Evolutionary processes from the perspective of flowering time diversity.

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time

Assessing the role of EO in biodiversity monitoring: options for integrating in-situ observations with EO within the context of the EBONE concept

The European Biodiversity Observation Network (EBONE) is a European contribution on terrestrial monitoring to GEO BON, the Group on Earth Observations Biodiversity Observation Network. EBONE’s aims are to develop a system of biodiversity observation at regional, national and European levels by assessing existing approaches in terms of their validity and applicability starting in Europe, then expanding to regions in Africa. The objective of EBONE is to deliver: 1. A sound scientific basis for the production of statistical estimates of stock and change of key indicators; 2. The development of a system for estimating past changes and forecasting and testing policy options and management strategies for threatened ecosystems and species; 3. A proposal for a cost-effective biodiversity monitoring system. There is a consensus that Earth Observation (EO) has a role to play in monitoring biodiversity. With its capacity to observe detailed spatial patterns and variability across large areas at regular intervals, our instinct suggests that EO could deliver the type of spatial and temporal coverage that is beyond reach with in-situ efforts. Furthermore, when considering the emerging networks of in-situ observations, the prospect of enhancing the quality of the information whilst reducing cost through integration is compelling. This report gives a realistic assessment of the role of EO in biodiversity monitoring and the options for integrating in-situ observations with EO within the context of the EBONE concept (cfr. EBONE-ID1.4). The assessment is mainly based on a set of targeted pilot studies. Building on this assessment, the report then presents a series of recommendations on the best options for using EO in an effective, consistent and sustainable biodiversity monitoring scheme. The issues that we faced were many: 1. Integration can be interpreted in different ways. One possible interpretation is: the combined use of independent data sets to deliver a different but improved data set; another is: the use of one data set to complement another dataset. 2. The targeted improvement will vary with stakeholder group: some will seek for more efficiency, others for more reliable estimates (accuracy and/or precision); others for more detail in space and/or time or more of everything. 3. Integration requires a link between the datasets (EO and in-situ). The strength of the link between reflected electromagnetic radiation and the habitats and their biodiversity observed in-situ is function of many variables, for example: the spatial scale of the observations; timing of the observations; the adopted nomenclature for classification; the complexity of the landscape in terms of composition, spatial structure and the physical environment; the habitat and land cover types under consideration. 4. The type of the EO data available varies (function of e.g. budget, size and location of region, cloudiness, national and/or international investment in airborne campaigns or space technology) which determines its capability to deliver the required output. EO and in-situ could be combined in different ways, depending on the type of integration we wanted to achieve and the targeted improvement. We aimed for an improvement in accuracy (i.e. the reduction in error of our indicator estimate calculated for an environmental zone). Furthermore, EO would also provide the spatial patterns for correlated in-situ data. EBONE in its initial development, focused on three main indicators covering: (i) the extent and change of habitats of European interest in the context of a general habitat assessment; (ii) abundance and distribution of selected species (birds, butterflies and plants); and (iii) fragmentation of natural and semi-natural areas. For habitat extent, we decided that it did not matter how in-situ was integrated with EO as long as we could demonstrate that acceptable accuracies could be achieved and the precision could consistently be improved. The nomenclature used to map habitats in-situ was the General Habitat Classification. We considered the following options where the EO and in-situ play different roles: using in-situ samples to re-calibrate a habitat map independently derived from EO; improving the accuracy of in-situ sampled habitat statistics, by post-stratification with correlated EO data; and using in-situ samples to train the classification of EO data into habitat types where the EO data delivers full coverage or a larger number of samples. For some of the above cases we also considered the impact that the sampling strategy employed to deliver the samples would have on the accuracy and precision achieved. Restricted access to European wide species data prevented work on the indicator ‘abundance and distribution of species’. With respect to the indicator ‘fragmentation’, we investigated ways of delivering EO derived measures of habitat patterns that are meaningful to sampled in-situ observations

