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Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant Tree of Life continues to improve. The intersection of these two research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade". These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis thaliana and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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PREMISE: Flowering plants have evolved a vast array of floral features involved in plant-pollinator interactions. A feature that seemingly increases the chance of pollen transfer is the androgynophore, a stalk-like structure that raises the reproductive organs of the flower. However, little is known about the developmental and genetic basis of this structure despite its presence in multiple, distantly related taxa. Here, we address this gap by investigating Gynandropsis gynandra (Cleomaceae), a species with a prominent androgynophore. METHODS: We combined morphological and anatomical analyses with a comparative transcriptomic study to provide a detailed description of the androgynophore throughout development, examine global gene expression patterns, and identify candidate genes putatively involved in androgynophore elongation. RESULTS: The radially symmetric androgynophore of G. gynandra rapidly lengthens primarily via cell elongation. Despite its structural uniformity, androgynophore development is characterized by complex gene expression patterns including differential expression of floral organ identity genes and genes associated with organ development and growth in Arabidopsis thaliana. CONCLUSIONS: Our morphological characterizations and high-quality transcriptome for G. gynandra suggest that the androgynophore is a novel structure formed via elaboration of both the receptacle and base of reproductive organs because it is structurally like an elongated internode but expresses the genetic repertoire typically associated with the reproductive organs. The drastic increase in cell length and uniform structure elevates the androgynophore as a potentially powerful model for cell elongation.
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Arabidopsis , Magnoliopsida , Flores , Magnoliopsida/genética , Arabidopsis/genética , Perfilación de la Expresión Génica , Transcriptoma , Regulación de la Expresión Génica de las PlantasRESUMEN
PREMISE: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. METHODS: Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. RESULTS: Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-É are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. CONCLUSIONS: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.
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Duplicación de Gen , Magnoliopsida/genética , Evolución Molecular , Genoma , Genoma de Planta/genética , Humanos , Filogenia , PoliploidíaRESUMEN
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-ß 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.
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Evolución Biológica , Resistencia a la Enfermedad/genética , Genes de Plantas , Genoma de Plastidios , Magnoliopsida/genética , Filogenia , Poliploidía , Brassicaceae/química , Brassicaceae/genética , Núcleo Celular , Evolución Molecular , Magnoliopsida/química , Plastidios , Especificidad de la EspecieRESUMEN
Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.
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Brassicaceae/genética , Mariposas Diurnas/genética , Duplicación de Gen , Genoma de los Insectos/genética , Genoma de Planta/genética , Animales , Teorema de Bayes , Biodiversidad , Brassicaceae/clasificación , Brassicaceae/parasitología , Mariposas Diurnas/clasificación , Mariposas Diurnas/fisiología , Evolución Molecular , Expresión Génica , Genes de Insecto/genética , Genes de Plantas/genética , Variación Genética , Interacciones Huésped-Parásitos/genética , Proteínas de Insectos/genética , Filogenia , Proteínas de Plantas/genética , Especificidad de la EspecieRESUMEN
Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice-free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross-species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south-central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.
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Genética de Población , Polimorfismo de Nucleótido Simple , Refugio de Fauna , Ovinos/genética , Animales , Colombia Británica , FilogeniaRESUMEN
Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.
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Brassicaceae/clasificación , Fósiles , África , Américas , Arabidopsis/clasificación , Arabidopsis/genética , Asia , Australia , Teorema de Bayes , Biodiversidad , Brassicaceae/genética , ADN Mitocondrial/aislamiento & purificación , ADN Mitocondrial/metabolismo , ADN de Plantas/aislamiento & purificación , ADN de Plantas/metabolismo , Europa (Continente) , Mitocondrias/genética , Filogenia , Filogeografía , Plastidios/genéticaRESUMEN
The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for minichromosome maintenance1, AGAMOUS, DEFICIENS and serum response factor) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical serine receptor kinase receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.
