Choosing the Right Life Partner: Ecological Drivers of Lichen Symbiosis

Lichens are an iconic example of symbiotic systems whose ecology is shaped by the requirements of the symbionts. Previous studies suggest that fungal (mycobionts) as well as photosynthesizing (phycobionts or cyanobionts) partners have a specific range of acceptable symbionts that can be chosen according to specific environmental conditions. This study aimed to investigate the effects of climatic conditions and mycobiont identity on phycobiont distribution within the lichen genera Stereocaulon, Cladonia, and Lepraria. The study area comprised the Canary Islands, Madeira, Sicily, and the Aeolian Islands, spanning a wide range of climatic conditions. These islands are known for their unique and diverse fauna and flora; however, lichen phycobionts have remained unstudied in most of these areas. In total, we genetically analyzed 339 lichen samples. The phycobiont pool differed significantly from that outside the studied area. Asterochloris mediterranea was identified as the most abundant phycobiont. However, its distribution was limited by climatic constraints. Other species of Asterochloris and representatives of the genera Chloroidium, Vulcanochloris, and Myrmecia were also recovered as phycobionts. The selection of symbiotic partners from the local phycobiont pool was driven by mycobiont specificity (i.e., the taxonomic range of acceptable partners) and the environmental conditions, mainly temperature. Interestingly, the dominant fungal species responded differently in their selection of algal symbionts along the environmental gradients. Cladonia rangiformis associated with its phycobiont A. mediterranea in a broader range of temperatures than Stereocaulon azoreum, which favors other Asterochloris species along most of the temperature gradient. Stereocaulon vesuvianum associated with Chloroidium spp., which also differed in their temperature optima. Finally, we described Stereocaulon canariense as a new endemic species ecologically distinct from the other Stereocaulon species on the Canary Islands.

Seabird Migration Strategies: Flight Budgets, Diel Activity Patterns, and Lunar Influence

Every year, billions of birds undertake extensive migrations between breeding and non-breeding areas, facing challenges that require behavioural adjustments, particularly to flight timing and duration. Such adjustments in daily activity patterns and the influence of extrinsic factors (e.g., environmental conditions, moonlight) have received much more research attention in terrestrial than marine migrants. Taking advantage of the widespread deployment in recent decades of combined light-level geolocator-immersion loggers, we investigated diel organisation and influence of the moon on flight activities during the non-breeding season of 21 migrant seabird species from a wide taxonomic range (6 families, 3 orders). Migrant seabirds regularly stopped (to either feed or rest) during migration, unlike some terrestrial and wetland birds which fly non-stop. We found an overall increase for most seabird species in time in flight and, for several species, also in flight bout duration, during migration compared to when resident at the non-breeding grounds. Additionally, several nocturnal species spent more of the day in flight during migration than at non-breeding areas, and vice versa for diurnal species. Nocturnal time in flight tended to increase during full moon, both during migration and at the non-breeding grounds, depending on species. Our study provides an extensive overview of activity patterns of migrant seabirds, paving the way for further research on the underlying mechanisms and drivers.

Adult Shell-size Regulation in Conispirally-coiled Shells: Evidence for a Widespread Negative Covariance between Whorls Growth-rate and the Final Number of Whorls in Land Snails

As shown, in particular, by the late S.J. Gould, the involvement of a regulation process, aiming at limiting the range of intraspecific variations in adult shell size, in those land snail species with determinate growth, can be indirectly, but conveniently, diagnosed by highlighting a negative covariance between the whorls growth-rate and the whorls number reached at adulthood. However, up to now, such kind of regulation had only been demonstrated in very few cases among land snails and shelled Gastropods in general. Accordingly, quite more extensive checking is required, across both the taxonomic spectrum and the geometrical range of shell profiles. The present report is a very preliminary contribution addressing these issues, which have been neglected for too long. Considering a still limited number of eight species, yet largely encompassing both taxonomic range and shell profiles, it is shown that strong negative covariances between whorls growth-rate and whorls number are systematically highlighted, thereby supporting the involvement of an efficient regulation process of adult shell size and shape in each eight species. Moreover, the degree of regulation of the adult shell size has been quantified and this regulation proves being remarkably effective as a whole, while yet remaining highly species-specific, with very significant disparities among species – and this, somewhat surprisingly, being quite irrespective of the type of geometrical profiles of shells, among the studied species.

