Genomic landscape of the global oak phylogeny.

@article{Hipp2019GenomicLO,
  title={Genomic landscape of the global oak phylogeny.},
  author={A. Hipp and P. Manos and Marlene Hahn and M. Avishai and C. Bod{\'e}n{\`e}s and J. Cavender-Bares and Andrew A Crowl and M. Deng and T. Denk and S. Fitz-Gibbon and O. Gailing and M. Gonz{\'a}lez-Elizondo and A. Gonz{\'a}lez-Rodr{\'i}guez and G. Grimm and Xiao-Long Jiang and A. Kremer and I. Lesur and John D McVay and C. Plomion and Hernando Rodr{\'i}guez-Correa and E. Schulze and M. Simeone and V. Sork and S. Valencia-{\'A}valos},
  journal={The New phytologist},
  year={2019}
}
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 250… Expand
Oaks: an evolutionary success story.
TLDR
Four overarching explanations of evolutionary success in oaks are convergence on: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; propensity for hybridization, contributing to adaptive introgression and facilitating migration. Expand
Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny.
TLDR
The results improve understanding of the pattern and tempo of diversification in Juniperus, and highlight the utility of reduced-representation sequencing for resolving phylogenetic relationships in non-model organisms with reticulation and recent divergence. Expand
Use of Genomic Resources to Assess Adaptive Divergence and Introgression in Oaks
TLDR
Evidence that oak species are genomically coherent entities is reviewed, focusing on sympatric populations with ongoing gene flow, and evidence for and hypotheses regarding genetic mechanisms linking adaptive divergence and reproductive isolation are discussed. Expand
Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks
TLDR
The authors' infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus, and points to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage. Expand
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks
TLDR
A high-quality de novo genome assembly of a California endemic oak, Quercus lobata, reveals features consistent with oak evolutionary success, including subcontext-specific patterns of DNA methylation associated with transposable elements that reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Expand
Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)
TLDR
It is shown, with a new approach based on iterative principal component analysis, that it is not (and will probably never be) possible to homogenize evolutionary rates and GC content for all taxa before phylogenetic inference, and advocates restoring a central role to morphology in the authors' understanding of the evolution of Ficus. Expand
An Updated Infrageneric Classification of the North American Oaks (Quercus Subgenus Quercus): Review of the Contribution of Phylogenomic Data to Biogeography and Species Diversity
The oak flora of North America north of Mexico is both phylogenetically diverse and species-rich, including 92 species placed in five sections of subgenus Quercus, the oak clade centered on theExpand
Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing.
TLDR
Insight is given into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes and a robust phylogenetic framework is recovered and supported Quercus section Ilex as not monophyletic. Expand
Tracking diversity and evolutionary pathways of Lebanese oak taxa through plastome analyses
TLDR
The results confirm the relevance of the Levant region as an important biogeographical crossroad between continents, and its key role in stimulating diversification and preservation of ancient genepools. Expand
A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification
The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperateExpand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 99 REFERENCES
Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America.
TLDR
It is concluded that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species. Expand
A time and a place for everything: phylogenetic history and geography as joint predictors of oak plastome phylogeny.
TLDR
Tipwise attenuation of phylogenetic informativeness in the plastome means that in practical terms, plastite data has little use in solving phylogenetic questions, but can still be a useful barcoding or phylogenetic marker for resolving questions among major clades. Expand
Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity.
TLDR
A highly resolved phylogeny demonstrates sympatric parallel diversification in climatic niche, leaf habit, and diversification rates in the oaks, which has shaped the diversity of North American forests. Expand
Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach
TLDR
A fossil‐calibrated phylogeny of Virentes was generated using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron region of nitrate reductase to examine genetic diversity within species, rates of gene flow among species and ancestral population size of disjunct sister species. Expand
A genetic legacy of introgression confounds phylogeny and biogeography in oaks
TLDR
It is demonstrated how divergence and reticulation both influence the understanding of the timing and nature of diversification and global colonization in these ecologically and economically important taxa. Expand
A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
TLDR
This study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old clade of oaks, and introduces a partitioned RAD visualization method to investigate the possibility that suboptimal topologies supported by large numbers of loci—due to reticulate evolution or lineage sorting—are masked by the globally optimal tree. Expand
Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus).
TLDR
The approach proved successful in detecting the genomic signature of ancient introgression and infer the divergent phylogenetic topology for the white oak clade, highlighting the importance of sampling and the use of a plurality of analytical tools and methods to sufficiently explore genomic datasets, uncover this signal, and accurately infer evolutionary history. Expand
RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercus sect. Quercus: Fagaceae)
TLDR
Thousands of SNPs generated by RAD sequencing are used to describe the phylogeny of a set of sympatric white oak species in California and then test whether these species exhibit pervasive interspecific gene exchange, finding that introgression is not equally pervasive between sympatrics tree and scrub oak species. Expand
Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus).
TLDR
The results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q.—tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits. Expand
Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia.
TLDR
Biogeographical reconstructions indicate that the wide northern hemisphere distribution of Quercus was disrupted in the Late Eocene, leading to the main extant groups at about 33 Ma, highlighting the importance of climatic changes and Indo-Eurasian collision-induced tectonic activities from the Neogene onward to the spatial-temporal diversification patterns of Asian EBLF lineages. Expand
...
1
2
3
4
5
...