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Brassicaceae/genética , Evolución Molecular , Genoma de Planta/genética , Carácter Cuantitativo Heredable , Flores/genética , Flores/crecimiento & desarrollo , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Proteínas de Dominio MADS/genética , Proteínas de Dominio MADS/metabolismo , Anotación de Secuencia Molecular , Filogenia , Mapeo Físico de Cromosoma , Poliploidía , Reproducción/genética , Autoincompatibilidad en las Plantas con Flores/genética , Análisis de Secuencia de ADN , Sintenía/genética , Factores de TiempoRESUMEN
Nature is aglow with numerous captivating examples of UV-fluorescence in the animal kingdom. Despite a putative role as a visual signal, exploration of UV-fluorescence in plants and its role in plant-animal interactions is lagging in comparison. Almost 50 years ago, UV-fluorescence of floral nectar, a crucial reward for pollinators, was reported for 23 flowering plant species. Since this intriguing discovery, UV-fluorescent nectar has only seldom been addressed in the scientific literature and has not been scrutinized in a phylogenetic or ecological context. Here, we report the prevalence of vibrant UV-fluorescent floral nectar across the family Cleomaceae, including the first photographic documentation in vivo colour for flowering plants. Though Cleomaceae flowers are morphologically diverse varying in colour, nectary prominence, and nectar volume, UV-fluorescent floral nectar may be a ubiquitous characteristic of the family. Fluorescence spectra show that the identity and number of fluorescent compounds in floral nectar may differ among Cleomaceae species. As Cleomaceae pollinators range from insects to bats and birds, we suggest that the UV-fluorescent floral nectar not only functions as a visual cue for the diurnal pollinators but also for the nocturnal/crepuscular pollinators in low light settings.
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Flores , Néctar de las Plantas , Polinización , Rayos Ultravioleta , Néctar de las Plantas/metabolismo , Fluorescencia , Animales , FilogeniaRESUMEN
That competition is stronger among closely related species and leads to phylogenetic overdispersion is a common assumption in community ecology. However, tests of this assumption are rare and field-based experiments lacking. We tested the relationship between competition, the degree of relatedness, and overdispersion among plants experimentally and using a field survey in a native grassland. Relatedness did not affect competition, nor was competition associated with phylogenetic overdispersion. Further, there was only weak evidence for increased overdispersion at spatial scales where plants are likely to compete. These results challenge traditional theory, but are consistent with recent theories regarding the mechanisms of plant competition and its potential effect on phylogenetic structure. We suggest that specific conditions related to the form of competition and trait conservatism must be met for competition to cause phylogenetic overdispersion. Consequently, overdispersion as a result of competition is likely to be rare in natural communities.
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Filogenia , Poaceae/genética , Poaceae/fisiología , DemografíaRESUMEN
PREMISE OF STUDY: A monophyletic group composed of five genera of the Cleomaceae represents an intriguing lineage with outstanding taxonomic and evolutionary questions. Generic boundaries are poorly defined, and historical hypotheses regarding the evolution of fruit type and phylogenetic relationships provide testable questions. This is the first detailed phylogenetic investigation of all 22 species in this group. We use this phylogenetic framework to assess generic monophyly and test Iltis's evolutionary "reduction series" hypothesis regarding phylogeny and fruit type/seed number. ⢠METHODS: Maximum likelihood and Bayesian analyses of four plastid intergenic spacer region sequences (rpl32-trnL, trnQ-rps16, ycf1-rps15, and psbA-trnH) and one nuclear (ITS) region were used to reconstruct phylogenetic relationships among the NA cleomoid species. Stochastic mapping and ancestral-state reconstruction were used to study the evolution of fruit type. ⢠KEY RESULTS: Both analyses recovered nearly identical phylogenies. Three of the currently recognized genera (Wislizenia, Carsonia, and Oxystylis) are monophyletic while two (Cleomella and Peritoma) are para- or polyphyletic. There was a single origin of the two-seeded schizocarp in the ancestor of the Oxystylis-Wislizenia clade and a secondary derivation of elongated capsule-type fruits in Peritoma from a truncated capsule state in Cleomella. ⢠CONCLUSIONS: Our well-resolved phylogeny supports most of the current species circumscriptions but not current generic circumscriptions. Additionally, our results are inconsistent with Iltis's hypothesis of species with elongated many-seed fruits giving rise to species with truncated few-seeded fruits. Instead, we find support for the reversion to elongated multiseeded fruits from a truncate few-seeded ancestor in Peritoma.