Evaluating the effects of turf-replacement programs in Los Angeles

Water utilities incentivize turf replacement to promote water conservation, but the effects of such programs have received limited evaluations. In 2014, the Metropolitan Water District of Southern California (MWD) undertook an unprecedented investment to incentive turf replacement throughout Southern California in response to a serious Statewide drought. MWD devoted $350 million to the program, resulting in more than 46,000 rebate payments (25,000 in Los Angeles County) to remove 15.3 million square meters of turf. The program implementation provided a unique opportunity to address research gaps on turf replacement implementation. We analyzed socioeconomic and spatial trends of program participants and assessed landscape changes from turf replacement using a random sample of properties (4% of LA County participants in 2014–16). Specifically, we used a novel and cost-effective approach Google Earth Street View to characterize landscapes in front yards and created a typology of land cover types. Results showed: post-replacement landscapes had a diversity of land cover types – diverse yards with several land cover types, as well as more homogenous yards with a single land cover such as woodchips, bare soil, gravel, and artificial turf. Analysis also indicated some evidence of “neighborhood adoption” effects. We describe the need for longitudinal studies to understand long-term effects of turf replacement and associated water use, and suggest that water utilities should also evaluate results in backyards, which requires site visits. This study provides a novel contribution that can be replicated over space and time to further knowledge of turf replacement program implementations and evaluation

Insights into the role of almond CBF transcription factors in the environmental control of cold acclimation and dormancy break

Dissertation presented to obtain the Ph.D degree in BiologyCold is an important environmental factor that may influence plant survival and productivity. It also plays a crucial role in the seasonal development of perennial plants by regulating the extent of (winter) dormancy and that of vegetative and reproductive growth periods. This aspect is particularly relevant in fruit trees, since it may directly impact fruit production. The Prunus genus includes economically relevant species, and the almond (Prunus dulcis Mill.) stands out for its high range of genetic variability, thus being an interesting model to study specific traits of agricultural interest. Considering that low temperature signalling pathways are still poorly understood in Prunus spp., this study aimed to identify and elucidate, in almonds, the function of members of the C-repeat Binding Factor (CBF) family of transcription factors (TFs) which are known to be relevant in the response to cold. Therefore, two CBF genes (PrdCBF1 and - 2) and their corresponding regulatory regions were cloned and sequenced in this species. Southern-blot analysis and further comparisons to the recently available peach genome revealed that the almond CBF family is composed of at least five members, located in close proximity in chromosome 5. In addition, a mapping analysis suggested an association between PrdCBFs and PrdDehydrin1 (PrdDHN1, a putative CBF target gene, involved in cold acclimation) to recently reported QTLs controlling chilling requirements and blooming time. However, further analyses are necessary to confirm this association.(...)This work was supported by a PhD fellowship (Ref. SFRH/BD/31594/2006) awarded to Pedro Barros, and also through the grant # PEst- OE/EQB/LA0004/2011, both from the Fundação para a Ciência e Tecnologia (FCT)

North Campus Open Space Restoration Project Restoration Plan

This Restoration Plan is the result of a collaborative effort between UCSB’s Cheadle Center for Biological Diversity and Ecological Restoration (CCBER) and a team of consultants lead by Environmental Science Associates (ESA). ESA conducted studies and prepared the design and construction documents for the earthwork to restore the landform of the project site to conditions suitable to support estuarine and transitional habitats, and to restore the South Parcel mesa to topography similar to its historic form. True Nature Design led the design of public access elements and designed the recycled water irrigation system to provide establishment irrigation to the restored native plant communities. Stantec provided civil engineering designs for the structural components of the project public access elements (crossing structures and finished trail surfaces). CCBER designed the plan for the matrix of aquatic, wetland, and upland habitats to be restored to the site, including species selection; planting methods; and habitat features to benefit wildlife. CCBER also lead the development  of the maintenance and monitoring methods and adaptive management strategy.The intent of this Restoration Plan is to describe the methodology for post grading restoration, enhancement, monitoring, and management of native habitats within the North Campus Open Space (NCOS) Restoration Project

