The seeds from Berenike and Shenshef are small in size. Because they were retrieved in small numbers from trash deposits, their identification to the level of subspecies is, however, not possible. Although they may belong to the microsperma group, it is also possible that we are dealing with the small specimens of macrosperma group that passed through the sieves during cleaning of the seeds prior to cooking.In many samples, from both Berenike and Shenshef, large quantities of bulb-coat leaves were found of a yet-unidentified plant species. These large quantities suggest that it was a valued food plant and that they must have been available on a regular scale. So far, only one intact specimen has been found. The size of the bulbs is relatively small, not exceeding 1 cm in length. The bulbs either belong to species that have increase bulbs , produced by the subterranean bulb, or to species, which produce bulbils in the inflorescence instead of the flowers. They could also belong to species that produce only small bulbs. It is plausible that we are dealing with a species of the genus Allium. Some species within this genus, such as the great-head garlic , can produce numerous bulbils, which is true for the Egyptian specimens in particular . The morphology and the anatomy of the bulbils from this onion species do not match, however, with the sub-fossil specimens.Like lentil, fl ax also belongs to the first group of crops that were domesticated in the Fertile Crescent. Flax holds a special position because it is not only grown as a food crop, but it is also exploited for its fibers. Today, fl ax is grown either for its seeds or for its fibers. Seed-yielding plants usually have short,10 plastic plant pots branched stems and produce large seeds, whereas fiber fl ax has taller, unbranched stems and produces smaller seeds .

The seeds are nutritious and contain 30 to 48 percent oil and 20 to 30 percent protein. Whole seeds can be used for garnishing loaves . Seeds can also be used as a source of vegetable oil and for making fl our. Linseed oil is obtained by cold pressing and can be used as cooking oil. The ancient Egyptians also used linseed oil for embalming bodies. Pounded linseed can be mixed with, for example, pulses and cereals. Pliny describes the making of barley porridge in which ground barley is mixed with pounded roasted coriander , salt, and linseed. In present-day Ethiopia, fl ax seeds are only used for making a stew called wot, which is a combination of pounded roasted linseed and pulses . Additionally, linseed was also used for all kinds of medical purposes. Pliny , for example, states that linseed together with ammi taken in wine is good for wounds caused by scorpions, creatures that have been frequently found during the excavations at Berenike. Today, linseed is still sold in spice markets for the treatment of abscesses and coughs . The fibers are extracted from the stem by a special procedure, which includes the bacterial breakdown of the softer tissue in stagnant water during a period of about 8 to 10 days. This is known as retting, a process in which the cellulose fibers become separated from each other. Flax fibers are the source of linen, which was used, among other things, for making dresses and sails. According to Pliny , sieves and meal sifters were made from fl ax fibers in Spain, whereas those in ancient Egypt were made from papyrus and rush . The use of flax as a source of fibers cannot be reconciled with the presence of fl ax seeds and a fruit fragment at Berenike and Shenshef. To produce fibers, much fresh water is needed for retting the stems, an essential step in the production process. This is not a problem in the Nile Valley, but is out of the question in desert settlements. The most likely explanation for its presence at Berenike and Shenshef is that the fl ax seeds were used in cooking, and possibly for oil extraction, and that they were traded.

The latter option is sustained by Pliny , who states that the disadvantage of growing fl ax, as it damages the land, is compensated in Egypt by the fact that it is used there in exchange for import items from Arabia and India. It is not clear from Pliny’s description whether fibers or seeds are meant. The Periplus Maris Erythraei makes no reference to the trade of fl ax. Judging by the water requirements on which fl ax cultivation relies, the Arabian Peninsula seems to be the most likely area to which it was exported. In trench BE96-14, a so-called twin-seed was found. Such double seeds stick together ventrally and originate from the same carpel. Twin-seeds are described from several samples collected in Ethiopia, including a sample from the Axum market . In most of these samples, twins-seeds were only sparsely present. A few samples from Haik , however, consisted predominantly of such twin-seeds. Twin-seeds of these samples were sown in an experimental field plot at Wageningen University , and those from Haik produced invariably plants with twin-seeds, indicating that this phenomenon is genetically determined.White lupin originates from the Mediterranean area. Its wild progenitor, now classified as Lupinus albus ssp. graecus Franco Silva, is native to the Aegean region . Apart from a single record from Pompeii, all other finds are recorded from Egypt. The first introduction into Egypt is, however, somewhat disputable. With the exception of a find in Dra Abu el-Naga from the Twenty second Dynasty , all other records are dated to the Roman period or later . White lupin is still a popular legume in Egypt. Almost all legumes are capable of fixing atmospheric nitrogen in their roots in association with bacteria of the genus Rhizobium. A precondition is, however, that the particular rhizobial strain is present in the soil. Owing to this capability of fixing nitrogen, legumes are considered natural fertilizers and can grow in poor soils. The ancient Greeks were already familiar with this phenomenon, and it has been explicitly mentioned for white lupin, among some other legumes, by Cato .