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Magnoliopsida/clasificación , Modelos Biológicos , Filogenia , Cromosomas de las Plantas/genética , Funciones de Verosimilitud , América del Norte , ProbabilidadRESUMEN
Floral nectaries have evolved multiple times and rapidly diversified with the adaptive radiation of animal pollinators. As such, floral nectaries exhibit extraordinary variation in location, size, shape, and secretory mechanism. Despite the intricate ties to pollinator interactions, floral nectaries are often overlooked in morphological and developmental studies. As Cleomaceae exhibits substantial floral diversity, our objective was to describe and compare floral nectaries between and within genera. Floral nectary morphology was assessed through scanning electron microscopy and histology across three developmental stages of nine Cleomaceae species including representatives for seven genera. A modified fast green and safranin O staining protocol was used to yield vibrant sections without highly hazardous chemicals. Cleomaceae floral nectaries are most commonly receptacular, located between the perianth and stamens. The floral nectaries are supplied by vasculature, often contain nectary parenchyma, and have nectarostomata. Despite the shared location, components, and secretory mechanism, the floral nectaries display dramatic diversity in size and shape, ranging from adaxial protrusions or concavities to annular disks. Our data reveal substantive lability in form with both adaxial and annular floral nectaries interspersed across Cleomaceae. Floral nectaries contribute to the vast morphological diversity of Cleomaceae flowers and so are valuable for taxonomic descriptions. Though Cleomaceae floral nectaries are often derived from the receptacle and receptacular nectaries are common across flowering plants, the role of the receptacle in floral evolution and diversification is overlooked and warrants further exploration.
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The dematiaceous hyphomycete genera Cadophora and Phialocephala are anamorphs associated with mollisioid inoperculate discomycetes (Helotiales) and are delineated based on the complexity of the phialide arrangement with members of Cadophora producing solitary phialides and species of Phialocephala producing complex heads of multiple phialides. A third phylogenetically related taxon, Leptodontidium orchidicola, produces mostly indehiscent conidia that may represent non-functional phialides. Morphological characteristics of both sexual and asexual states of these and other fungi in a focal group of helotialean taxa were re-examined, in light of relationships shown by molecular phylogenetic analyses of rDNA ITS sequences, to determine the evolutionary significance of phialide arrangement. The focal species of Phialocephala formed a monophyletic clade, while five of six species of Cadophora including the type were in a separate clade along with L. orchidicola. C. finlandica was placed in a third clade with species of Meliniomyces and Rhizoscyphus. We hypothesized that the ancestral state for species in Cadophora and Phialocephala is the production of sclerotium-like heads of multiple phialides, which has been retained in most species assignable to Phialocephala. A reduction to solitary phialides occurred in the lineage leading to the clade containing most of the Cadophora species. Two possible reductions to non-functional phialides were identified: one in the Meliniomyces-C. finlandica-Chloridium paucisporum clade and another in the L. orchidicola and Mollisia "rhizophila": clade. A reversion to increased phialide complexity might have occurred in the clade containing C. finlandica and Ch. paucisporum. Our data and analyses also show a previously unrecognized relationship between teleomorph and anamorph morphology in that Mollisia species with smaller asci would be expected to have Phialocephala states while those with larger asci would be expected to have Cadophora states. Based on morphology and phylogenetic placement, L. orchidicola and C. hiberna are transferred respectively to Cadophora and Phialocephala.
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Ascomicetos/clasificación , Ascomicetos/ultraestructura , Evolución Biológica , Filogenia , Ascomicetos/genética , Teorema de Bayes , ADN de Hongos/genética , ADN Ribosómico/genética , ADN Espaciador Ribosómico/genética , Funciones de Verosimilitud , Esporas Fúngicas/ultraestructuraRESUMEN
Nectaries are a promising frontier for plant evo-devo research, and are particularly fascinating given their diversity in form, position, and secretion methods across angiosperms. Emerging model systems permit investigations of the molecular basis for nectary development and nectar secretion across a range of taxa, which addresses fundamental questions about underlying parallelisms and convergence. Herein, we explore nectary development and nectar secretion in the emerging model taxa, Cleome violacea (Cleomaceae), which exhibits a prominent adaxial nectary. First, we characterized nectary anatomy and quantified nectar secretion to establish a foundation for quantitative and functional gene experiments. Next, we leveraged RNA-seq to establish gene expression profiles of nectaries across three key stages of development: pre-anthesis, anthesis, and post-fertilization. We then performed functional studies on five genes that were putatively involved in nectary and nectar formation: CvCRABSCLAW (CvCRC), CvAGAMOUS (CvAG), CvSHATTERPROOF (CvSHP), CvSWEET9, and a highly expressed but uncharacterized transcript. These experiments revealed a high degree of functional convergence to homologues from other core Eudicots, especially Arabidopsis. CvCRC, redundantly with CvAG and CvSHP, are required for nectary initiation. Concordantly, CvSWEET9 is essential for nectar formation and secretion, which indicates that the process is eccrine based in C. violacea. While demonstration of conservation is informative to our understanding of nectary evolution, questions remain. For example, it is unknown which genes are downstream of the developmental initiators CvCRC, CvAG, and CvSHP, or what role the TCP gene family plays in nectary initiation in this family. Further to this, we have initiated a characterization of associations between nectaries, yeast, and bacteria, but more research is required beyond establishing their presence. Cleome violacea is an excellent model for continued research into nectary development because of its conspicuous nectaries, short generation time, and close taxonomic distance to Arabidopsis.