CLONING, EXPRESSION ANALYSIS, AND TRANSFORMATION VECTOR CONSTRUCTION OF DAM HOMOLOGS IN PEACH AND POPLAR

Genetic fine mapping and sequencing of the EVG locus in peach [Prunus persica (L.) Batsch] identified six tandem arrayed Dormancy-Associated MADS-box (DAM) genes as candidates for regulating growth cessation and terminal bud formation in the non-dormant evergrowing (evg) mutant. Since the mutant is lacking expression of six genes in the mapped locus, further functional analysis is needed to narrow the list of gene candidates for the non-dormant evg phenotype. Here I report three sets of experiments designed to functionally test DAM genes in peach and their homologs in a model tree, hybrid poplar. First I constructed overexpression and knockdown vectors for the reverse genetic experiments needed to assign DAM gene function in peach via Agrobacterium-mediated transformation of plants. Peach DAM full-length open reading frame (ORF) cDNAs were cloned for construction of overexpression vectors. The 3\u27 UTR sequences of DAM genes, which are gene-specific, were cloned and used for the construction of hairpin-forming inverted repeat cassettes which are known to reduce endogenous gene expression via RNA interference (RNAi). Second, I report results from experiments where I have constructed overexpression and knockdown vectors for putative DAM homologs from a hybrid poplar clone (Populus tremula_alba, INRA 717-1B4). The six peach DAMs are members of the SVP/StMADS11 clade of type-II MADS-box genes and the sequenced P. trichocarpa genome contains eight genes in this clade. However, only six DAM homologs were isolated from the INRA 717-1B4 clone. Full-length ORF cDNAs of these six hybrid poplar homologs of the peach DAM genes were cloned. Overexpression and knockdown vectors were constructed using full-length ORF cDNAs and 3\u27 UTR sequences, respectively, as described above for peach. These vectors were used for Agrobacterium-mediated transformation of the hybrid poplar clone INRA 717-1B4. Putative transgenic plants were obtained for three of the six poplar DAM homologs: PtMADS7, PtMADS26 and PtMADS48. Finally, I measured gene expression of the six PtMADS genes over a six month period from summer to winter solstice in order to find correspondences between the expression patterns of these genes in peach and hybrid poplar. The expression pattern was notably different from that observed in the peach DAMs. This suggests the function of PtMADS in poplar may be different from the DAMs in peach. Additionally, the expression patterns of all of the six PtMADSs genes were very similar, which opens the possibility that these highly similar genes may be functionally redundant. This work is the first to specifically monitor hybrid poplar DAM homolog gene expression through a seasonal transition from active growth through growth cessation, bud set, and endodormancy entrance. The seasonal behavior of the hybrid poplar genes differs dramatically from that of the peach DAMs. The role of these genes in hybrid poplar is possibly divergent from that of peach. The function of the hybrid poplar DAM homologs is currently not known; the overexpression and gene silencing vectors construction in this work is a necessary first step to understand the function of the DAM homologs in hybrid poplar

Kohalike ja invasiivsete röövtoiduliste suurselgrootute elupaigakasutus ja toitumissuhted Läänemere põhjaosas

