Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

  title={Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms},
  author={Gregory W. Stull and Xiao-Jian Qu and C. Tomomi Parins-Fukuchi and Ying-Ying Yang and Jun-bo Yang and Zhiyun Yang and Yi Hu and Hong Ma and Pamela S. Soltis and Douglas E. Soltis and De‐Zhu Li and Stephen A. Smith and Tingshuang Yi},
  journal={Nature Plants},
  pages={1015 - 1025}
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various… 

Evolution of complex genome architecture in gymnosperms

An overview of the publicly available gymnosperm genome resources is provided and the genomic features most related to changes affecting the whole genome are described, which highlight new realizations relative to repetitive sequence dynamics, paleopolyploidy, and long introns.

Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants

It is confirmed that extant tracheophytes and bryophytes are both highly derived; as a result, understanding the origin of land plants requires tracing character evolution across the diversity of modern lineages.

Compositional shifts associated with major evolutionary transitions in plants

It is demonstrated that many nucleotide and amino acid compositional shifts in plants occur at the origins of major clades and while individual genes do not share the same composition they often shift in the same direction.

Deep reticulation: the long legacy of hybridization in vascular plant evolution.

A critical review of ancient hybridization in vascular plants is provided, outlining well-documented cases ofAncient hybridization across plant phylogeny as well as the challenges unique to documenting ancient vs. recent hybridization.

The Cycas genome and the early evolution of seed plants

The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking, and closes an important gap in understanding of genome structure and evolution in seed plants.

Chinese fir genome and the evolution of gymnosperms

Seed plants comprise angiosperms and gymnosperms. The latter includes gnetophytes, cycads, Ginkgo, and conifers. Conifers are distributed worldwide, with 630 species distributed across eight families

Genomic evidence for homoploid hybrid speciation between ancestors of two different genera

This study highlights the likelihood of an HHS event between ancestors of the extant genera during their initial divergences, which may have led to reticulate phylogenies at higher taxonomic levels.



Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae

It is shown that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts, resulting in an overall high net diversification rates in Brassicaceae.

Early genome duplications in conifers and other seed plants

Analysis of transcriptomes from 24 gymnosperms and 3 outgroups indicates that polyploidy has contributed to the evolution of conifers and other gymnos perms, contrary to previous genomic research that reported an absence of polyploidsy in the ancestry of contemporary gymnOSperms.

Phylogenomic conflict coincides with rapid morphological innovation

It is demonstrated that instances of high gene-tree conflict in mammals, birds, and several major plant clades correspond to rate increases in morphological innovation, and that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypesic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales.

Disparity, diversity, and duplications in the Caryophyllales.

While it is difficult to consider diversification and duplication to be tightly correlated, the findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.

Impact of whole-genome duplication events on diversification rates in angiosperms.

Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD.

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

The results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species.

Evidence for an ancient whole genome duplication in the cycad lineage

Remains of an ancient whole genome duplication in both cycad Encephalartos natalensis and Ginkgo biloba are identified and the most parsimonious explanation would be that this whole genome duplicate event was shared between both species and had occurred prior to their divergence, about 300 million years ago.

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.

Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time, and it is suggested that stochastically changing diversification rates across the phylogeny explain these patterns.

Polyploid incidence and evolution.

New estimates for the incidence of polyploidy in ferns and flowering plants are presented based on a simple model describing transitions between odd and even base chromosome numbers, and it is indicated that ploidy changes may represent from 2 to 4% of speciation events in flowering plants and 7% in f Ferns.