Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

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The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labor-intensive, and this phenomenon remains understudied. Here, we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms, and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. We also show that the relative abundance of the two structural haplotypes remains constant across multiple samples from a single individual plant, suggesting that the process which maintains equal frequency of the two haplotypes operates rapidly, consistent with the hypothesis that flip-flop recombination mediates chloroplast structural heteroplasmy. Our results suggest that previous claims of differences in chloroplast genome structure between species may need to be revisited.

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The least understood aspects of the nutritional needs of bees are the elemental composition of pollen and the bees' need for a stoichiometrically balanced diet containing the required proportions of nutrients. Reduced plant diversity has been proposed as an indirect factor responsible for the pollinator crisis. We suggest stoichiometric mismatch resulting from a nutritionally unbalanced diet as a potential direct factor. The concentrations and stoichiometric ratios of C, N, S, P, K, Na, Ca, Mg, Fe, Zn, Mn, and Cu were studied in the bodies of honeybees of various castes and sexes and in the nectar and pollen of various plant species. A literature review of the elemental composition of pollen was performed. We identified possible co-limitations of bee growth and development resulting mainly from the scarcity of Na, S, Cu, P and K, and possibly Zn and N, in pollen. Particular castes and sexes face specific limitations. Concentrations of potentially limiting elements in pollen revealed high taxonomic diversity. High floral diversity may be necessary to maintain populations of pollen eaters. Single-species crop plantations, even if these species are rich in nectar and pollen, might limit bee growth and development, not allowing for gathering nutrients in adequate proportions. However, particular plant species may play greater roles than others in balancing honeybee diets. Therefore, we suggest specific plant species that may (1) ensure optimal growth and production of individuals by producing pollen that is exceptionally well balanced stoichiometrically (e.g., clover) or (2) prevent growth and development of honeybees by producing pollen that is extremely unbalanced for bees (e.g., sunflower). Since pollen is generally poor in Na, this element must be supplemented using "dirty water". Nectar cannot supplement the diet with limiting elements. Stoichiometric mismatch should be considered in intervention strategies aimed at improving the nutritional base for bees.

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Temperate grassy woodlands were once the dominant vegetation across many agricultural regions of south-eastern Australia, but most of these are now highly degraded and fragmented. Adequate conservation of these woodlands is dependent on successful ecological restoration; however, ecological barriers often limit ecosystem recovery once degrading processes are removed. To help identify these barriers, we used a state and transition framework to compare topsoils of little-disturbed (reference) and variously degraded remnants of grassy Eucalyptus albens Benth. and E. melliodora Cunn. ex Schauer woodlands. Topsoils of degraded remnants showed a repeated pattern, with the most compacted, most acidic and most depleted topsoils occurring in remnants dominated by Aristida ramosa R.Br. or Austrodanthonia H.P.Linder and Austrostipa scabra (Lindl.) S.W.L.Jacobs & J.Everett; the least compacted and most nutrient rich topsoils in remnants dominated by annual exotics; and generally intermediate topsoils in remnants dominated by Bothriochloa macra (Steud.) S.T.Blake or Austrostipa bigeniculata (Hughes) S.W.L.Jacobs & J.Everett. Surprisingly, topsoils beneath trees in reference sites (supporting Poa sieberiana Spreng.) were similar to topsoils supporting annual exotics for most soil properties. Chemical properties of topsoils from open areas of reference sites [supporting Themeda australis (R.Br.) Stapf] were usually intermediate and similar to Bothriochloa macra and Austrostipa bigeniculata topsoils. The most striking exception to these trends was for soil nitrate, which was extremely low in all reference topsoils and showed a high correlation with annual exotic abundance. We discuss the potential for positive feedbacks between soil nitrogen cycling and understorey composition and the need for intervention to assist possible nitrate-dependent transitions between annual and perennial understorey states. Dominant grasses, trees and annual weed abundance may be useful indicators of soil conditions and could inform selection of target sites, species and techniques for restoration projects.

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Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered 'normal', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be envisioned in which the process could provide intrinsic impetus to speciation.

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