Väitekirja elektrooniline versioon ei sisalda publikatsiooneRöövtoidulised suurselgrootud, peamiselt vähilaadsed, on rannikumere toitumisvõrgustikes oluliseks lüliks põhjaelustiku ja kalade vahel ning ühtlasi nad reguleerivad väiksemate selgrootute arvukust. Läänemere põhjaosas elas selle rühma esindajaid seni ainult kaks liiki – läänemere krevett (Palaemon adspersus) ja põhjamere garneel (Crangon crangon). Hiljuti lisandusid neile kohalikele liikidele kaks võõrliiki – elegantne krevett (Palaemon elegans) ja rändkrabi (Rhithropanopeus harrisii). Kohalike ja võõrliikidest röövtoiduliste suurselgrootute leviku, elupaigaeelistuste ja toitumise uurimiseks kasutati olemasolevaid põhjaelustiku leviku andmeid, spetsiaalselt uuritavatele liikidele suunatud proovide kogumist loodusest ja laborikatseid, kus rakendati muuhulgas loomade raadiomärgistamist. Võõrliigist kreveti levik oli ulatuslikum kui kohalike krevettide levik. Võõrliik oli kohalike krevettidega võrreldes enam seotud elupaikadega, millele on iseloomulikud etrofeerumise tunnused (kõrge toitainete kontsentratsioon, lühiealiste niitjate vetikate suur hulk). Krevettide toitumisuuringud näitasid, et uuritud Palaemon liikide toitumisintensiivsus ja toidu kooseis ei erinenud. Seega on kohaliku ja võõrkreveti roll rannikumere toiduvõrkudes sarnane, ent võõrliik võib troofilisi suhteid ümber kujundada piirkondades, kus kohalikud krevetid puuduvad. Kõige kitsama elupaigakasutusega oli põhjamere garneel ja Palaemon liikidest oli võõrliigi P. elegans spetsialiseerumise tase mõnevõrra kõrgem kui kohalikul liigil. R. harrisii eelistas põisadruga (Fucus vesiculosus) elupaika mis viitab sellele, et põisadruga elupaik pakub krabile aastaringset stabiilset elupaika ja et mitmekesine põhjakooslus võib saada seetõttu krabidest oluliselt mõjutatud. Doktoritöö tulemused näitasid, et elupaikade iseloom ja seisund mõjutab kohalike ja võõrliikide levikumustreid ning võõrliikidest selgrootute kiskjate saabumine ja kiire levila laienemine Läänemere põhjaosas toovad kaasa täiesti uue ökoloogilise funktsiooni (suuremõõtmeline kiskja) või juba varem regionaalselt esinenud funktsiooni leviku piirkondadesse, kus see varem puudus.Decapod crustaceans, such as crabs and shrimps play an important role in coastal ecosystems as they prey on small benthic invertebrates and at the same time they are an important food item for fishes. Until recently, this group of macroinvertebrates consisted of only a few species in the northern Baltic Sea, including only two species of native shrimps – Crangon crangon and Palaemon adspersus. However, very recently two non-native crustacean predators arrived – the shrimp Palaemon elegans and the crab Rhithropanopeus harrisii. Data from available databases were used together with field sampling and laboratory experiments (incl. radio frequency positioning technology) to describe the geographical distribution, habitat selection, and feeding of native and invasive predatory crustaceans in the coastal areas of the northern Baltic Sea. The distribution of the non-native P. elegans was wider than that of native species. P. elegans was associated with lower salinity, higher concentrations of nutrients and higher proportions of ephemeral filamentous algae, relative to P. adspersus. According to results of the experiment on feeding activity, P. elegans performs a similar role in the coastal food web as the native congener, although it may rearrange trophic interactions and introduce new ecological function in the most eutrophicated areas previously lacking any native shrimp. Among the studied shrimps, C. crangon had the highest habitat specialization. The non-native P. elegans showed slightly higher habitat specialization compared to the native P. adspersus. The invasive crab R. harrisii preferred habitats with bladder wrack where the diverse native community may become heavily impacted by this novel large-bodied predator. This thesis showed that the successful establishment of non-native predatory invertebrates can introduce new ecological functions (large-bodied predators) or considerably strengthen already existed ones, while the heterogeneity of habitats has varying effects on the distribution patterns of native and invasive species

Limitation of grassland productivity by low temperature and seasonality of growth

