a predictive model of the population’s habitat use. Pink-footed geese arrive in Svalbard in early spring when they forage for belowground plant parts; this foraging (called grubbing) can cause vegetation loss and soil disturbance. Surveys of the extent and intensity of grubbing were carried out to develop predictive models that were subsequently tested against data collected during the following year from different areas. Both habitat type at a particular point and the amount of preferred fen habitat in the surrounding area were powerful predictors of grubbing likelihood and the developed model correctly classified over 69% of validation observations with an AUC of 0.75. Pink-footed geese showed a strong preference for wetter habitats within low-lying landscapes. Extrapolation of the predictive model across the archipelago showed that a maximum potential area of 2300 km² (3.8% of the archipelago) could be disturbed by grubbing. Thus, increasing populations of geese may cause large-scale vegetation loss and soil disturbance in arctic ecosystems.     

Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola

The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10,000-12,000 years ago in the Fertile Crescent. The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses. We use a comparative genomics approach to assess how the process of host specialization affected the genome structure of M. graminicola since divergence from the closest known progenitor species named M. graminicola S1. The genome of S1 was obtained by Illumina sequencing resulting in a 35 Mb draft genome sequence of 32X. Assembled contigs were aligned to the previously sequenced M. graminicola genome. The alignment covered >90% of the non-repetitive portion of the M. graminicola genome with an average divergence of 7%. The sequenced M. graminicola strain is known to harbor thirteen essential chromosomes plus eight dispensable chromosomes. We found evidence that structural rearrangements significantly affected the dispensable chromosomes while the essential chromosomes were syntenic. At the nucleotide level, the essential and dispensable chromosomes have evolved differently. The average synonymous substitution rate in dispensable chromosomes is considerably lower than in essential chromosomes, whereas the average non-synonymous substitution rate is three times higher. Differences in molecular evolution can be related to different transmission and recombination patterns, as well as to differences in effective population sizes of essential and dispensable chromosomes. In order to identify genes potentially involved in host specialization or speciation, we calculated ratios of synonymous and non-synonymous substitution rates in the >9,500 aligned protein coding genes. The genes are generally under strong purifying selection. We identified 43 candidate genes showing evidence of positive selection, one encoding a potential pathogen effector protein. We conclude that divergence of these pathogens was accompanied by structural rearrangements in the small dispensable chromosomes, while footprints of positive selection were present in only a small number of protein coding genes.     

Ultrasonography of the metacarpophalangeal and proximal interphalangeal joints in rheumatoid arthritis: a comparison with magnetic resonance imaging, conventional radiography and clinical examination

Signs of inflammation and destruction in the finger joints are the principal features of rheumatoid arthritis (RA). There are few studies assessing the sensitivity and specificity of ultrasonography in detecting these signs. The objective of the present study was to investigate whether ultrasonography can provide information on signs of inflammation and destruction in RA finger joints that are not available with conventional radiography and clinical examination, and comparable to the information provided by magnetic resonance imaging (MRI). The second to fifth metacarpophalangeal and proximal interphalangeal joints of 40 RA patients and 20 control persons were assessed with ultrasonography, clinical examination, radiography and MRI. With MRI as the reference method, the sensitivity, specificity and accuracy of ultrasonography in detecting bone erosions in the finger joints were 0.59, 0.98 and 0.96, respectively; they were 0.42, 0.99 and 0.95 for radiography. The sensitivity, specificity and accuracy of ultrasonography, with signs of inflammation on T1-weighted MRI sequences as the reference method, were 0.70, 0.78 and 0.76, respectively; they were 0.40, 0.85 and 0.72 for the clinical examination. With MRI as the reference method, ultrasonography had higher sensitivity and accuracy in detecting signs of inflammation and destruction in RA finger joints than did clinical and radiographic examinations, without loss of specificity. This study shows that ultrasonography has the potential to improve assessment of patients with RA.     

Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata

We report studies of seven members of the S-domain gene family in Arabidopsis lyrata, a member of the Brassicaceae that has a sporophytic self-incompatibility (SI) system. Orthologs for five loci are identifiable in the self-compatible relative A. thaliana. Like the Brassica stigmatic incompatibility protein locus (SRK), some of these genes have kinase domains. We show that several of these genes are unlinked to the putative A. lyrata SRK, Aly13. These genes have much lower nonsynonymous and synonymous polymorphism than Aly13 in the S-domains within natural populations, and differentiation between populations is higher, consistent with balancing selection at the Aly13 locus. One gene (Aly8) is linked to Aly13 and has high diversity. No departures from neutrality were detected for any of the loci. Comparing different loci within A. lyrata, sites corresponding to hypervariable regions in the Brassica S-loci (SLG and SRK) and in comparable regions of Aly13 have greater replacement site divergence than the rest of the S-domain. This suggests that the high polymorphism in these regions of incompatibility loci is due to balancing selection acting on sites within or near these regions, combined with low selective constraints.     

Biofilm formation by Pseudomonas aeruginosa wild type,flagella and type IV pili mutants

Biofilm formation by Gfp-tagged Pseudomonas aeruginosa PAO1 wild type, flagella and type IV pili mutants in flow chambers irrigated with citrate minimal medium was characterized by the use of confocal laser scanning microscopy and comstat image analysis. Flagella and type IV pili were not necessary for P. aeruginosa initial attachment or biofilm formation, but the cell appendages had roles in biofilm development, as wild type, flagella and type IV pili mutants formed biofilms with different structures. Dynamics and selection during biofilm formation were investigated by tagging the wild type and flagella/type IV mutants with Yfp and Cfp and performing time-lapse confocal laser scanning microscopy in mixed colour biofilms. The initial microcolony formation occurred by clonal growth, after which wild-type P. aeruginosa bacteria spread over the substratum by means of twitching motility. The wild-type biofilms were dynamic compositions with extensive motility, competition and selection occurring during development. Bacterial migration prevented the formation of larger microcolonial structures in the wild-type biofilms. The results are discussed in relation to the current model for P. aeruginosa biofilm development.