Search for: All records

Abstract PremiseDioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genusAsparagus(Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. MethodsWe use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genusAsparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. ResultsWe estimate that dioecy evolved once or twice approximately 2.78−3.78 million years ago inAsparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. ConclusionsOur findings support previous work implicating a young age and the possibility of two origins of dioecy inAsparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy inAsparagusapproximately 2.78−3.78 million years ago. 

Abstract A phylogenomic analysis of the so far phylogenetically unresolved subfamily Bromelioideae (Bromeliaceae) was performed to infer species relationships as the basis for future taxonomic treatment, stabilization of generic concept, and further analyses of evolution and biogeography of the subfamily. A target‐enrichment approach was chosen, using the Angiosperms353 v.4 kit RNA‐baits and including 86 Bromelioideae species representing previously identified major evolutionary lineages. Phylogenetic analyses were based on 125 target nuclear loci, assembled off‐target plastome as well as mitogenome reads. A Bromelioideae phylogeny with a mostly well‐resolved backbone is provided based on nuclear (194 kbp), plastome (109 kbp), and mitogenome data (34 kbp). For the nuclear markers, a coalescent‐based analysis of single‐locus gene trees was performed as well as a supermatrix analysis of concatenated gene alignments. Nuclear and plastome datasets provide well‐resolved trees, which showed only minor topological incongruences. The mitogenome tree is not sufficiently resolved. A total of 26 well‐supported clades were identified. The generaAechmea,Canistrum,Hohenbergia,Neoregelia, andQuesneliawere revealed polyphyletic. In core Bromelioideae,Acanthostachysis sister to the remainder. Among the 26 recognized clades, 12 correspond with currently employed taxonomic concepts. Hence, the presented phylogenetic framework will serve as an important basis for future taxonomic revisions as well as to better understand the evolutionary drivers and processes in this exciting subfamily. 

PremiseUnderstanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up‐front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages. MethodsWe designed an Orchidaceae target capture bait set for 963 single‐copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae. ResultsBetween 1,518,041 and 87,946,590 paired‐end 150‐base reads were generated for target‐enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set. DiscussionThe Orchidaceae963 kit will enable greater accessibility and utility of next‐generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade. 

PremiseCornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales. MethodsUsing the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae. ResultsWe curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL‐III, a method statistically consistent with the multispecies coalescent model. ConclusionsThe species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae‐Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification ofCornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set. 

Summary Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM.Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought‐stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM.Most time‐of‐day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific.YuccaandBeschorneriahave CAM‐like expression ofPPC2, a copy ofPPCthat has never been shown to be recruited for CAM in angiosperms.Together the physiological and transcriptomic comparison of closely related C₃and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function. 

Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genusSarraceniaL. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis ofSarraceniaestimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring inSarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembledde-novofrom sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history ofSarracenia.