The productivity of temperate grassland is limited by the response of plants to low temperature, affecting winter persistence and seasonal growth rates. During the winter, the growth of perennial grasses is restricted by a combination of low temperature and the lack of available light, but during early spring low ground temperature is the main limiting factor. Once temperature increases, growth is stimulated, resulting in a peak in growth in spring before growth rates decline later in the season. Growth is not primarily limited by the ability to photosynthesize, but controlled by active regulatory processes that, e.g., enable plants to restrict growth and conserve resources for cold acclimation and winter survival. An insufficient ability to cold acclimate can affect winter persistence, thereby also reducing grassland productivity. While some mechanistic knowledge is available that explains how low temperature limits plant growth, the seasonal mechanisms that promote growth in response to increasing spring temperatures but restrict growth later in the season are only partially understood. Here, we assess the available knowledge of the physiological and signaling processes that determine growth, including hormonal effects, on cellular growth and on carbohydrate metabolism. Using data for grass growth in Ireland, we identify environmental factors that limit growth at different times of the year. Ideas are proposed how developmental factors, e.g., epigenetic changes, can lead to seasonality of the growth response to temperature. We also discuss perspectives for modeling grass growth and breeding to improve grassland productivity in a changing climate

Molecular genetics and physiological analyses of the transition to flowering in winter rapeseed

Understanding the stages of reproductive development and the genetic factors that control this process is essential to optimize yield and produce varieties that are better adapted to the changing climate. A global gene expression profiling of the SAM, accompanied with detailed histological analyses of the stages of meristematic development of winter rapeseed Express617 during floral transition was performed in this study. The aims were to determine the timing of floral transition and to identify gene paralogs that mark each stage of meristem development. Although some previous studies on rapeseed flowering-time included transcriptome analysis (Jones et al., 2018; O'Neill et al., 2019; Shah et al.,2018), such high resolution of physiological and molecular analysis of the floral transition during the course of vernalization was still lacking. The results of this study provide comprehensive insights of cold-driven floral transition in winter rapeseed, and open new avenues for further flowering time and yield related studies. In this work, we showed through histological analysis, that winter rapeseed plants, at a certain developmental age, initiate floral transition in the first five weeks of vernalization. Through transcriptome analysis, we identified the genes that are associated with different stages of the flowering response, and showed that specific paralogs of Bna.SOC1 (Bna.SOC1.A05 and Bna.SOC1.C04-random) and Bna.SPL5 (Bna.SPL5.C05 and Bna.SPL5.A05) are induced during the early events of the floral transition. Moreover, we investigated the age-dependent responsiveness to vernalization and showed that pre-vernalization growth periods affect the timing of the floral transition in winter rapeseed, and that Bna.SOC1 and Bna.SPL5 genes respond to age-related signals downstream of Bna.FLC. The study on genomic variation in flowering time genes, between spring and winter types, uncovered a novel presence/absence variation upstream of Bna.SOC1.A05 that is associated with growth type in rapeseed

Plant Cellular and Molecular Biotechnology: Following Mariotti's Steps

This review is dedicated to the memory of Prof. Domenico Mariotti, who significantly contributed to establishing the Italian research community in Agricultural Genetics and carried out the first experiments of Agrobacterium-mediated plant genetic transformation and regeneration in Italy during the 1980s. Following his scientific interests as guiding principles, this review summarizes the recent advances obtained in plant biotechnology and fundamental research aiming to: (i) Exploit in vitro plant cell and tissue cultures to induce genetic variability and to produce useful metabolites; (ii) gain new insights into the biochemical function of Agrobacterium rhizogenes rol genes and their application to metabolite production, fruit tree transformation, and reverse genetics; (iii) improve genetic transformation in legume species, most of them recalcitrant to regeneration; (iv) untangle the potential of KNOTTED1-like homeobox (KNOX) transcription factors in plant morphogenesis as key regulators of hormonal homeostasis; and (v) elucidate the molecular mechanisms of the transition from juvenility to the adult phase in Prunus tree species