Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds”

Jarvis et al. (Research Articles, 12 December 2014, p. 1320) presented molecular clock analyses that suggested that most modern bird orders diverged just after the mass extinction event at the Cretaceous-Paleogene boundary (about 66 million years ago). We demonstrate that this conclusion results from the use of a single inappropriate maximum bound, which effectively precludes the Cretaceous diversification overwhelmingly supported by previous molecular studies.

Assessment of crop insect damage using unmanned aerial systems: A machine learning approach

Agricultural pests are responsible for millions of dollars in crop losses and management costs every year. In order to implement optimal site-specific treatments and reduce control costs, new methods to accurately monitor and assess pest damage need to be investigated. In this paper we explore the combination of unmanned aerial vehicles (UAV), remote sensing and machine learning techniques as a promising technology to address this challenge. The deployment of UAVs as a sensor platform is a rapidly growing field of study for biosecurity and precision agriculture applications. In this experiment, a data collection campaign is performed over a sorghum crop severely damaged by white grubs (Coleoptera: Scarabaeidae). The larvae of these scarab beetles feed on the roots of plants, which in turn impairs root exploration of the soil profile. In the field, crop health status could be classified according to three levels: bare soil where plants were decimated, transition zones of reduced plant density and healthy canopy areas. In this study, we describe the UAV platform deployed to collect high-resolution RGB imagery as well as the image processing pipeline implemented to create an orthoimage. An unsupervised machine learning approach is formulated in order to create a meaningful partition of the image into each of the crop levels. The aim of the approach is to simplify the image analysis step by minimizing user input requirements and avoiding the manual data labeling necessary in supervised learning approaches. The implemented algorithm is based on the K-means clustering algorithm. In order to control high-frequency components present in the feature space, a neighbourhood-oriented parameter is introduced by applying Gaussian convolution kernels prior to K-means. The outcome of this approach is a soft K-means algorithm similar to the EM algorithm for Gaussian mixture models. The results show the algorithm delivers decision boundaries that consistently classify the field into three clusters, one for each crop health level. The methodology presented in this paper represents a venue for further research towards automated crop damage assessments and biosecurity surveillance.

Context-dependency of a complex fruit-frugivore mutualism: temporal variation in crop size and neighborhood effects

The quantity of fruit consumed by dispersers is highly variable among individuals within plant populations. The outcome Of Such selection operated by firugivores has been examined mostly with respect to changing spatial contexts. The influence of varying temporal contexts on frugivore choice, and their possible demographic and evolutionary consequences is poorly understood. We examined if temporal variation in fruit availability across a hierarchy of nested temporal levels (interannual, intraseasonal, 120 h, 24 h) altered frugivore choice for a complex seed dispersal system in dry tropical forests of southern India. The interactions between Phyllanthus emblica and its primary disperser (ruminants) was mediated by another frugivore (a primate),which made large quantities of fruit available on the ground to ruminants. The direction and strength of crop size and neighborhood effects on this interaction varied with changing temporal contexts.Fruit availability was higher in the first of the two study years, and at the start of the season in both years. Fruit persistence on trees,determined by primate foraging, was influenced by crop size andconspecific neighborhood densities only in the high fruit availability year. Fruit removal by ruminants was influenced by crop size in both years and neighborhood densities only in the high availability year. In both years, these effects were stronger at the start of the season.Intraseasonal reduction in fruit availability diminished inequalities in fruit removal by ruminants and the influence of crop size and fruiting neighborhoods. All trees were not equally attractive to frugivores in a P. emblica population at all points of time. Temporal asymmetry in frugivore-mediated selection could reduce potential for co-evolution between firugivores and plants by diluting selective pressures. Inter-dependencies; formed between disparate animal consumers can add additional levels of complexity to plant-frugivore mutualistic networks and have potential reproductive consequences for specific individuals within populations.