Seeds of white lupin have a relatively high oil content of 11 to 18 percent and also a high protein content of up to 45 percent . Up until the 1920s, when a sweet alkaloid-free type became available, the steeping or boiling of white lupin seeds was necessary before consumption. According to Dalby , this pulse was not considered a high standard food in the Greek diet. White lupin can be fed to animals, but the presence of the bitter alkaloid may cause the disease lupinosis in sheep and horses, especially when these animals consume large concentrations. Seeds of the white lupin are also recommended by Pliny for the treatment of stomach disorders. Even at present-day markets in Egypt, white lupins are sold for medical purposes, such as skin inflammations, acne, diabetes, and liver complaints . The white lupin has been regularly found at Berenike and Shenshef. There is a marked contrast between whole seeds, which are perfectly preserved but are only seldom found, and damaged seeds, from which a reasonable number of seed-coat fragments are preserved. This difference in frequency can be explained by the way the seeds are eaten. After having been soaked in water,plastic pots large the seeds are cooked and eaten as a snack in which the soft content is sucked out and the leathery seed coats are discarded. Possibly, damaged seeds are less resistant to decay. Because of the unfavorable preservation of the broken seeds, it is possible that the white lupin is underrepresented in the archaeobotanical record. The white lupin was probably imported from the Nile Valley.The primary center of origin of the apple is located in parts of temperate Asia, its real center of origin however is obscured by the many existing varieties of both wild and cultivated apples. Even today, hybridization between wild and cultivated apples still occurs. The apple tree is adapted to cooler temperate climates as a chilling phase is necessary to break bud dormancy so that branches can produce their flowers . In present Egypt, apples are cultivated in the Marsah Matruh, located in the western Mediterranean coastal zone and are among the fruit crops in Egypt whose productivity is increasing . Apples can be propagated by seeds, as is the case with wild apples, or by vegetative reproduction attained by grafting or budding, which is common practice with cultivated races. The advantage of vegetative reproduction is twofold: the life cycle of new trees is shortened, and established features are no longer affected by recombination. The technique of vegetative propagation was already known in classical times. Theophrastus , for example, points out that apples, among some other fruit trees, can be best propagated by root suckers, whereas those raised from seeds will only produce inferior fruits. The presence of some pips at Berenike demonstrates the appreciation of this fruit, which most probably must have been imported from the Mediterranean area.

The only other archaeobotanical record of apple, mentioned as M. sylvestris Mill, is from Greek-Roman Douch in the Kharga Oasis , where leafy branches, a core fragment, and a pip were found .Persea is a member of the Sapotaceae, a plant family that has a pantropical distribution and is not represented in Egypt today. Persea is a tall tree adapted to arid conditions and is especially found on rocky slopes. It is native to Yemen, Saudi Arabia, Ethiopia, and adjacent parts of Somalia, but is also widely cultivated outside this area including Egypt . The oval greenish berries of the persea tree are about 3 to 4 cm long, have a sweet taste, and contain large inedible seeds. Theophrastus gives a description of the persea tree which makes sense in most of its details , including that it is fruit bearing in Egypt but has only flowers in Rhodes , which has a Mediterranean climate. According to Theophrastus, the persea tree is abundant in Thebes . His statement that the persea, together with the sycamore fig , the acacia, the sugar date , and some others trees are peculiar to Egypt , is certainly not true. The impressive archaeobotanical record of persea is restricted to Egypt. The first records date back to the Third Dynasty and comprise seeds and leaves made into garlands, in particular. It is noticed by Hepper that the folded leaves indicate that the tree once grew in Egypt as such folding is only possible when the leathery leaves are still fresh. Whole fruits were found in Tutankhamen’s tomb . Until recently, some trees planted by Schweinfurth were still present in the garden of the Agricultural Museum in Cairo , and currently its presence in the garden of the Egyptian museum could be demonstrated by Germer . The persea fruits could have been obtained from the Nile Valley or from Adulis or Avalitês , Muza on the coast of Yemen, or the far-side ports along the Somalian coast.The bentree belongs to the Moringaceae, a plant family related to the legume family . This tree is found in Israel northward up to the Jordan Valley, in tropical northeast Africa, and in parts of the Arabian Peninsula . In Egypt, the bentree grows in upstream wadis of the Red Sea mountains and in the mountains of the Sinai. In these areas, the bentree is restricted to the foothills of mountains higher than 1,300 m, especially if they are located more inland. Although the xerophytic trees have a low water requirement, they are only assured of sufficient supply of atmospheric water if they grow in the vicinity of such high mountains. The trees are quite common between Hurghada and Quseir and are also recorded from the Gebel Nugrus, about 130 km northwest of Berenike. South of Berenike, they are recorded from the Gebel Elba . The tree produces pendulous fruits up to 30 cm long, which contain a row of triangular seeds. The benseeds are highly valued for their oil. Ben oil is sweet, transparent, and odorless. It is the roots that have the same odor of horseradish and are sometimes eaten as a substitute for this plant.