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PREMISE OF STUDY: Many angiosperms have fruit morphologies that result in seeds from the same plant having different dispersal capabilities. A prime example is found in the Brassiceae (Brassicaceae), which has many members with segmented or heteroarthrocarpic fruits. Since only 40% of the genera are heteroarthrocarpic, this tribe provides an opportunity to study the evolution of an ecologically significant novelty and its variants. METHODS: We analyzed nuclear (PHYA) and plastid (matK) sequences from 66 accessions using maximum parsimony, maximum likelihood, and Bayesian inference approaches. The evolution of heteroarthrocarpy and its variants was evaluated using maximum parsimony and maximum likelihood ancestral state reconstructions. KEY RESULTS: Although nuclear and plastid phylogenies are incongruent with each other, the following findings are consistent: (1) Cakile, Crambe, Vella, and Zilla lineages are monophyletic; (2) the Nigra lineage is not monophyletic; and (3) within the Cakile clade, Cakile, Didesmus, and Erucaria are paraphyletic. Despite differences in the matK and PHYA topologies at both deep and shallow nodes, similar patterns of morphological evolution emerge. Heteroarthrocarpy, a complex morphological trait, has evolved multiple times across the tribe. Moreover, there are convergent transitions in dehiscence capabilities and fruit disarticulation across the tribe. CONCLUSIONS: We present the first explicit analysis of fruit evolution within the Brassiceae, which exemplifies evolutionary lability. The repeated loss and gain of segment dehiscence and disarticulation suggests conservation in the genetic pathway controlling abscission with differential expression across taxa. This study provides a strong foundation for future studies of mechanisms underlying variation in dispersal capabilities of Brassiceae.
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Evolución Biológica , Brassicaceae/anatomía & histología , Brassicaceae/genética , Frutas/anatomía & histología , Frutas/genética , Secuencia de Bases , Teorema de Bayes , Endorribonucleasas/genética , Frutas/crecimiento & desarrollo , Genes de Plantas/genética , Funciones de Verosimilitud , Nucleotidiltransferasas/genética , Filogenia , Fitocromo A/genética , Dispersión de Semillas/genéticaRESUMEN
PREMISE: Cleomaceae is emerging as a promising family to investigate a wide range of phenomena, such as C4 photosynthesis and floral diversity. However, functional techniques are lacking for elucidating this diversity. Herein, we establish virus-induced gene silencing (VIGS) as a method of generating functional data for Cleome violacea, bolstering Cleomaceae as a model system. METHODS: We leveraged the sister relationship of Cleomaceae and Brassicaceae by using constructs readily available for Arabidopsis thaliana to provide initial information about the feasibility of VIGS in C. violacea. We then developed endogenous constructs to optimize VIGS efficiency and viability for fruit development. RESULTS: PHYTOENE DESATURASE was successfully downregulated in C. violacea using both heterologous and endogenous constructs. The endogenous construct had the highest degree of downregulation, with many plants displaying strong photobleaching. FRUITFULL-treated plants were also successfully downregulated, with a high rate of survival but less effective silencing; only a small percentage of survivors showed a strong phenotype. DISCUSSION: Our optimized VIGS protocol in C. violacea enables functional gene analyses at different developmental stages. Additionally, C. violacea is amenable to heterologous knockdown, which suggests that a first pass using non-endogenous constructs is a possible route to test additional species of Cleomaceae.
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The interpretation of a group's evolutionary history can be altered based on the phylogenetic placement of problematic taxa. Mountain goats (Oreamnos americanus) epitomize a 'rogue taxon' as many placements within the Caprini tribe have been suggested. Using a total evidence approach, we reconstructed the Caprini phylogeny using parsimony, likelihood, and Bayesian methods. Bayesian and likelihood methods placed mountain goats as an independent lineage sister to all Caprini except muskox and goral. Maximum parsimony placed mountain goats in a derived Caprini clade. Closer examination revealed that parsimony analysis failed to integrate over phylogenetic uncertainty. We then tested our mountain goat placement against nine published alternatives using non-parametric tests, and the parametric SOWH test. Non-parametric tests returned ambiguous results, but the SOWH test rejected all alternative hypotheses. Our study represents the first explicit testing of all hypotheses for the placement of mountain goats and supports a relatively basal position for the taxon.
