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The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE (Binary State Speciation and Extinction) methods. Specifically, our model, which we refer to as HiSSE (Hidden State Speciation and Extinction), assumes that related to each observed state in the model are \"hidden\" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as characterindependent diversification models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.

Background The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry ( Fragaria vesca ) , the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle. Results Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups. Conclusions These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

With increases in both the size and scope of phylogenetic trees, we are afforded a renewed opportunity to address long-standing comparative questions, such as whether particular fruit characters account for much of the variation in diversity among flowering plant clades. Studies to date have reported conflicting results, largely as a consequence of taxonomic scale and a reliance on potentially conservative statistical measures. Here we examine a larger and older angiosperm clade, the Campanulidae, and infer the rates of character transitions among the major fruit types, emphasizing the evolution of the achene fruits that are most frequently observed within the group. Our analyses imply that campanulids likely originated bearing capsules, and that all subsequent fruit diversity was derived from various modifications of this dry fruit type. We also found that the preponderance of lineages bearing achenes is a consequence of not only being a fruit type that is somewhat irreversible once it evolves, but one that also seems to have a positive association with diversification rates. Although these results imply the achene fruit type is a significant correlate of diversity patterns observed across campanulids, we conclude that it remains difficult to confidently and directly view this character state as the actual cause of increased diversification rates.

Fragaria vesca, a diploid woodland strawberry with a small and sequenced genome, is an excellent model for studying fruit development. The strawberry fruit is unique in that the edible flesh is actually enlarged receptacle tissue. The true fruit are the numerous dry achenes dotting the receptacle's surface. Auxin produced from the achene is essential for the receptacle fruit set, a paradigm for studying crosstalk between hormone signaling and development. To investigate the molecular mechanism underlying strawberry fruit set, next-generation sequencing was employed to profile early-stage fruit development with five fruit tissue types and five developmental stages from floral anthesis to enlarged fruits. This two-dimensional data set provides a systems-level view of molecular events with precise spatial and temporal resolution. The data suggest that the endosperm and seed coat may play a more prominent role than the embryo in auxin and gibberellin biosynthesis for fruit set. A model is proposed to illustrate how hormonal signals produced in the endosperm and seed coat coordinate seed, ovary wall, and receptacle fruit development. The comprehensive fruit transcriptome data set provides a wealth of genomic resources for the strawberry and Rosaceae communities as well as unprecedented molecular insight into fruit set and early stage fruit development.

Confectionary sunflower ( Helianthus annuus L.) has gained popularity due to its utilization in roasting as snacks, poultry, bird food, and bakery products. However, seed quality of confectionary sunflower differs from non-oil seed types. In the present study, 71 sunflower accessions were selected for the evaluation of seed quality traits. Significant genetic variability was observed for traits such as 100-seed mass and seed length, as indicated by high genotypic coefficients of variability. Genotypic correlation analysis revealed a positive association between 100-seed mass and seed size, protein content, and oleic acid content. Path coefficient analysis based on genotypic and phenotypic correlations suggested that accessions with high sugar content may be selected to develop superior germplasm for confectionary products. Biplot analysis was conducted to identify suitable accessions with favorable confectionary traits. Accessions ‘Hybrid 100’, ‘GOR101’, and ‘Odesskijj112’ exhibited high sugar content, while ‘Yawn’ demonstrated comparatively higher oleic acid content. Accessions ‘Vinimik 6931’ and ‘HA 305’ displayed high 100-seed mass, while seed length was greater in accessions ‘Comet’ and H.  × multiflorous. Combining ability analysis were performed to assess the breeding value of accessions. ‘Comet’ exhibited the highest general combining ability (GCA) effects for seed yield per plant, head diameter and 100-achene mass; while ‘G.OR.104’ had positive GCA for achene yield per plant but negative combining ability for other traits. ‘Tenissiei’ displayed positive GCA for all traits. Among the testers, accession ‘Universal’ showed positive GCA for seed yield per plant, while ‘HA-292’ exhibited positive GCA for head diameter. The accessions with higher values for confectionary traits and positive general combining ability effects for yield related traits may be further exploited in confectionary sunflower breeding programs as parents.

The critical role of auxin in strawberry fruit set and receptacle enlargement was demonstrated previously. While fertilization is known to trigger auxin biosynthesis, the specific tissue source of fertilization-induced auxin is not well understood. Here, the auxin reporter DR5ver2::GUS was introduced into wild strawberry (Fragaria vesca) to reveal auxin distribution in the seed and fruit receptacle pre- and post-fertilization as well as in the root. In addition, the expression of TAR and YUCCA genes coding for enzymes catalysing the two-step auxin biosynthesis pathway was investigated using their respective promoters fused to the β-glucuronidase (GUS) reporter. Two FveTARs and four FveYUCs were shown to be expressed primarily in the endosperm and embryo inside the achenes as well as in root tips and lateral root primordia. Expression of these reporters in dissected tissues provided more detailed and precise spatial (cell and tissue) and temporal (pre- and post-fertilization) information on where auxin is synthesized and accumulates than previous studies in strawberry. Moreover, we generated CRISPR-mediated knock-out mutants of FveYUC10, the most abundant YUC in seeds; the mutants had a lower free auxin level in young fruit, but displayed no obvious morphological phenotypes. However, overexpression of FveYUC10 resulted in elongated hypocotyls in Arabidopsis caused by elevated auxin level. Overall, the study revealed auxin accumulation in the chalazal seed coat, embryo, receptacle vasculature, root tip, and lateral root primordia and highlighted the endosperm as the main auxin biosynthesis site for fruit set.