The ophrastus states that chickpeas differ in size, shape, color, and taste. He distinguishes a red, a black, and a white type, the last one being the most appetizing. This distinction corresponds quite well with the cultivars grown today. On the other hand, Theophrastus erroneously states that the chickpea does not occur in India, while the Indian archaeobotanical record of this food legume dates back to the third millennium BC . A substantial record of archaeobotanical finds is also available for the Middle East and the Mediterranean, but not for Ethiopia and Eritrea, where archaeobotanical research in Axum has only recently been started. Literary sources make mention of the cultivation in Ethiopia as early as AD 1520. Therefore, the origin of the chickpea in Ethiopia is still rather obscure. According to Van derMaesen , the chickpeas of Egypt and Ethiopia differ from each other, making it unlikely that this crop was traded between both countries. This would imply that the Egyptian chickpea was introduced directly from the Near East, whereas the transoceanic trade between India and East Africa might have been responsible for its introduction into Ethiopia and Eritrea. The chickpea is represented in Berenike by only 26 seeds. This number is in marked contrast with that of two other pulses, namely lentils and white lupin, which have been found plentifully in many samples. Wastage of the relatively small lentils is obvious because seed samples are contaminated with weed seeds and small stones, and cleaning such contaminated lentils automatically means some smaller specimens will end up in the soil. The presence of the large seeds of the white lupin can be explained by the manner of consumption. Eaten as a snack, the content of the seeds is sucked out,greenhouse tables whereas the empty seed coat is discarded. In contrast, the large chickpea seeds can be sieved effectively, resulting in almost no wastage.

The chickpea was probably imported from the Nile Valley.The colocynth is a common desert plant that belongs to the white bryony family , which includes watermelons, gourds, and squashes. The colocynth has slender, procumbent stems with small yellow flowers that produce fruits with a diameter of 5.5 to 10.4 cm . Although tendrils are present, plants have mostly a prostrate habitus because of the lack of suitable host plants. Only occasionally plants may be seen trailing over other plants. Schweinfurth even describes many specimens hanging down from the slope of Wadi Mursseefa, south of Quseir. Unripe fruits are green and juicy and quite heavy. During the ripening process, the fruits become yellow and dry out completely, by which process the seeds get released from the inner fruit layers. The fruits are now very light and can easily be dispersed by the wind. As soon as the fragile fruit coat becomes damaged, the seeds are scattered into the sand. Despite its close taxonomic relationship to the watermelon, both fruits and seeds of the colocynth are not fit to eat due to their extreme bitter taste caused by the glucoside colocinthine. According to the Ababda nomads, only donkey and gazelle eat the fruits when they are still juicy and when more preferable herbs are no longer present in sufficient amounts. Osborne states that they are also eaten by Barbary sheep, rodents, and, after being boiled or roasted, by Tibbu people. Personal observations confirm that juicy fruits are eaten by donkeys, but not by sheep and goats. It was also observed that holes were pecked in both unripe and ripe fruits, probably by carrion crows. The presence of colocynth depends on the rainfall during the winter period. When there has been sufficient rainfall, some hundreds of full-grown fruits can be collected in the nearby wadi branches.