Phylogenetic signal in the vocalizations of vocal learning and vocal non-learning birds

Some animal vocalizations develop reliably in the absence of relevant experience, but an intriguing subset of animal vocalizations is learned: they require acoustic models during ontogeny in order to develop, and the learner's vocal output reflects those models. To what extent do such learned vocalizations reflect phylogeny? We compared the degree to which phylogenetic signal is present in vocal signals from a wide taxonomic range of birds, including both vocal learners (songbirds) and vocal non-learners. We used publically available molecular phylogenies and developed methods to analyse spectral and temporal features in a carefully curated collection of high-quality recordings of bird songs and bird calls, to yield acoustic distance measures. Our methods were initially developed using pairs of closely related North American and European bird species, and then applied to a non-overlapping random stratified sample of European birds. We found strong similarity in acoustic and genetic distances, which manifested itself as a significant phylogenetic signal, in both samples. In songbirds, both learned song and (mostly) unlearned calls allowed reconstruction of phylogenetic trees nearly isomorphic to the phylogenetic trees derived from genetic analysis. We conclude that phylogeny and inheritance constrain vocal structure to a surprising degree, even in learned birdsong. This article is part of the theme issue ‘Vocal learning in animals and humans’.

Expanding the taxonomic range in the fecal metagenome

Background Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limited numbers of non-bacterial species in their databases compared to available genomic sequences and their methodologies do not favour classification of rare sequences which may represent only a small fraction of their parent genome. In seeking to optimise identification of non-bacterial species, we evaluated five widely-used metagenome classifier programs (BURST, Kraken2, Centrifuge, MetaPhlAn2 and CCMetagen) for their ability to correctly assign and count simulations of bacterial, viral and eukaryotic DNA sequence reads, including the effect of taxonomic order of analysis of bacteria, viruses and eukaryotes and the effect of sequencing depth. Results We found that the precision of metagenome classifiers varied significantly between programs and between taxonomic groups. When classifying viruses and eukaryotes, ordering the analysis such that bacteria were classified first significantly improved classification precision. Increasing sequencing depth decreased classification precision and did not improve recall of rare species. Conclusions Choice of metagenome classifier program can have a marked effect on results with respect to precision of species assignment in different taxonomic groups. The order of taxonomic classification can markedly improve precision. Increasing sequencing depth can decrease classification precision and yields diminishing returns in probability of species detection.

Mimicry in motion and morphology: do information limitation, trade-offs or compensation relax selection for mimetic accuracy?

Many animals mimic dangerous or undesirable prey as a defence from predators. We would expect predators to reliably avoid animals that closely resemble dangerous prey, yet imperfect mimics are common across a wide taxonomic range. There have been many hypotheses suggested to explain imperfect mimicry, but comparative tests across multiple mimicry systems are needed to determine which are applicable, and which—if any—represent general principles governing imperfect mimicry. We tested four hypotheses on Australian ant mimics and found support for only one of them: the information limitation hypothesis. A predator with incomplete information will be unable to discriminate some poor mimics from their models. We further present a simple model to show that predators are likely to operate with incomplete information because they forage and make decisions while they are learning, so might never learn to properly discriminate poor mimics from their models. We found no evidence that one accurate mimetic trait can compensate for, or constrain, another, or that rapid movement reduces selection pressure for good mimicry. We argue that information limitation may be a general principle behind imperfect mimicry of complex traits, while interactions between components of mimicry are unlikely to provide a general explanation for imperfect mimicry.