Despite the existence of a rich record, fossils of Carex have been largely neglected by neobotanists. Here we present an exhaustive critically commented checklist of the so-far published pre-Pleistocene records ascribed to Carex. We have made every attempt to include all pertinent paleobotanical literature. The extensive collection of the Museum fur Naturkunde (Berlin, Germany) has also been studied. We found that up to 83 names belonging to different Carex groups may be applied to reliable remains, plus another 23 names of doubtful remains. These fossils come from more than 550 sites, mainly from C and E Europe and the Russian Federations. The age of the reliable fossil record ranges from the Eocene to recent times. Problems detected on the taxonomy, age and naming of these fossils are discussed. We hope that this work will stimulate neobotanical and paleobotanical communities to work together on broad-scope systematic projects as this one.

Arsenic (As) is a naturally occurring element that is found in soil, water, and rocks. However, it can also be released into the environment through human activities. Arsenic is considered an environmental hazard because it is toxic to humans and animals and can cause serious health problems. Additionally, As-contaminated soil can limit plant growth and reduce crop yields, leading to economic losses for farmers. So, decreasing metal/metalloid solubility in soil by synthetic and organic amendments leads to better crop productivity on contaminated soils. The current study aimed to evaluate farmyard manure (FYM)-mediated changes in soil arsenic (As) behavior, and subsequent effects on achene yield of sunflower. Treatment plan comprised of two As levels, i.e., As-60 (60 mg kg −1 ) and As-120 (120 mg kg −1 ), four FYM levels (0, 20, 35, and 50 g kg −1 ), three textural types (sandy, loamy and clayey), and replicated thrice. Seven As fractions including water soluble-As (WS-As), labile-As (L-As), calcium-bound As (Ca-As), aluminum-bound As (Al-As), iron-bound As (Fe-As), organic-matter-bound As (OM-As), and residual-As (R-As) were determined which differed significantly ( P ≤ 0.05) with FYM and soil texture. FYM supplementation decreased WS-As, L-As, Ca-As, and Al-As while increased Fe-As, OM-As, and R-As. The immobilizing effect of FYM increased with increasing its rate of application, and maximum effect was found in clayey soil. As speciation in soil also significantly ( P ≤ 0.05) affected by FYM and soil texture, with a reduction in arsenate while increase in arsenite, mono-methyl arsenate, and di-methyl arsenate with increasing the rate of FYM supplementation. Bioaccumulation factor reduced with FYM addition, and highest reduction of 38.65 and 42.13% in sandy, 34.24 and 36.26% in loamy while 29.16 and 35.10% in clayey soils at As-60 and As-120, respectively, by 50 g kg −1 FYM compared with respective As treatments without FYM. As accumulation in plant parts was significantly ( P ≤ 0.05) reduced by FYM with the subsequent improvement in achene yield.

Generic delimitations within the cosmopolitan Carduus-Cirsium group (i.e., \"thistles\") have a long history of taxonomic confusion and debate. We present the most comprehensive molecular phylogeny of the group to date to test generic limits, reconstruct the evolution of pappus type, and elucidate the role of chromosomal evolution. We offer two solutions for the recognition of monophyletic genera: (1) consolidate all taxa into one large genus (Carduus or Cirsium), or (2) recognize each major clade as a genus (Carduus, Cirsium, Eriolepis, Notobasis, Picnomon, Silybum, and Tyrimnus). Under the second proposal, the cryptic genus Eriolepis is segregated from Cirsium, and the African Carduus are included within Cirsium. The best diagnosablemorphological character to delimit the genera is pollen type, which is not practical in field-based application. We caution that prior to implementing either solution, a thorough, comprehensivemorphological analysis of all current members of Cirsium sect. Epitrachys (= genus Eriolepis) be completed. Future morphological studies may find additional achene or leaf surface characters that could be used for practical field identification of the segregate genera. The data show that the plumose pappus state is symplesiomorphic for the group, with one transition to barbellate pappus, likely followed by a reversal to its ancestral state as the group colonized Eurasia. The data are consistent with a North African origin in the region of the Mediterranean and a single colonization event to North America. An ancestral chromosome state of 𝑛 = 17 is hypothesized for the group, and a descending dysploidy series in Carduus is hypothesized to correspond with the aridification of the Mediterranean region. The Carduus-Cirsium group highlights the difficulty of delimiting morphologically similar, cryptic genera.