After a dry winter, however, the number of plants is clearly reduced, and also the fruit diameter is relatively small. The colocynth still occurs in Wadi Shenshef and may have entered the trash deposits from this settlement by natural dispersal agents. Nevertheless, the occurrence of colocynth seeds in reasonable concentrations in most samples from Shenshef seems to exceed its presence as part of the seed bank and consequently indicates deliberate collecting. The rare occurrence of the colocynth in the immediate surroundings of this settlement can be explained by the presence of wild donkeys and gazelles, the former frequently seen passing the settlement area on special paths and the latter detected by the many hoof prints in the sand. The colocynth is also present in the many branches of Wadi Mandit in the coastal plain around Berenike, so the collecting of these fruits did not require a great deal of effort. It is possible that the residents of Berenike collected unripe, juicy fruits of the colocynth as donkey food. In addition to camels, these animals were used for transport in Berenike . Such unripe fruits can be stored for at least a couple of months without drying out. Ababda nomads also use the fruits for medical purposes, and in wadis where this species is abundant, carloads are collected and brought to Aswân to sell at the markets. Fruits that are still juicy are fastened to one’s heel to relieve the pain caused by rheumatism. The production of an ointment for treating camel scabies is mentioned in particular in relation to the Ababda nomads. This ointment is made by filling a pot with colocynth seeds and covering the pot’s mouth with some palm leaves. Then the pot is put upside down on a dish and covered with charcoal. During this process, black oil, resembling motor oil, drips out of the seeds onto the dish. After shaving the camel’s skin and removing the scab, the black ointment is then rubbed onto the wound of the camel. During his visits to the Gebel Elba area, Drar saw piles of colocynth fruits and a number of small ovens between Wadi Ibib and Karam Elba especially erected for extracting this tar, which they call “diwân.” Also Osborne often saw piles of charred seeds and remnants of fruits in wadis of the Eastern Desert together with an oven of stones and clay.

According to Girgis, cited in Zahran and Willis , this tar was also used for tanning skins meant for making water bags. Bottles with such tar are still sold at local markets, such as those of Shelateen. In the Sinai, the bedouins still use colocynth seeds to cure human constipation . Reasonable quantities of colocynth fruits are still collected in the Egyptian deserts and put up for sale in markets where they are sold for 1 Egyptian pound apiece. Both the reddish, sweet-tasting fruit pulp and the large seeds are edible. The fruit pulp has a low content of vitamins and minerals; the seeds are nutritious and contain a relatively high percentage of protein, fat, and carbohydrate. Today, in Arabic countries, several seeds are used as a snack, including seeds of watermelon, summer squash , and large seeded varieties of the sunflower , the two last ones being New World species. A special inedible variety of watermelon with small fruits is even exclusively cultivated for its seeds, especially in Nubia, from where it is imported to Egypt . The seeds are crushed between the teeth, the seed content is eaten, and the hard seed coats are discarded. In Egypt this is practiced by both Egyptians and nomads. About half of the sub-fossil seeds from Berenike and Shenshef are still whole and suggest that seeds were not eaten. The seed fragments found can be explained because old seeds easily disintegrate, especially along the lengthwise groove. As watermelons are well adapted to hot and dry climates,flood tray they might have been locally cultivated in kitchen gardens near Berenike and Shenshef. Because the fruits have a hard rind, they can easily be transported and might also have been imported from the Nile Valley. Today, they are, for example, available from the market in Shelateen. The storage life is maximized by leaving the long peduncle on the fruit . Unfortunately, no remains of peduncles or rinds have been found so far. Modern watermelons produce fruits up to 10 kg in weight. Such large-sized fruits can only be successfully grown if the stems creep along the ground. The tendrils produced in leaf axils indicate that we are dealing with a trailing plant so that in the past the fruits must have been much smaller. Watermelon is a native of tropical and subtropical Africa and has been cultivated in Egypt since predynastic times.Cocculus pendulus is a plant that grows in cliff-side habitats or in areas where other trees are present. In the latter case it becomes a liana. As the seed germinates in the soil, it produces a creeping stem that ascends when under a tree, possibly induced by the reduction of light intensity. The lower part of the stem, which is mostly fl at to some extent, may reach a diameter up to 25 cm, whereas the interweaving branches are much smaller. The plant is recorded from the Aswân Nile islands, all deserts, including the east section of Wadi Allaqi in the Nubian Desert, the Sinai, and the Gebel Elba area . The present vegetation around Berenike and Shenshef does not suggest that C. pendulus once grew in the vicinity of either of these places. The presence of small amounts of seeds in several trenches of both sites indicates that the edible fruits must have been imported regularly. Judging by the frequency of C. pendulus in the Gebel Elba, this area seems to be the most plausible place of origin. The fruits have a diameter of 5 mm. The stony endocarps are relatively large, so that only a small part of the bitter tasting fruit is edible. Arabs use the fruits for making an alcoholic beverage called Chamr el Madjnûne . Fruits are also used for medicinal purposes.