Jatkuvasatoisten mansikoiden lannoitus rajoitetussa kasvualustassa

Mansikka (Fragaria × ananassa Duch.) on tärkein Suomessa viljelty marja sekä määrällisesti että taloudellisesti. Suomessa ongelmana on lyhyt satokausi ja matala satotaso. Pääsadon aikaan runsas mansikan tarjonta markkinoilla laskee huomattavasti mansikan hintaa. Paras hinta saadaan normaalin satokauden ulkopuolella. Jatkuvasatoiset mansikkalajikkeet mahdollistaisivat pidemmän ja tasaisen satokauden, mikä vakauttaisi mansikan hintaa. Jatkuvasatoinen mansikka sopii viljelyyn kausihuoneissa korotetuilla kasvualustoilla, jolloin lannoitus ja kastelu hoidetaan tippukastelulla. Jatkuvasatoinen mansikka tuottaa kukkia ja marjoja koko satokauden, mikä vaikuttaa sen ravinnetarpeeseen. Tehdyssä tutkimuksessa testattiin kolmea eri lannoitustasoa 1,5 mS/cm, 2,3mS/cm ja 3,0 mS/cm, joiden N:K –suhde marjojen kypsymisvaiheessa oli 1:1,5. Neljäs käsittely oli kastelu johtokyvyllä 2,3 mS/cm N:K –suhteen ollessa 1:2 marjojen kypsyessä. Tutkimuksessa havainnointiin taimien vegetatiivista kasvua sekä sadon muodostusta ja marjojen laatua. Samalla seurattiin ylivaluntaveden määrää sekä veden mukana huuhtoutunutta fosforia ja typpeä. Tutkimuksessa käytetyt lajikkeet olivat ’Malling Opal’ ja ’Rondo’. Tämän tutkimuksen tulokset tukevat aikaisempia tutkimuksia, että mansikan ravinnetarve on suhteellisen matala. Voimakkain vegetatiivinen kasvu, suurin sato ja suurimmat marjat saatiin alimmalla testatulla johtokyvyllä (1,5 mS/cm). Lannoitustasolla oli hyvin vähän vaikutusta marjan laatuun tai sadon ajoittumiseen. Myöskään N:K – suhteen muutoksella ei ollut vaikutusta marjan laatuun. Taimien veden otto oli suurinta alimmalla lannoitustasolla, ja mahdollisesti kasteluveden korkea ionipitoisuus vaikeutti kasvin veden ottoa korkeilla veden johtokyvyillä. Valumaveden mukana poistuneet typpi- ja fosforipäästöt kasvoivat huomattavasti kasteluveden johtokyvyn noustessa.

Testing the efficacy of a chilli-tobacco rope fence as a deterrent against crop-raiding elephants

Chilli-based repellents have shown promise as deterrents against crop-raiding elephants in Africa. We experimented with ropes coated with chilli-based repellent as a cheap alternative to existing elephant cropraid deterrent methods in India. Three locations (Buxa Tiger Reserve, Wyanad Wildlife Sanctuary and Hosur Forest Division) representing varying rainfall regimes from high to low, and with histories of intense elephant-agriculture conflict, were selected for the experiments that were conducted over 2-3 months during the pre-harvest period of the kharif season in late 2006. Chilli and tobacco powder mixed with waste oil was applied to ropes strung around agricultural fields of 1.4-5.5 km perimeter and elephant approaches were monitored. Elephants breached the rope fences a few times at all three study sites. Female-led herds were far more deterred (practically 100% reduction) than were solitary males (c. 50%) by the chilli-tobacco rope. Efficacy of this method as a deterrent was significantly better in the low-rainfall regime relative to medium and high-rainfall regimes. The initial promising results present a case for more rigorous experimentation; these would help determine if the elephants avoiding the rope are responding physiologically to the chilli-tobacco smell or merely reacting cautiously to a novel substance in their environment.

Ecology of the Asian Elephant in Southern India. II. Feeding Habits and Crop Raiding Patterns

The Asian elephant's foraging strategy in its natural habitat and in cultivation was studied in southern India during 1981-83. Though elephants consumed at least 112 plant species in the study area, about 85% of their diet consisted of only 25 species from the order Malvales and the families Leguminosae, Palmae, Cyperaceae and Gramineae. Alteration between a predominantly browse diet during the dry season with a grass diet during the early wet season was related to the seasonally changing protein content of grasses. Crop raiding, which was sporadic during the dry season, gradually increased with more area being cultivated with the onset of rains. Raiding frequency reached a peak during October-December, with some villages being raided almost every night, when finger millet (Eleusine coracana) was cultivated by most farmers. The monthly frequency of raiding was related to the seasonal movement of elephant herds and to the size of the enclave. Of their total annual food requirement, adult bull elephants derived an estimated 9.3% and family herds 1.7% in quantity from cultivated land. Cultivated cereal and millet crops provided significantly more protein, calcium and sodium than the wild grasses. Ultimately, crop raiding can be thought of as an extension of the elephant's optimal foraging strategy.