Comparative Genomics Reveals 13 Different Isoforms of Mytimycins (A-M) in Mytilus galloprovincialis

Mytimycins are cysteine-rich antimicrobial peptides that show antifungal properties. These peptides are part of the immune network that constitutes the defense system of the Mediterranean mussel (Mytilus galloprovincialis). The immune system of mussels has been increasingly studied in the last decade due to its great efficiency, since these molluscs, particularly resistant to adverse conditions and pathogens, are present all over the world, being considered as an invasive species. The recent sequencing of the mussel genome has greatly simplified the genetic study of some of its immune genes. In the present work, we describe a total of 106 different mytimycin variants in 16 individual mussel genomes. The 13 highly supported mytimycin clusters (A–M) identified with phylogenetic inference were found to be subject to the presence/absence variation, a widespread phenomenon in mussels. We also identified a block of conserved residues evolving under purifying selection, which may indicate the “functional core” of the mature peptide, and a conserved set of 10 invariable plus 6 accessory cysteines which constitute a plastic disulfide array. Finally, we extended the taxonomic range of distribution of mytimycins among Mytilida, identifying novel sequences in M. coruscus, M. californianus, P. viridis, L. fortunei, M. philippinarum, M. modiolus, and P. purpuratus.

Ecology of asynchronous asexual replication: the intraerythrocytic development cycle of Plasmodium berghei is resistant to host rhythms

Background Daily periodicity in the diverse activities of parasites occurs across a broad taxonomic range. The rhythms exhibited by parasites are thought to be adaptations that allow parasites to cope with, or exploit, the consequences of host activities that follow daily rhythms. Malaria parasites (Plasmodium) are well-known for their synchronized cycles of replication within host red blood cells. Whilst most species of Plasmodium appear sensitive to the timing of the daily rhythms of hosts, and even vectors, some species present no detectable rhythms in blood-stage replication. Why the intraerythrocytic development cycle (IDC) of, for example Plasmodium chabaudi, is governed by host rhythms, yet seems completely independent of host rhythms in Plasmodium berghei, another rodent malaria species, is mysterious. Methods This study reports a series of five experiments probing the relationships between the asynchronous IDC schedule of P. berghei and the rhythms of hosts and vectors by manipulating host time-of-day, photoperiod and feeding rhythms. Results The results reveal that: (i) a lack coordination between host and parasite rhythms does not impose appreciable fitness costs on P. berghei; (ii) the IDC schedule of P. berghei is impervious to host rhythms, including altered photoperiod and host-feeding-related rhythms; (iii) there is weak evidence for daily rhythms in the density and activities of transmission stages; but (iv), these rhythms have little consequence for successful transmission to mosquitoes. Conclusions Overall, host rhythms do not affect the performance of P. berghei and its asynchronous IDC is resistant to the scheduling forces that underpin synchronous replication in closely related parasites. This suggests that natural variation in the IDC schedule across species represents different parasite strategies that maximize fitness. Thus, subtle differences in the ecological interactions between parasites and their hosts/vectors may select for the evolution of very different IDC schedules.

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

Comparative analysis of the rhizosphere and endophytic microbiomes across apple rootstock genotypes in replant orchard soils

Apple replant disease (ARD), caused by a complex of soil-borne pathogens, negatively impacts tree health and productivity in new orchard plantings at sites previously planted to apple. Use of new disease tolerant apple rootstock genotypes may diminish growth limiting effects of ARD, however the influence of rootstock genotype on modulating the rhizosphere and endophytic microbiome to enable ARD tolerance is not fully understood. Composition of the rhizosphere and root endophytic microbiomes was characterized across a diversity of apple rootstock genotypes. A series of tolerant (G.210, G.41, G.890, and G.935) and susceptible (M.26 and M.9) rootstock cultivars were consecutively planted into orchard replant soil containing a known pathogen complex. Amplicon sequencing was used to determine simultaneously the presence of a broad taxonomic range of organisms and their relative abundance. Microbial communities exhibited significant differences in composition between the rhizosphere and endophytic environments in terms of species diversity, content, and abundance. Significant differences in composition of the endophytic and rhizosphere microbiomes were observed between rootstock genotypes. Among rootstock endophytic fungal communities, rootstock G.890 samples consistently harbored the highest percentage of arbuscular mycorrhizal fungal species (>5% of total). Ilyonectria spp., which may function as a pathogen of apple, were detected at high relative abundance in the endosphere of all genotypes, with the highest relative abundance in M.26. These results provide further insight into rhizosphere and endophytic microbial communities of apple rootstocks, which could be exploited or manipulated to improve tree fruit agricultural management practices with respect to plant nutrition and disease control.