Another member of this plant family, namely, Anamirta cocculus Wright & Arn., is one of the species that according to Warmington might have been traded by the Romans. The dried, highly poisonous fruits of this plant cannot be confused with those of C. pendulus, but are still sold under the old name of C. indicus Wright & Arn. at Middle East markets, including the Harraz Drug Store in Cairo . During a visit to the Gebel Elba area in February/ March 1999, it was seen that most fruits fall when they are still green. Once the fruits are on the soil, they lose moisture and are difficult to collect because they are scattered in low densities and tend to sink in the loose sand when they are touched. Collecting fruits still attached to branches is also difficult, especially when the liana grows in large, spiny acacias. An effective way of harvesting would be pulling down the fruits with long sticks and collecting the fruits on mats or cloths. The archaeobotanical record of this species is scanty. The oldest record is from the Eastpans site A95/1-1 in the southwestern part of the Western Desert where some 10 charred seeds were found in a Middle Neolithic layer . Schiemann reported the presence of a single fruit of C. hirsutus Diel among samples of Grewia, taken from several baskets of Tutankhamen’s tomb. According to Germer , more fruits are present in the samples stored in the Dokki Agricultural Museum in Cairo. Recently, the author had the opportunity to check this sample and it turned out that the fruits of Grewia were contaminated with a fruit of juniper , a fruit of nabq , and two spikelets of grasses. Also, the other part of the Grewia sample from Tutankhamen’s tomb kept in Kew does not contain any seed of Cocculus, so the identification by Schiemann could not be confirmed . Another reason for doubting its identification is that C. hirsutus is not native to Egypt but must have been imported from either Saudi Arabia, Yemen, or tropical Africa. Moreover, there is no reference to specific uses of the small fruits. The coconut is valued for both the fruit and the seed. The fruit consists of three layers: the exocarp, the mesocarp, and the endocarp. The lignified, relatively thin endocarp is tightly connected with the thin seed coat. Initially, inside the seed coat there is a liquid endosperm, which, as the fruit ripens, gets reduced and forms a white edible layer against the seed coat.

Ababda nomads still harvest suitable branches from these plants . Branches of the toothbrush plant are cut into pieces about 15 cm long and made into a brush at one end. Salvadora persica often remain bushy as a result of this exploitation. Some antispasmodic properties of this plant have been proven, for which reason extracts are also recom mended for certain diseases . In 1988, a commercial toothpaste containing Salvadora was even put on the market in Saudi Arabia . Branches of the plant are still offered for sale in markets in the Middle East. Another plant that is still used for oral hygiene in this area, and also still available in markets, is toothpick ammi . Complete umbels are collected from this plant. The rays thicken after flowering and can be used as toothpicks. In Egypt, this plant has been recorded from the Nile Valley and the Mediterranean region but has become an endangered species in this country by now. Potential dye plants that grow in the immediate surroundings of Berenike are Arnebia hispidissima, Chrozophora tinctoria, and Indigofera articulata. The thickened root of A. hispidissima is a source of yellow dye. Crushed leaves of C. tinctoria can be used to give the skin a purple tone. Fermented leaves of indigo species can be used as a source of blue dye. When synthetic indigo became available in 1897, the production of natural indigo dropped dramatically . According to Drar , by the beginning of the twentieth century, the extensive cultivation of indigo was confined to the Nile Valley and the Dakhla oasis. Local Ababda nomads do not use either of these plants today. Polycarpaea repens and Citrullus colocynthis are used for treating wounds,blueberry container size in particular those of camels. Leaves from P. repens are either crushed on the skin or first made into ash .