Rapsista tuotetun biodieselin ja vehnästä tuotetun bioetanolin energiavirrat ja ympäristövaikutukset Euroopan unionissa

The aim of this thesis was to study the crops currently used for biofuel production from the following aspects: 1. what should be the average yield/ ha to reach an energy balance at least 0 or positive 2. what are the shares of the primary and secondary energy flows in agriculture, transport, processing and usage, and 3. overall effects of biofuel crop cultivation, transport, processing and usage. This thesis concentrated on oilseed rape biodiesel and wheat bioethanol in the European Union, comparing them with competing biofuels, such as corn and sugarcane-based ethanol, and the second generation biofuels. The study was executed by comparing Life Cycle Assessment-studies from the EU-region and by analyzing them thoroughly from the differences viewpoint. The variables were the following: energy ratio, hectare yield (l/ha), impact on greenhouse gas emissions (particularly CO2), energy consumption in crop growing and processing one hectare of a particular crop to biofuel, distribution of energy in processing and effects of the secondary energy flows, like e.g. wheat straw. Processing was found to be the most energy consuming part in the production of biofuels. So if the raw materials will remain the same, the development will happen in processing. First generation biodiesel requires esterification, which consumes approximately one third of the process energy. Around 75% of the energy consumed in manufacturing the first generation wheat-based ethanol is spent in steam and electricity generation. No breakthroughs are in sight in the agricultural sector to achieve significantly higher energy ratios. It was found out that even in ideal conditions the energy ratio of first generation wheat-based ethanol will remain slightly under 2. For oilseed rape-based biodiesel the energy ratios are better, and energy consumption per hectare is lower compared to wheat-based ethanol. But both of these are lower compared to e.g. sugarcane-based ethanol. Also the hectare yield of wheat-based ethanol is significantly lower. Biofuels are in a key position when considering the future of the world’s transport sector. Uncertainties concerning biofuels are, however, several, like the schedule of large scale introduction to consumer markets, technologies used, raw materials and their availability and - maybe the biggest - the real production capacity in relation to the fuel consumption. First generation biofuels have not been the expected answer to environmental problems. Comparisons made show that sugarcane-based ethanol is the most prominent first generation biofuel at the moment, both from energy and environment point of view. Also palmoil-based biodiesel looks promising, although it involves environmental concerns as well. From this point of view the biofuels in this study - wheat-based ethanol and oilseed rape-based biodiesel - are not very competitive options. On the other hand, crops currently used for fuel production in different countries are selected based on several factors, not only based on thier relative general superiority. It is challenging to make long-term forecasts for the biofuel sector, but it can be said that satisfying the world's current and near future traffic fuel consumption with biofuels can only be regarded impossible. This does not mean that biofuels shoud be rejected and their positive aspects ignored, but maybe this reality helps us to put them in perspective. To achieve true environmental benefits through the usage of biofuels there must first be a significant drop both in traffic volumes and overall fuel consumption. Second generation biofuels are coming, but serious questions about their availability and production capacities remain open. Therefore nothing can be taken for granted in this issue, expect the need for development.

Optimal crop planning and conjunctive use of water resources in a coastal river basin

Due to increasing trend of intensive rice cultivation in a coastal river basin, crop planning and groundwater management are imperative for the sustainable agriculture. For effective management, two models have been developed viz. groundwater balance model and optimum cropping and groundwater management model to determine optimum cropping pattern and groundwater allocation from private and government tubewells according to different soil types (saline and non-saline), type of agriculture (rainfed and irrigated) and seasons (monsoon and winter). A groundwater balance model has been developed considering mass balance approach. The components of the groundwater balance considered are recharge from rainfall, irrigated rice and non-rice fields, base flow from rivers and seepage flow from surface drains. In the second phase, a linear programming optimization model is developed for optimal cropping and groundwater management for maximizing the economic returns. The models developed were applied to a portion of coastal river basin in Orissa State, India and optimal cropping pattern for various scenarios of river flow and groundwater availability was obtained.

Development of recombinant coat protein antibody based IC-RT-PCR for detection and discrimination of sugarcane streak mosaic virus isolates from Southern India

Sugarcane streak mosaic virus (SCSMV), causes mosaic disease of sugarcane and is thought to belong to a new undescribed genus in the family Potyviridae. The coat protein (CP) gene from the Andhra Pradesh (AP) isolate of SCSMV (SCSMV AP) was cloned and expressed in Escherichia coli. The recombinant coat protein was used to raise high quality antiserum. The CP antiserum was used to develop an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) based assay for the detection and discrimination of SCSMV isolates in South India. The sequence of the cloned PCR products encoding 3'untranslated region (UTR) and CP regions of the virus isolates from three different locations in South India viz. Tanuku (Coastal Andhra Pradesh), Coimbatore (Tamil Nadu) and Hospet (Karnataka) was compared with that of SCSMV AP The analysis showed that they share 89.4, 89.5 and 90% identity respectively at the nucleotide level. This suggests that the isolates causing mosaic disease of sugarcane in South India are indeed strains of SCSMV In addition, the sensitivity of the IC-RT-PCR was compared with direct antigen coating-enzyme linked immunosorbent assay (DAC-ELISA) and dot-blot immunobinding assays and was found to be more sensitive and hence could be used to detect the presence of virus in sugarcane breeding, germplasm centres and in quarantine programs.