Local climate and vernalization requirements explain the latitudinal patterns of flowering initiation in the crop wild relative Linum bienne

Background and Aims: Days to flowering initiation in species with large geographic distributions often correlate with latitude. Latitude reflects climatic gradients, but it is unclear if large-scale differentiation in flowering results from adaptation to local climate, and whether adaptation to local climate could constrain shifts in distribution and colonization of new environments. Methods: In its Western range in Europe, L. bienne populations were surveyed to describe latitudinal patterns of flowering initiation and determine its correlation with the local climate of populations. This was measured under standardized greenhouse conditions, with a vernalization experiment to learn if chilling advances flowering, and with a reciprocal transplant experiment at three sites along the latitudinal gradient, recording flowering at the central site and plant survival in all sites. Also, genetic differentiation of populations along the latitudinal range was studied using microsatellite markers. Key Results: Flowering initiation varied with latitude, with southern populations flowering earlier than northern populations. Latitude also predicted population response to vernalization, with chilling inducing a greater advance of flowering initiation in northern than southern populations. In general, plant survival in the reciprocal transplant experiment decreased with the geographic distance of populations to the experimental site and, at the central site, flowering initiation varied with latitude of origin. However, across experiments, the local climate of populations better predicted the differentiation in flowering initiation and vernalization response than latitude of origin. Finally, the microsatellite data revealed genetic differentiation of populations forming two groups that agree with a Mediterranean and Atlantic lineage. Conclusions: The consistent result across experiments of a latitudinal cline in flowering initiation and in the vernalization response suggests that flowering is under genetic regulation and yet dependent on particular environmental and climatic cues at local scale. However, the genetic differentiation suggests that past population history might influenced the flowering initiation patterns detected.

Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.

Integrated miRNA and transcriptome profiling to explore the molecular determinism of convergent adaptation to corn in two lepidopteran pests of agriculture

Background The degree to which adaptation to same environment is determined by similar molecular mechanisms, is a topic of broad interest in evolutionary biology, as an indicator of evolutionary predictability. We wished to address if adaptation to the same host plant in phytophagous insects involved related gene expression patterns. We compared sRNA-Seq and RNA-Seq data between two pairs of taxa of Ostrinia and Spodoptera frugiperda sharing maize as host-plant. For the latter, we had previously carried out a reciprocal transplant experiment by feeding of the larvae of the Corn strain (Sf-C) and the Rice strain (Sf-R) on corn versus rice and characterized the mRNA and miRNA responses. Results First, we predicted the genes encoding miRNA in Ostrinia nubilalis (On) and O. scapulalis (Os). Respectively 67 and 65 known miRNA genes, as well as 196 and 190 novel ones were predicted with Os genome using sncRNAs extracted from whole larvae feeding on corn or mugwort. In On, a read counts analysis showed that 37 (55.22%) known miRNAs and 19 (9.84%) novel miRNAs were differentially expressed (DE) on mugwort compared to corn (in Os, 25 known miRs (38.46%) and 8 novel ones (4.34%)). Between species on corn, 8 (12.5%) known miRNAs and 8 (6.83%) novel ones were DE while only one novel miRNA showed expression variation between species on mugwort. Gene target prediction led to the identification of 2953 unique target genes in On and 2719 in Os, among which 11.6% (344) were DE when comparing species on corn. 1.8% (54) of On miR targets showed expression variation upon a change of host-plant. We found molecular changes matching convergent phenotype, i.e., a set of nine miRNAs that are regulated either according to the host-plant both in On and Sf-C or between them on the same plant, corn. Among DE miR target genes between taxa, 13.7% shared exactly the same annotation between the two pairs of taxa and had function related to insect host-plant interaction. Conclusion There is some similarity in underlying genetic mechanisms of convergent evolution of two distant Lepidopteran species having adopted corn in their host range, highlighting possible adaptation genes.

Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations

Background Restoration through planting is the dominant strategy to conserve mangrove ecosystems. However, many of the plantations fail to survive. Site and seeding selection matters for planting. The process of afforestation, where individuals were planted in a novel environment, is essentially human-controlled transplanting events. Trying to deepen and expand the understanding of the effects of transplanting on plants, we have performed a seven-year-long reciprocal transplant experiment on Kandelia obovata along a latitudinal gradient. Results Combined phenotypic analyses and next-generation sequencing, we found phenotypic discrepancies among individuals from different populations in the common garden and genetic differentiation among populations. The central population with abundant genetic diversity and high phenotypic plasticity had a wide plantable range. But its biomass was reduced after being transferred to other latitudes. The suppressed expression of lignin biosynthesis genes revealed by RNA-seq was responsible for the biomass reduction. Moreover, using whole-genome bisulfite sequencing, we observed modification of DNA methylation in MADS-box genes that involved in the regulation of flowering time, which might contribute to the adaptation to new environments. Conclusions Taking advantage of classical ecological experiments as well as multi-omics analyses, our work observed morphology differences and genetic differentiation among different populations of K. obovata, offering scientific advice for the development of restoration strategy with long-term efficacy, also explored phenotypic, transcript, and epigenetic responses of plants to transplanting events between latitudes.

Evolutionary Rescue as a Mechanism Allowing a Clonal Grass to Adapt to Novel Climates

Filing gaps in our understanding of species' abilities to adapt to novel climates is a key challenge for predicting future range shifts and biodiversity loss. Key knowledge gaps are related to the potential for evolutionary rescue in response to climate, especially in long-lived clonally reproducing species. We illustrate a novel approach to assess the potential for evolutionary rescue using a combination of reciprocal transplant experiment in the field to assess performance under a changing climate and independent growth chamber assays to assess growth- and physiology-related plant trait maxima and plasticities of the same clones. We use a clonal grass, Festuca rubra, as a model species. We propagated individual clones and used them in a transplant experiment across broad-scale temperature and precipitation gradients, simulating the projected direction of climate change in the region. Independent information on trait maxima and plasticities of the same clones was obtained by cultivating them in four growth chambers representing climate extremes. Plant survival was affected by interaction between plant traits and climate change, with both trait plasticities and maxima being important for adaptation to novel climates. Key traits include plasticity in extravaginal ramets, aboveground biomass, and osmotic potential. The direction of selection in response to a given climatic change detected in this study mostly contradicted the natural trait clines indicating that short-term selection pressure as identified here does not match long-term selection outcomes. Long-lived clonal species exposed to different climatic changes are subjected to consistent selection pressures on key traits, a necessary condition for adaptation to novel conditions. This points to evolutionary rescue as an important mechanism for dealing with climate change in these species. Our experimental approach may be applied also in other model systems broadening our understanding of evolutionary rescue. Such knowledge cannot be easily deduced from observing the existing field clines.

The ecological, genetic and genomic architecture of local adaptation and population differentiation in Boechera stricta

Differential local adaptation restricts gene flow between populations inhabiting distinct environments, resulting in isolation by adaptation. In addition to the statistical inferences of genotype–environment associations, an integrative approach is needed to investigate the effect of local adaptation on population divergence at the ecological, genetic and genomic scale. Here, we combine reciprocal transplant, genome–environment association and QTL mapping to investigate local adaptation in Boechera stricta (Drummond's rockcress). With reciprocal transplant experiment, we found local genetic groups exhibit phenotypic characteristics corresponding to the distinct selection forces from different water availability. At the genetic level, the local allele of a major fitness QTL confers higher and sturdier flowering stalks, maximizing the fecundity fitness component under sufficient water supply, and its genetic variation is associated with precipitation across the landscape. At the genomewide scale, we further showed that multiple loci associated with precipitation are highly differentiated between genetic groups, suggesting that local adaptation has a widespread effect on reducing gene flow. This study provides one of the few comprehensive examples demonstrating how local adaptation facilitates population divergence at the trait, gene and genome level.