A more-detailed description of the processing of tar from the seeds of C. colocynthis follows in the “Local Food Production” section. Echium rauwolfi i is widely valued in Yemen for its medical properties, where it is used as a diuretic, tranquilizer, and aphrodisiac .For the interpretation of the sub-fossil record of cultivated plants from Berenike and Shenshef, it is important to explore the present-day practices of local food production in the Eastern Desert. Water availability and labor can be considered as the main limiting factors. Nevertheless, it may be assumed that the inhabitants of Berenike and Shenshef may also have practiced the small-scale examples that can be encountered today. Although the part of Egypt that is suitable for agricultural production is relatively small, being confined to the Nile Valley, the Nile Delta, and the oases in the Western Desert, it still is capable of producing very high yields. Before the construction of the Aswan High Dam, the Nile Valley and the Delta owed their fertility to the yearly flooding of the Nile. Because sufficient rainfall is only available in the Mediterranean coastal area, irrigation is necessary elsewhere. But even in far less suitable environments, such as the Eastern Desert, agricultural practices can be observed almost everywhere where people have settled. This is not only true for cities such as Quseir, but also for small villages of settled Ababdas and restaurants along desert roads. In order of importance, we can distinguish kitchen gardens, cultivated trees, and fields.Both permanent and semipermanent settlements in the Eastern Desert are characterized by the presence of small kitchen gardens. The cultivation of vegetables and herbs with a short life cycle enables their cultivation even in temporarily occupied settlements. In most instances the gardens are private domains and of limited size. Both the presence of the kitchen gardens and their size are mainly determined by the amount of water that is available. Kitchen gardens that were seen in the Eastern Desert have a size of about 4 to 20 m2 . A necessary condition for the cultivation of crop plants in these kitchen gardens is the availability of water and minerals. Due to their fixed location, manuring might be necessary if gardens are used intensively.

According to the sheikh of Arab Saleh, one of the few owners of a kitchen garden in this settlement, their gardens are not fertilized. He referred to the former situation in the Nile Valley , where only additional camel dung was used as a natural fertilizer. Applying this traditional and natural manure, vegetables were produced with a good taste. Nowadays artificial manure has to be brought onto the land as the Nile flooding is blocked. Much organic waste is present in the water used for irrigation and on the fields proper, which in their turn affects people’s health. Despite their relatively small size, kitchen gar dens produce quite a variety of crops. Although the productivity is limited, the yield may be self-supporting if the family is not too big. If water is available throughout the year, kitchen gardens can produce several yields a year. Kitchen plants are mostly grown in a protected area near the house, although occasionally it was also seen that plants such as karkadeih and basil were cultivated in a flower box. The gardens are surrounded by walls or fences to prevent the browsing of domestic animals such as sheep and goats, which are a serious threat to a good harvest. Fences are constructed from spiny branches, such as those from twisted acacia , wire netting, wood, or sheet iron. It is conceivable that in Roman times spiny branches were used especially for this purpose. When fenced off, kitchen gardens may be completely hidden from view. I once stayed for a couple of days at the accommodation of the Geological Survey in Shelateen and only discovered the small kitchen garden producing faba beans by accident after two days.In a temporary settlement of workmen from an asphalt company, some 30 km north of Berenike, a larger kitchen garden was observed, which w a s a c o m m u n a l property. In this case, the kitchen garden was unfenced because no domestic animals were present. Only a scarecrow was erected for protection . Most garden plants are characterized by their edibility. The following species have been recorded in kitchen gardens in the Eastern Desert: basil , sunflower , caper bush , possibly cumin , lavender , fennel , Johnson grass , faba bean , morning glories , karkadeih , cress , coriander , tomato , potato , onions , garden rocket , watermelon , cucumber , and courgette .

