Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3-1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.

Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (1) "plant breeding" (generating new genetic material), (2) "molecular interactions" (exploring the molecular dialogue governing plant-pathogen interactions) and (3) "epidemiology and evolution" (explaining and forecasting of pathogen population dynamics resulting from selection pressure[s] exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary-epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars.

Understanding microbial dispersal is critical to understand the dynamics and evolution of microbial communities. However, microbial dispersal is difficult to study because of uncertainty about their vectors of migration. This applies to both microbial communities in natural and human-associated environments. Here, we studied microbial dispersal along the sourdoughs bread-making chain using a participatory research approach. Sourdough is a naturally fermented mixture of flour and water. It hosts a community of bacteria and yeasts whose origins are only partially known. We analysed the potential of wheat grains and flour to serve as an inoculum for sourdough microbial communities using 16S rDNA and ITS1 metabarcoding. First, in an experiment involving farmers, a miller and bakers, we followed the microbiota from grains to newly initiated and propagated sourdoughs. Second, we compared the microbiota of 46 sourdough samples collected everywhere in France, and of the flour used for their back-slopping. The core microbiota detected on the seeds, in the flour and in the sourdough was composed mainly of microbes known to be associated with plants and not living in sourdoughs. No sourdough yeast species were detected on grains and flours. Sourdough lactic acid bacteria were rarely found in flour. When they were, they did not have the same amplicon sequence variant (ASV) as found in the corresponding sourdough. However, the low sequencing depth for bacteria in flour did not allow us to draw definitive conclusion. Thus, our results showed that sourdough yeasts did not come from flour, and suggest that neither do sourdough LAB.

The gut microbiome is one of the most important sites of host-microbe interactions, however, mechanisms governing the responses of host-associated microbes to changing environmental conditions are poorly understood. To address this, we investigated individual and combined effects of dietary changes and increase in salinity (from freshwater to salinity 3) or antibiotic concentration on the gastrointestinal bacterial community of the aquatic snail Ampullaceana balthica. In parallel, the energy reserves of the host were quantified. A change of natural food source to biofilm forming green algae Scenedesmus obliquus as well as the combined treatment of salinity and S. obliquus decreased the richness and changed the composition of the A. balthica gastrointestinal bacterial community. In these treatments Pseudomonas became the dominant bacterium. However, energy reserves of the host were higher in these treatments compared to the reference aquaria specimens and the combined treatment of antibiotics with S. obliquus. The presence of antibiotics inhibited the dominance of Pseudomonas and resulted in lower energy reserves despite S. obliquus feeding. Therefore the host seems to be able to adapt and replace its bacterial community composition to respond to mild changes in salinity and food source. Antibiotics in the water can disturb this self-regulating mechanism. Our study underlines the ability of aquatic macroinvertebrates to respond to sudden changes in food source and mild shifts in salinity. Moreover, it emphasizes the strong impact of the food source on the gastrointestinal microbiome and the importance of generalists during disturbance.

Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.

Synchronous multispecific coral spawning generally occurs annually and forms an integral part of the coral life cycle. Apart from spawning times and species participation, however, much else remains unknown. Here, we applied environmental DNA (eDNA) metabarcoding to study two tropical reef sites of contrasting coral cover before, during and after coral spawning. Using coral-ITS2 and vertebrate-12S markers, we evaluated eDNA as an alternative monitoring tool by assessing its capabilities in detecting spawning species and tracking relative abundances of coral and fish eDNA. Over 3 years, elevated eDNA coral signals during the event (proportional read increase of up to five-fold) were observed, detecting a total of 38 coral and 133 fish species with all but one of the coral species visually observed to be spawning. This is also the first demonstration that eDNA metabarcoding can be used to infer the diurnal partitioning of night- and day-time spawning, spawning in coral species overlooked by visual surveys, and the associated changes in fish trophic structures as an indicator of spawning events. Our study paves the way for applied quantitative eDNA metabarcoding approaches to better study ephemeral and important biological events.

Fusarium head blight (FHB) is a major disease worldwide on cultivated cereals, caused by several Fusarium species. FHB can cause not only yield reduction but also accumulation of mycotoxins in the grain contaminating the food supply. Much of the earlier research has focused on Fusarium pathogenesis, conditions required for disease development and toxin accumulation, and FHB management. However, the Fusarium community composition within the micro-habitat of a single diseased wheat head in the field has had limited investigation. Similarly, the relationship between the Fusarium community structure and mycotoxin accumulation within diseased heads remains unclear. In the present study, we investigated the Fusarium community in diseased heads sampled from different geographical sites in China. Several sites in Shandong province formed a transitional region which contained highly variable profiles of Fusarium OTUs, where a single diseased head could contain more than 10 Fusarium OTUs. Mycotoxin accumulation was independent of geographical properties, however, deoxynivalenol, 15-acetyldeoxynivalenol and zearalenone concentrations showed a significant negative correlation with Fusarium diversity on diseased heads while a significant positive correlation between nivalenol concentration and Fusarium diversity was observed. Taken together, the Fusarium OTU diversity within diseased heads in the field significantly influences mycotoxin accumulation, providing an important point to consider in FHB disease management and mycotoxin research.

Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long-read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small-scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species.