Disparity, diversity, and duplications in the Caryophyllales
2017/09/11 by Stephen A. Smith, Joseph W. Brown, Ya Yang +8 · 94 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Biology #Chromosomal and Genetic Variations #Clade #Diversification (marketing strategy) #Evolutionary biology #Extant taxon #Gene #Genetic diversity and population structure #Genetics #Genomics and Phylogenetic Studies #Lineage (genetic) #Phylogenetics
paper · pdf · doi:10.1111/nph.14772
published in New Phytologist 217(2), 836-854 (Wiley)
openalex publication_date 2017/09/11 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
Abstract
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically mapped putative WGDs as identified from analyses on transcriptomic and genomic data and analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Of these, four WGDs were concurrent with diversification shifts, with other diversification shifts occurring at more recent nodes than WGDs. Five WGDs were associated with shifts to colder climatic occupancy. While we find that many diversification shifts occur after WGDs, it is difficult to consider diversification and duplication to be tightly correlated. Our findings suggest that duplications may often occur along with shifts in either diversification rate, climatic occupancy, or rate of evolution.
Citations
Cited by
- Evolutionary origins, macroevolutionary dynamics, and climatic niche space of the succulent plant syndrome in the Caryophyllales
- Pollinator, herbivore, and climatic selective pressures differ across a floral color transition zone
- Deep reticulation: the long legacy of hybridization in vascular plant evolution
- Traditional medicinal use is linked with apparency, not specialized metabolite profiles in the order Caryophyllales
- The link between ancient whole‐genome duplications and cold adaptations in the Caryophyllaceae
- Evaluating the African arid corridor hypothesis: A meta‐analysis including the phylogenetic and biogeographical history of Sesamothamnus
- Plastome evolution in the Caesalpinia group (Caesalpinioideae, Fabaceae): Comparative genomics reveals genome dynamics, phylogenetic insights and adaptive evolution
- Investigating historical drivers of latitudinal gradients in polyploid plant biogeography: A multiclade perspective
- Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales
- Polyploidy linked with species richness but not diversification rates or niche breadth in Australian Pomaderreae (Rhamnaceae)
- Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
- On the Origin of Carnivory: Molecular Physiology and Evolution of Plants on an Animal Diet
- Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships
- Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms
- Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy
- Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms
- Phylotranscriptomic Analyses Reveal Asymmetrical Gene Duplication Dynamics and Signatures of Ancient Polyploidy in Mints. [europepmc]
- Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions. [europepmc]
- Genomes of the Venus Flytrap and Close Relatives Unveil the Roots of Plant Carnivory. [europepmc]
- Linking the evolution of development of stem vascular system in Nyctaginaceae and its correlation to habit and species diversification. [europepmc]
- Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution. [europepmc]
- Trends in the evolution of intronless genes in Poaceae . [europepmc]
- Phylogenetic analysis and temporal diversification of the tribe Alsineae (Caryophyllaceae) with the description of three new genera, Hesperostellaria , Reniostellaria and Torreyostellaria . [europepmc]
- A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum. [europepmc]
- Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline. [europepmc]
- Repeated shifts out of tropical climates preceded by whole genome duplication. [europepmc]
- The Role of Plant Evolutionary History in Shaping the Variation in Specific Leaf Area Across China. [europepmc]
- Evaluating the African arid corridor hypothesis: A meta-analysis including the phylogenetic and biogeographical history of Sesamothamnus. [europepmc]
Related