Hobbs also mentions Malta jute , snake melon , okra , chickpea , white lupin , lentil , and tobacco . The cultivation of tobacco is forbidden in Egypt today as it is related with the period in which Nasser was in power, during which close relations with the former Soviet Union were maintained. Vegetables and herbs are sown in early spring to profit from the winter rains and to avoid high temperatures during the growing season. But additional watering is always necessary. This might be done with a watering can or, more advanced, with the aid of small gutters that transect the garden and are regularly filled with water. Wastewater may be used for this purpose, but special water is also bought. That the presence of kitchen gardens is directly determined by the availability of water is clearly illustrated in Quseir, where kitchen gardens are in abundance and owners are assured of a steady supply of cheap water. This water originates from the Red Sea and is desalinated in a special factory. This amount of water is sufficient for a kitchen garden of approximately 12 to 15 m2 . In Arab Saleh, an Ababda village some 15 km northwest of Berenike, water has become a scarce item and has led to the reduction of kitchen gardens in this area. Contrary to Quseir,growing raspberries in container the water used for human consumption and for irrigation originates from the same source. A special type of irrigation is obtained by diverting flood waters to particular depressions, which are subsequently used for farming purposes. The practice of this kind of runoff or flood water farming, which is restricted to years with heavy winter rains, is observed for the Arab bedouins in the northern part of the Eastern Desert and the Sinai .Only a minority of these trees is indigenous to the Eastern Desert: twisted acacia, nabq, and date palm. Some others originate from the Nile Valley or are cultivated there from classical times onward: Nile acacia, fig, henna tree and castor-oil plant. All the others trees can be considered as exotic species. A good example is the Eucalyptus tree, which originates from Australia and has a widespread distribution today throughout the Mediterranean region, where it can be found near settlements and also in more natural environments. As most people like to cultivate exotic species in their gardens, the planting of foreign trees by desert dwellers may therefore not be surprising. The Eucalyptus tree in Arab Saleh, for example, was grown from a young sprout that originated from the Nile Valley. The large proportion of exotic trees in Cairo also illustrates people’s preference for non-indigenous plants . Such non-desert trees, however, need special attention and are restricted to settlements only. But desert trees that are cultivated near shelters may also need supplementary watering. Schweinfurth states that a small date-palm grove near Quseir was irrigated with brackish water obtained from Wadi Ambagi. The author witnessed in Marsa Alam, located between Quseir and Berenike, a full-grown Balanites aegyptiaca that was watered with wastewater via a gully. Trees that are adapted to desert conditions may survive when settlements become abandoned or may even escape from cultivation through seed dispersion. According to Schweinfurth such a palm grove is present in the Wadi Gimal estuary, 93 km north of Berenike, and consists of date palms and doam palms . Today, these palm trees are not cultivated anymore: the old leaves are still attached to the stem. Hobbs states that nabq trees in the Ma’aza territory are regarded by the nomads as “antiquities,” which were cultivated by the Romans. Once full-grown, trees may serve as shade plants. They also may be exploited for useful products, which is true for almost every species enumerated above. Dead branches can be used as firewood, and most of the cultivated trees are valued for their edible fruits. Others, such as the henna tree and the Nile acacia , produce other useful products. The powdered leaves of the henna tree can be used as a cosmetic dye and is applied to the hands and feet of women in a characteristic pattern. Fruits of the Nile acacia are used for tanning. Both the henna tree and the Nile acacia are present in gardens of Quseir, and it is likely that leaves and ripe pods are harvested for personal use or sold in markets. Even in Cairo’s spice markets, these products are offered for sale. The Ababdas from Arab Saleh do not cultivate these trees, despite their frequent use of henna and acacia fruits. Both products are obtained from the markets in Shelateen, approximately 90 km to the south.At several locations the author has witnessed that cereal cultivation in the Eastern Desert is possible. A fairly large wheat field next to an orchard has been seen in Wadi el-Matuli, along the former caravan track between Berenike and Koptos , some 17 km from the Nile Valley. A barley field of only 4 m2 was seen near a frontier station about 10 km north of Quseir . Both these fields were irrigated. An example of rain-fed farming was found about 1.5 km south of Arab Saleh, near Berenike, where sorghum was occasionally cultivated on a small scale. A necessary condition for sorghum cultivation in this area is sufficient rainfall during the winter period, with most rain falling in November. The field near Arab Saleh measures a couple of hectares and had been sown with sorghum in 1995 and in 1997 after heavy winter rains. Suitable locations for such rain-fed agriculture are shallow depressions in which rainwater is concentrated.

