Disparity, diversity, and duplications in the Caryophyllales

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141874/1/nph14772_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141874/2/nph14772.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141874/3/nph14772-sup-0001-SupInfo.pd

Anatomical diversity and evolution of the anthocarp in Nyctaginaceae

Nyctaginaceae are one of the most diverse families in core Caryophyllales. The most diagnostic character of the family is a persistent anthocarp derived from a calyx-like perianth. Anthocarp morphology is highly variable across the family, but its evolution is poorly studied. We investigate anthocarp evolution in Nyctaginaceae through extensive anatomical studies (159 species from 28 genera representing six of seven tribes) and phylogenetic character state reconstructions. We found highly diverse anthocarp anatomy across Nyctaginaceae, with most traits analysed evolving multiple times throughout the family. The representatives of three early-diverging clades of Nyctaginaceae (Leucastereae, Boldoeae and Colignonieae) possess a calyx-like anthocarp with simplified anatomy. The so-called \u27glands\u27 in Nyctagineae and Pisonieae are emergences, whereas wings originate by accrescence of perianth segments, elongation of the ribs and outgrowths (emergences) of anthocarp mesophyll. Anthocarp anatomy can be considered as a generic-level feature in Colignonieae, Pisonieae, Bougainvilleeae and Nyctagineae. The most dramatic transitions from perianth to anthocarp involve the shrivelling and abscission of the upper perianth part and the maintenance of the basal modified perianth portion that originated in the clade comprising Colignonieae and sister clades

Data from: Disparity, diversity, and duplications in the Caryophyllales

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

phylogenetic information

- align.fasta = alignment - align.models = gene regions - align_w_shtest.tre = maximum likelihood tree with SH-like test listed - align_w_shtest_treepl_3samp.tre = maximum likelihood tree with divergence time estimation and 3 minimum samples - raxml_fasttree_sh_boot_all.tre = bootstrap tree set with SH-like test with divergence time estimatio

climate information

bioclimatic climate data for each specie

diversification information

- BS_summ_div.tre = bootstrap results for medusa diversification - ML_summ_div.tre = ML results for medusa diversificatio

Phylogenetic Analysis Of The Plastid Inverted Repeat For 244 Species: Insights Into Deeper-level Angiosperm Relationships From A Long, Slowly Evolving Sequence Region

Recent plastid phylogenomic studies have helped clarify the backbone phylogeny of angiosperms. However, the relatively limited taxon sampling in these studies has precluded strongly supported resolution of some regions of angiosperm phylogeny. Other recent work has suggested that the 25,000-bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently, we aligned all available angiosperm IR sequences to produce a matrix of 24,702 aligned bases for 246 accessions, including 36 new accessions. Maximum likelihood analyses of the complete data set yielded a generally well-supported topology that is highly congruent with those of recent plastid phylogenomic analyses. However, reducing taxon sampling to match a recent 83-gene plastid analysis resulted in significant changes in bootstrap support at some nodes. Notably, IR analyses resolved Pentapetalae into three well-supported clades: (1) superasterids (comprising Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (comprising Vitaceae, Saxifragales, and Rosidae), and (3) Dilleniaceae. These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms and demonstrate the utility of IR data for resolving the deeper levels of angiosperm phylogeny. They also reiterate the importance of carefully considering taxon sampling in phylogenomic studies

The Amborella Genome and the Evolution of Flowering Plants

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications

The <em>Amborella</em> Genome and the Evolution of Flowering Plants

Amborella trichopoda is strongly supported as the single living species of the sister lineage to all other extant flowering plants, providing a unique reference for inferring the genome content and structure of the most recent common ancestor (MRCA) of living angiosperms. Sequencing the Amborella genome, we identified an ancient genome duplication predating angiosperm diversification, without evidence of subsequent, lineage-specific genome duplications. Comparisons between Amborella and other angiosperms facilitated reconstruction of the ancestral angiosperm gene content and gene order in the MRCA of core eudicots. We identify new gene families, gene duplications, and floral protein-protein interactions that first appeared in the ancestral angiosperm. Transposable elements in Amborella are ancient and highly divergent, with no recent transposon radiations. Population genomic analysis across Amborella's native range in New Caledonia reveals a recent genetic bottleneck and geographic structure with conservation implications