Phylogenetic analysis is complicated by interspecific gene flow and the presence of shared ancestral polymorphisms, particularly those maintained by balancing selection. In this study, we aimed to examine the prevalence of these factors during the diversification of We constructed phylogenetic trees of 29 We identified 45 candidate genes with ancient polymorphisms maintained by balancing selection. These genes were mainly associated with mating compatibility, growth and stress resistance. Both gene flow and selection‐mediated ancient polymorphisms are prevalent in the genus
While flowering plants have diversified in virtually every terrestrial clime, climate constrains the distribution of individual lineages. Overcoming climatic constraints may be associated with diverse evolutionary phenomena including whole genome duplication (WGD), gene‐tree conflict, and life‐history changes. Climatic shifts may also have facilitated increases in flowering plant diversification rates. We investigate climatic shifts in the flowering plant order Ericales, which consists of We estimate phylogenetic trees from transcriptomic data, 64 chloroplast loci, and Angiosperms353 nuclear loci that, respectively, incorporate 147, 4508, and 2870 Ericales species. We use these phylogenetic trees to analyse how climatic shifts are associated with WGD, gene‐tree conflict, life‐history, and diversification rates. Early branches in the phylogenetic trees are extremely short, and have high levels of gene‐tree conflict and at least one WGD. On lineages descended from these early branches, there is a significant association between climatic shifts (primarily out of tropical climates), further WGDs, and life‐history. Extremely short early branches, and their associated gene‐tree conflict and WGDs, appear to underpin the explosive origin of numerous species rich Ericales clades. The evolution of diverse climatic tolerances in these species rich clades is tightly associated with WGD and life‐history.
- PAR ID:
- 10550372
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 244
- Issue:
- 6
- ISSN:
- 0028-646X
- Format(s):
- Medium: X Size: p. 2561-2575
- Size(s):
- p. 2561-2575
- Sponsoring Org:
- National Science Foundation
More Like this
-
Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selectionmore » « less
Summary Populus , a model tree genus in the Northern Hemisphere.Populus taxa using 80 individuals based on re‐sequenced genomes. Our species tree analyses recovered four main clades in the genus based on consensus nuclear phylogenies, but in conflict with the plastome phylogeny. A few interspecific relationships remained unresolved within the multiple‐species clade because of inconsistent gene trees. Our results indicated that gene flow has been widespread within each clade and also occurred among the four clades during their early divergence.Populus . These are potentially important contributors to adaptive variation. Our results provide a framework for the diversification of model tree genus that will facilitate future comparative studies. -
more » « less
Summary The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny.
We utilize fossil data and restriction‐site associated
DNA sequencing (RAD ‐seq) for 632 individuals representing nearly 250Quercus species to infer a time‐calibrated phylogeny of the world's oaks. We use a reversible‐jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among‐clade sampling biases. We then map the > 20 000RAD ‐seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity.
The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
-
more » « less
Abstract Both tree size and life history variation drive forest structure and dynamics, but little is known about how life history frequency changes with size. We used a scaling framework to quantify ontogenetic size variation and assessed patterns of abundance, richness, productivity and light interception across life history strategies from >114,000 trees in a primary, neotropical forest. We classified trees along two life history axes: a
fast–slow axis characterized by a growth–survival trade‐off, and astature–recruitment axis with tall,long‐lived pioneers at one end and short,short‐lived recruiters at the other.Relative abundance, richness, productivity and light interception follow an approximate power law, systematically shifting over an order of magnitude with tree size.
Slow saplings dominate the understorey, butslow trees decline to parity with rapidly growingfast andlong‐lived pioneer species in the canopy.Like the community as a whole,
slow species are the closest to obeying the energy equivalence rule (EER)—with equal productivity per size class—but other life histories strongly increase productivity with tree size. Productivity is fuelled by resources, and the scaling of light interception corresponds to the scaling of productivity across life history strategies, withslow andall species near solar energy equivalence. This points towards a resource‐use corollary to the EER: the resource equivalence rule.Fitness trade‐offs associated with tree size and life history may promote coexistence in tropical forests by limiting niche overlap and reducing fitness differences.
Synthesis . Tree life history strategies describe the different ways trees grow, survive and recruit in the understorey. We show that the proportion of trees with a pioneer life history strategy increases steadily with tree size, as pioneers become relatively more abundant, productive, diverse and capture more resources towards the canopy. Fitness trade‐offs associated with size and life history strategy offer a mechanism for coexistence in tropical forests. -
more » « less
Premise Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.
Methods We used a hierarchical clustering approach, with tree‐based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene‐wise edge‐based analyses, concatenation, and coalescent‐based methods, and is summarized in a consensus framework.
Results Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole‐genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.
Conclusions We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.
-
more » « less
Summary The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing
Phlox , appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation.Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing
Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification.Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species.
Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non‐model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.