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Evolución Molecular , Filogenia , Rumiantes/genética , Animales , Teorema de Bayes , ADN Mitocondrial/genética , Funciones de Verosimilitud , Modelos Genéticos , Rumiantes/clasificación , Análisis de Secuencia de ADNRESUMEN
Comparative gene expression studies are invaluable for predicting how existing genetic pathways may be modified or redeployed to produce novel and variable phenotypes. Fruits are ecologically important organs because of their impact on plant fitness and seed dispersal, modifications in which results in morphological variation across species. A novel fruit type in the Brassicaceae known as heteroarthrocarpy enables distinct dispersal methods in a single fruit through segmentation via a lateral joint and variable dehiscence at maturity. Given the close relationship to Arabidopsis, species that exhibit heteroarthrocarpy are powerful models to elucidate how differences in gene expression of a fruit patterning pathway may result in novel fruit types. Transcriptomes of distal, joint, and proximal regions from Erucaria erucarioides and Cakile lanceolata were analyzed to elucidate within fruit and between species differences in whole transcriptome, gene ontology, and fruit patterning expression profiles. Whole transcriptome expression profiles vary between fruit regions in patterns that are consistent with fruit anatomy. These transcriptomic variances do not correlate with changes in gene ontology, as they remain generally stable within and between both species. Upstream regulators in the fruit patterning pathway, FILAMENTOUS FLOWER and YABBY3, are expressed in the distal and proximal regions of E. erucarioides, but not in the joint, implicating alterations in the pathway in heteroarthrocarpic fruits. Downstream gene, INDEHISCENT, is significantly upregulated in the abscissing joint region of C. lanceolata, which suggests repurposing of valve margin genes for novel joint disarticulation in an otherwise indehiscent fruit. In summary, these data are consistent with modifications in fruit patterning genes producing heteroarthrocarpic fruits through different components of the pathway relative to other indehiscent, non-heteroarthrocarpic, species within the family. Our understanding of fruit development in Arabidopsis is now extended to atypical siliques within the Brassicaceae, facilitating future studies on seed shattering in important Brassicaceous crops and pernicious weeds.
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Brassicaceae/genética , Frutas/genética , Regulación de la Expresión Génica de las Plantas , Transcriptoma , Brassicaceae/metabolismo , Frutas/metabolismo , Perfilación de la Expresión Génica , Dispersión de las PlantasRESUMEN
Cleomaceae is a diverse group well-suited to addressing fundamental genomic and evolutionary questions as the sister group to Brassicaceae, facilitating transfer of knowledge from the model Arabidopsis thaliana. Phylogenetic and taxonomic revisions provide a framework for examining the evolution of substantive morphological and physiology diversity in Cleomaceae, but not necessarily in Brassicaceae. The investigation of both nested and contrasting whole-genome duplications (WGDs) between Cleomaceae and Brassicaceae allows comparisons of independently duplicated genes and investigation of whether they may be drivers of the observed innovations. Further, a wealth of outstanding genetic research has provided insight into how the important alternative carbon fixation pathway, C4 photosynthesis, has evolved via differential expression of a suite of genes, of which the underlying mechanisms are being elucidated.
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Genoma de Planta/genética , Genómica , Magnoliopsida/genética , Brassicaceae/clasificación , Brassicaceae/genética , Evolución Molecular , Magnoliopsida/clasificación , FilogeniaRESUMEN
Advances in the understanding of floral developmental genetics in model species such as Arabidopsis continue to provide an important foundation for comparative studies in other flowering plants. In particular, floral organ identity genes are the focus of many projects that are addressing both ancient and recent evolutionary questions. Expanded analyses of the evolution of these gene lineages have highlighted the dynamic nature of the gene birth-and-death process, and may have significant implications for the evolution of genetic pathways. Crucial functional studies of floral organ identity genes in diverse taxa are allowing the first real insight into the conservation of gene function, while findings on the genetic control of organ elaboration offer to open up new avenues for investigation. Taken together, these trends show that the field of floral developmental evolution continues to make significant progress towards elucidating the processes that have shaped the evolution of flower development and morphology.