E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus

BACKGROUND

Eucalyptus urophylla × Eucalyptus grandis, an economically important forest tree, provides important raw material for energy and reduces damage to native forests. However, the absence of a high-quality E. urophylla × E. grandis reference genome has significantly hindered its evolution and genetic analysis.

RESULTS

We successfully presented a high-quality reference genome of E. urophylla × E. grandis (545.75 Mb; scaffold N50, 51.62 Mb) using a combination of the Illumina, PacBio HiFi, and Hi-C sequencing platforms. A total of 34,502 genes and 58.56% of the repetitive sequences in this genome were annotated. Using genome evolution analyses, we identified a recent whole-genome duplication (WGD) event in E. urophylla × E. grandis. We further found that gene families associated with starch and sucrose metabolism, flavonoid biosynthesis, and plant-pathogen interaction were significantly expanded in E. urophylla × E. grandis. Moreover, comparative genomic and evolutionary analyses showed large structural variations among the different chromosomes of the 34 Eucalyptus accessions, which were divided into six clades.

CONCLUSIONS

Overall, our findings provide a valuable resource for expanding our understanding of the E. urophylla × E. grandis genome evolution, genetic improvement, and its comparative biology.

A box on the river: The phylogenetics and phylogeography of Eucalyptus baueriana (Eucalyptus sect. Adnataria ser. Heterophloiae)

We present a phylogeographic study of the tree species Eucalyptus baueriana Schauer, which occurs in disjunct areas on the near coastal plains and ranges of the south-east Australian mainland. DArTseq data are used to build a phylogeny including E. baueriana and closely related taxa to test its monophyly, test the genetic distinctness of the three subspecies of E. baueriana, and investigate relationships between its disjunct populations. Additionally, we use population structure analysis to investigate the genetic distinctness of populations, and MaxEnt to investigate the environmental factors potentially influencing the species' distribution. We show E. baueriana is monophyletic and most closely related to three other Blue Box eucalypt species: E. conica H.Deane & Maiden, E. dalveenica T.L.Collins, R.L.Andrew & J.J.Bruhl and E. magnificata L.A.S.Johnson & K.D.Hill, with some evidence for genetic introgression between these taxa. Within E. baueriana, the deepest genetic breaks do not correspond with the subspecies classification as the two geographically restricted subspecies, together with samples of the more widespread E. baueriana subsp. baueriana from west of the Gippsland lowlands, form a south-western clade with that is sister to other populations of subsp. baueriana. The oldest genetic break in the species occurs in far eastern Gippsland (Victoria), corresponding to one of the shortest geographic disjunctions in the species' distribution. Genetic breaks in other species have been observed in this region which is broadly referred to as the southern transition zone. Both total annual rainfall and the seasonality of this rainfall are hypothesised to affect the species' distribution; gaps in its distribution are in areas of higher rainfall that support closed forest and in regions with more winter dominated rainfall.

Horizontal Gene Transfer Phylogenetics: A Random Walk Approach

The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fine systematic resolution, the standard markers are too crude to provide a phylogenetic signal. Nevertheless, among prokaryotes, genome dynamics in the form of horizontal gene transfer (HGT) between organisms and gene loss seem to provide far richer information by affecting both gene order and gene content. The "synteny index" (SI) between a pair of genomes combines these latter two factors, allowing comparison of genomes with unequal gene content, together with order considerations of their common genes. Although this approach is useful for classifying close relatives, no rigorous statistical modeling for it has been suggested. Such modeling is valuable, as it allows observed measures to be transformed into estimates of time periods during evolution, yielding the "additivity" of the measure. To the best of our knowledge, there is no other additivity proof for other gene order/content measures under HGT. Here, we provide a first statistical model and analysis for the SI measure. We model the "gene neighborhood" as a "birth-death-immigration" process affected by the HGT activity over the genome, and analytically relate the HGT rate and time to the expected SI. This model is asymptotic and thus provides accurate results, assuming infinite size genomes. Therefore, we also developed a heuristic model following an "exponential decay" function, accounting for biologically realistic values, which performed well in simulations. Applying this model to 1,133 prokaryotes partitioned to 39 clusters by the rank of genus yields that the average number of genome dynamics events per gene in the phylogenetic depth of genus is around half with significant variability between genera. This result extends and confirms similar results obtained for individual genera in different manners.

Chloroplast genome analysis of box-ironbark Eucalyptus

Eucalyptus L'Hérit. (Myrtaceae) is a taxonomically complex and highly speciose genus that dominates much of Australia's woody vegetation. However, very little information is available about the molecular biology and chloroplast diversity of certain groups, such as Eucalyptus section Adnataria, which is found in many woodland habitats of eastern Australia. We report four new complete chloroplast genomes of Eucalyptus, including three genomes from species previously lacking any chloroplast reference sequences. Plastomes of E. albens, E. conica, E. crebra and E. melliodora assembled using a de novo approach were shown to be largely identical to each other, and similar in size and structure to previously published chloroplast genomes from Eucalyptus. A total of 132 genes (114 single-copy genes and 18 duplicated genes in the IR regions) were identified, and shown to be highly conserved in terms of gene order, content and organization. Slightly higher divergence in the intergenic spacers was identified through comparative genomic analyses. Chloroplast sequences of 35 additional individuals representing 12 species were assembled using a reference guided approach. Rates of nucleotide substitution varied among the protein coding genes, with 17 genes under possible positive selection, and 29 invariant genes. Phylogenetic analysis of either the whole reconstructed plastome sequences or the individual genes revealed extreme discordance with expected species boundaries or higher-level relationships. Plastome relationships were better predicted by geography than by nuclear DNA or taxonomic relationships, suggesting a substantial influence of gene flow over and above the effects of incomplete lineage sorting. These results provide resources for future research and valuable insights into the prevalence of interspecific gene flow among Eucalyptus species.

Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes

PREMISE OF THE STUDY

Philodendron is a large genus of ~560 species and among the most conspicuous epiphytic components of Neotropical forests, yet its phylogenetic relationships, timing of divergence, and diversification history have remained unclear. We present a comprehensive phylogenetic study for Philodendron and investigate its diversification, including divergence-time estimates and diversification rate shift analyses.

METHODS

We performed the largest phylogenetic reconstruction for Philodendron to date, including 125 taxa with a combined dataset of three plastid regions (petD, rpl16, and trnK/matK). We estimated divergence times using Bayesian evolutionary analysis sampling trees and inferred shifts in diversification rates using Bayesian analysis of macroevolutionary mixtures.

KEY RESULTS

We found that Philodendron, its three subgenera, and the closely related genus Adelonema are monophyletic. Within Philodendron subgenus Philodendron, 12 statistically well-supported clades are recognized. The genus Philodendron originated ~25 mya and a diversification rate upshift was detected at the origin of subgenus Philodendron ~12 mya.

CONCLUSIONS

Philodendron is a species-rich Neotropical lineage that diverged from Adelonema during the late Oligocene. Within Philodendron, the three subgenera currently accepted are recovered in two lineages: one contains the subgenera Meconostigma and Pteromischum and the other contains subgenus Philodendron. The lineage containing subgenera Meconostigma and Pteromischum underwent a consistent diversification rate. By contrast, a diversification rate upshift occurred within subgenus Philodendron ~12 mya. This diversification rate upshift is associated with the species radiation of the most speciose subgenus within Philodendron. The sections accepted within subgenus Philodendron are not congruent with the clades recovered. Instead, the clades are geographically defined.

Simulating and Summarizing Sources of Gene Tree Incongruence

We introduce a gene tree simulator that is designed for use in conjunction with approximate Bayesian computation approaches. We show that it can be used to determine the relative importance of hybrid speciation and introgression compared with incomplete lineage sorting (ILS) in producing patterns of incongruence across gene trees. Important features of the new simulator are (1) a choice of models to capture the decreasing probability of successful hybrid species formation or introgression as a function of genetic distance between potential parent species; (2) the ability for hybrid speciation to result in asymmetrical contributions of genetic material from each parent species; (3) the ability to vary the rates of hybrid speciation, introgression, and divergence speciation in different epochs; and (4) incorporation of the coalescent, so that patterns of incongruence due to ILS can be compared with those due to hybrid evolution. Given a set of gene trees generated by the simulator, we calculate a set of statistics, each measuring in a different way the discordance between the gene trees. We show that these statistics can be used to differentiate whether the gene tree discordance was largely due to hybridization, or only due to lineage sorting.

Allopatric diversification, multiple habitat shifts, and hybridization in the evolution of Pericallis (Asteraceae), a Macaronesian endemic genus

PREMISE OF THE STUDY

Geographic isolation, habitat shifts, and hybridization have contributed to the diversification of oceanic island floras. We investigated the contribution of these processes to the diversification of Pericallis, a genus endemic to Macaronesia.

METHODS

Data from the chloroplast psaI-accD and trnV-ndhC regions and the nuclear ribosomal internal transcribed spacer region (ITS) were sampled for multiple accessions of all taxa and used to establish phylogenetic hypotheses. Habitat preferences were optimized to investigate habitat shifts, and divergence times were estimated. Species nonmonophyly was investigated using Bayes factors.

KEY RESULTS

Much of the diversification in Pericallis has occurred recently, within the past 1.7 Ma. Three habitat shifts have occurred in the evolution of the genus. However, geographic isolation has played a greater role in its diversification. Novel allopatric patterns were revealed within some species, highlighting the significance of geographic isolation in the evolution of Pericallis. One species (P. appendiculata) that resolved as monophyletic in the ITS analysis was polyphyletic in the chloroplast analysis. Bayes factors provide strong support for the nonmonophyly of P. appendiculata haplotypes, and their phylogenetic placement suggests that ancient hybridization is responsible for the haplotype diversity observed.

CONCLUSIONS

Multiple markers and extensive sampling provided new insights into the evolution of Pericallis. In contrast to previous studies, our results reveal a more significant role for allopatry than habitat shifts and new evidence for ancient hybridization in the evolution of Pericallis. Our study highlights the power of broad taxon sampling for unraveling diversity patterns and processes within oceanic island radiations.

Phylogenetic responses of forest trees to global change

In a rapidly changing biosphere, approaches to understanding the ecology and evolution of forest species will be critical to predict and mitigate the effects of anthropogenic global change on forest ecosystems. Utilizing 26 forest species in a factorial experiment with two levels each of atmospheric CO₂ and soil nitrogen, we examined the hypothesis that phylogeny would influence plant performance in response to elevated CO₂ and nitrogen fertilization. We found highly idiosyncratic responses at the species level. However, significant, among-genetic lineage responses were present across a molecularly determined phylogeny, indicating that past evolutionary history may have an important role in the response of whole genetic lineages to future global change. These data imply that some genetic lineages will perform well and that others will not, depending upon the environmental context.