The oak syngameon Cannon, Charles H.; Petit, Rémy J.
New phytologist,
20/May , Letnik:
226, Številka:
4
Journal Article
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One of Anthropocene’s most daunting challenges for conservation biology is habitat extinction, caused by rapid global change. Tree diversity has persisted through previous episodes of rapid change, ...even global extinctions. Given the pace of current change, our management of extant diversity needs to facilitate and even enhance the natural ability of trees to adapt and diversify. Numerous processes contribute to this evolutionary flexibility, including introgression, a widespread yet under-studied process. Reproductive networks, in which species remain distinct despite interspecific gene flow, are called syngameons, a concept largely inspired from work focusing on Quercus. Delineating and analyzing such species groups, empirically and theoretically, will provide insights into the nonadditive effects on evolution of numerous partially interfertile species exchanging genetic material episodically under changing environmental conditions. To conserve tree diversity, crossing experiments designed with an empirical and theoretical understanding of the constituent syngameon should be set up to assist diversification and adaptation in the Anthropocene. Our increasingly detailed knowledge of the oak genome and of oak interspecific and intraspecific phenotypic variation will improve our ability to sustain the diversity of this tree through an unpredictable and unprecedented future.
Speciation is often portrayed as an “incomplete” or “incipient” process if two groups of organisms, technically distinguishable either by morphology or genetics, can exchange genes. The ultimate ...outcome of diversification, given this perspective, is complete reproductive isolation. But an increasing amount of evidence suggests that speciation is rarely complete and inter‐fertility between different taxonomically accepted species is consistently maintained. In this issue of Molecular Ecology, Linan et al. (2021) provide results that bridge evolutionary processes from populations to phylogenies that indicate suites of closely related tree species in the Mascarene Islands actively exchange genes, evolving as a nested set of syngameons with a hierarchical pattern of interfertility. The deep insight into diversification provided by this study is particularly powerful because of the genomic scale of the data and the complete taxonomic sampling of an island clade evolving in situ. The prevalence of syngameon dynamics in a broad range of organisms indicates that we should adopt a fluid and comprehensive approach to defining evolutionary units for conservation and research. We should move beyond focusing on single endangered species in evolutionary and ecological isolation from other species but consider the entire network of potentially interfertile species and the potential for future adaptation and innovation, particularly in a human dominated world.
Trees in the beech or oak family (Fagaceae) have a mutualistic relationship with scatter-hoarding rodents. Rodents obtain nutrients and energy by consuming seeds, while providing seed dispersal for ...the tree by allowing some cached seeds to germinate. Seed predation and caching behavior of rodents is primarily affected by seed size, mechanical protection, macronutrient content, and chemical antifeedants. To enhance seed dispersal, trees must optimize trade-offs in investment between macronutrients and antifeedants. Here, we examine this important chemical balance in the seeds of tropical stone oak species with two substantially different fruit morphologies. These two distinct fruit morphologies in Lithocarpus differ in the degree of mechanical protection of the seed. For 'acorn' fruit, a thin exocarp forms a shell around the seed while for 'enclosed receptacle' (ER) fruit, the seed is embedded in a woody receptacle. We compared the chemical composition of numerous macronutrient and antifeedant in seeds from several Lithocarpus species, focusing on two pairs of sympatric species with different fruit morphologies. We found that macronutrients, particularly total non-structural carbohydrate, was more concentrated in seeds of ER fruits while antifeedants, primarily fibers, were more concentrated in seeds of acorn fruits. The trade-off in these two major chemical components was more evident between the two sympatric lowland species than between two highland species. Surprisingly, no significant difference in overall tannin concentrations in the seeds was observed between the two fruit morphologies. Instead, the major trade-off between macronutrients and antifeedants involved indigestible fibers. Future studies of this complex mutualism should carefully consider the role of indigestible fibers in the foraging behavior of scatter-hoarding rodents.
Ancient trees contribute multifaceted ecosystem benefits to old-growth forests, rewilding, and human cultural landscapes. As such, we call for international efforts to preserve these hubs of ...diversity and resilience. A global coalition utilizing advanced technologies and community scientists to discover, protect, and propagate ancient trees is needed before they disappear.
Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), ...provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp. Using five sympatric dioecious fig taxa and their pollinators, we examine the degree of pollinator sharing and inter-taxa gene flow. We experimentally test pollinator preference for floral volatiles, the main host recognition signal, from different figs. All five fig taxa shared pollinators with other taxa, and gene flow occurred between fig taxa within and between sections. Floral volatiles of each taxon attracted more than one pollinator species. Floral volatiles were more similar between closely related figs, which experienced higher levels of pollinator sharing and inter-taxa gene flow. This study demonstrates that pollinator sharing and inter-taxa gene flow occurs among closely related sympatric dioecious fig taxa and that pollinators choose the floral volatiles of multiple fig taxa. The implications of pollinator sharing and inter-taxa gene flow on diversification, occurring even in this highly specialized obligate pollination system, require further study.
Two fruit types can be distinguished among stone oaks (Lithocarpus) species: the 'acorn' (AC) and the 'enclosed receptacle' (ER) types. Our morphometric analysis of 595 nuts from 98 species (one ...third of all Lithocarpus spp.) found substantial transition in mechanical protection of the seed between two woody fruit tissues (exocarp and receptacle) of two fruit types. AC fruits were smaller in seed and fruit size and the thin brittle exocarp largely enclosed the seed, whereas ER fruits were larger and the seed was mostly enclosed by thick woody receptacle tissue. The differences in these two tissues were considerably greater between compared to within fruit type and species. Geospatial distribution showed that seed size of all examined species increased with elevation and decreased with latitude, the physical defense increased with both elevation and latitude, and ER-fruit species were more common at higher elevation. The two fruit types represent distinct suites of associated traits that respond differently to the various biotic and abiotic factors associated with geographic variation, profoundly impacting the evolution of the two fruit types. The co-occurrence of two fruit types in the same forest could be a consequence of distinct fruit and animal interactions.
The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.
In this paper, we demonstrate that ...constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer.
We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.
Next-generation sequencing technologies are rapidly generating whole-genome datasets for an increasing number of organisms. However, phylogenetic reconstruction of genomic data remains difficult ...because de novo assembly for non-model genomes and multi-genome alignment are challenging.
To greatly simplify the analysis, we present an Assembly and Alignment-Free (AAF) method ( https://sourceforge.net/projects/aaf-phylogeny ) that constructs phylogenies directly from unassembled genome sequence data, bypassing both genome assembly and alignment. Using mathematical calculations, models of sequence evolution, and simulated sequencing of published genomes, we address both evolutionary and sampling issues caused by direct reconstruction, including homoplasy, sequencing errors, and incomplete sequencing coverage. From these results, we calculate the statistical properties of the pairwise distances between genomes, allowing us to optimize parameter selection and perform bootstrapping. As a test case with real data, we successfully reconstructed the phylogeny of 12 mammals using raw sequencing reads. We also applied AAF to 21 tropical tree genome datasets with low coverage to demonstrate its effectiveness on non-model organisms.
Our AAF method opens up phylogenomics for species without an appropriate reference genome or high sequence coverage, and rapidly creates a phylogenetic framework for further analysis of genome structure and diversity among non-model organisms.
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