Phylogeny, Genome Size, and Chromosome Evolution of Asparagales

Asparagales are a diverse monophyletic order that has numerous species (ca. 50% of monocots) including important crop plants such as Allium, Asparagus, and Vanilla, and a host of ornamentals such as irises, hyacinths, and orchids. Historically, Asparagales have been of interest partly because of their fascinating chromosomal evolution. We examine the evolutionary dynamics of Asparagales genomes in an updated phylogenetic framework that combines analyses of seven gene regions (atp1, atpB, matK, ndhF, rbcL, trnL intron, and trnL-F intergenic spacer) for 79 taxa of Asparagales and outgroups. Asparagales genomes are evolutionarily labile for many characters, including chromosome number and genome size. The history and causes of variation in chromosome number and genome size remain unclear, primarily because of the lack of data in small clades in the phylogenetic tree and the lack of comparative genetic maps, apart from Allium and Asparagus. Genomic tools such as bacterial artificial chromosome (BAC) libraries should be developed, as both molecular cytogenetic markers and a source of nuclear genes that can be widely used by evolutionary biologists and plant breeders alike to decipher mechanisms of chromosomal evolution

System of animal husbandry in Seyhan basin and how climate changes affect it

PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS - Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At‐α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At‐β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS - We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole‐genome sequencing projects

Multigene Analyses of Monocot Relationships

We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear I8S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atp1 DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has some bootstrap support, although support for paraphyly of liliids is still only low to moderate (79-82%). Dioscoreales and Pandanales are sister taxa (moderately supported, 87- 92%), and Asparagales are weakly supported (79%) as sister to the commelinids. Analysis of just the four plastid genes reveals that addition of data from the other two genomes contributes to generally better support for most clades, particularly along the spine. A new collection reveals that previous material of Petermannia was misidentified, and now Petermanniaceae should no longer be considered a synonym of Colchicaceae. Arachnitis (Corsiaceae) falls into Liliales, but its exact position is not well supported. Sciaphila (Triuridaceae) falls with Pandanales. Trithuria (Hydatellaceae) falls in Poales near Eriocaulaceae, Mayacaceae, and Xyridaceae, but until a complete set of genes are produced for this taxon, its placement will remain problematic. Within the commelinid clade, Dasypogonaceae are sister to Poales and Arecales sister to the rest of the commelinids, but these relationships are only weakly supported