This is documented in the Periplus by several examples and concerns food items , textiles and clothing, lac dye , and slaves . After the downfall of the Roman Empire and the arrival of the Arabs in Egypt in AD 640, Berenike lost its transfer function and was at the mercy of the destructive forces of the desert. Both sandstorms and supply of sand by the wadi branches north and south of Berenike buried the city in the course of time, leaving only a vague contour of the walls of the latest buildings and a variety of densely scattered trash. The lagoon south of Berenike has been filled by wadi fl ood sediments and wind borne sediments .Roman activity in the Eastern Desert lasted from 30 BC to AD 638 and is still reflected by many archaeological installations, including settlements, watering stations , forts, quarries, roads, graves, and cemeteries. This is also true for the environment of Berenike. To optimize a comparison of the sub-fossil plant remains of this harbor site with the present-day situation, it was decided to make an inventory of the present vegetation of the immediate surroundings of Berenike, the nearby watering station Kalalat, and the mountain settlements of Khesm Umm Kabu, Hitan Rayan, Shenshef, and Qariya Mustafa ‘Amr Gama . These sites will be briefl y described, starting with the northernmost site and ending with the most southerly one. Khesm Umm Kabu is located in the upstream part of Wadi Gimal . In this part of the wadi, the Romans exploited several beryl mines in the mountains. These mines are located at different branches of this wadi and are referred to as Mons Smaragdus. Surface finds indicate that the occupation period of the mining settlements lasted from the first to the fifth centuries AD . Contrary to the nearby mining settlements Sikait and Nugrus,plastic potting pots no obvious remnants of Roman buildings are present these days at Khesm Umm Kabu.

The only two ruins and an associated well are of recent date. Berenike is located on the seaward edge of the coastal plain between the branches of Wadi Mandit and Wadi Umm el-Mandit. The Ptolemaic buildings were founded on an elevated limestone outcrop that originally had a maximum elevation of well over 3 m above the current high tide . Ptolemaic as well as Roman buildings have been completely covered by wind-blown sand, which has accumulated during the course of time. With the exception of the remains of the temple of Serapis, located on the highest point of the town center, only the contours of the most elevated walls are visible on the surface . Photographs taken during an expedition in 1897 conducted by Raimondi clearly show that this temple has suffered much from its exposure during the twentieth century. Therefore, the Berenike project decided to rebury the temple. Although detailed maps are now available presenting the buildings visible on the surface and despite eight years of excavation, it is still difficult to make a reliable estimate of the total number of buildings. Demographic data, such as the size of the population in a particular period, are equally unclear. This is especially true for earlier habitation periods, as these have been built over or destroyed by subsequent activities in the town. An estimate for the last habitation phase, dated to the fifth to the early sixth centuries AD, is also difficult to make, since part of the topmost portion of the surface on the west side has been leveled by bulldozing in about 1973, when military installations were built in this area. Estimating the original size of the settlement is further complicated by the fact that it is likely that only a part of Berenike consisted of stone structures. Locally available fossilized coral was the most commonly used building material .

Temporary residence, using tents in a similar way as was practiced during the excavation seasons, could have been established perhaps west of the town center on a fl at area that covers about 7 ha. At its maximal extension, Berenike may have comprised an area of about 2 km². This area not only included living quarters, but there is also evidence of some industrial activity, including the production of metal, rope, and perhaps glass and beads . A conservative estimate of 500 persons is given by Wendrich , taking into consideration only the small buildings visible in the still-intact town center and supposing an occupation per house of an average of five persons. The location of the harbor, whether it was a real harbor or some convenient landing place, as described by Strabo , is not yet known for certain. Possibly its location shifted from north to south of the town in the course of time, as did the extension of the town center. Although some burials were found in the built-up area of Berenike, most bodies seem to have been buried outside the town. Scattered over the higher levels of the coastal plain, dozens of graves are still present. Here they are well protected against flooding, although this location could not have prevented plundering. In Wadi Kalalat, close to the mountains, a small fort and a large watering station are present at a distance of about 1 km from each other. The function of the small fort is still unclear. The watering station has a rectangular outside wall and a large, walled, circular depression on the inside. Measuring approximately 80 x 90 m, it is measured up to the largest forts of the Eastern Desert . The watering station is located on the floor of the most active part of Wadi Kalalat. At this latitude most of the water drains off underground to the Red Sea, but occasionally serious flooding may occur after heavy rainfall. Probably, the thick outside walls were built to protect the inner construction, in which the latter probably functioned as a well .

To ensure the indispensable supply of water throughout the year, Harrell suggests that a large diameter of the well should have been necessary because of the low groundwater-fl ow velocity. It is very likely that this watering station played an import role in the supply of fresh water to Berenike. Although the principal drainage course of Wadi Kalalat flows into the Red Sea just south of Berenike, the watering station is located 8.5 km southwest of the site. This western location was probably chosen to avoid the effect of saltwater penetration nearer to the sea. Partly, salt water penetrates through the soil and partly salt crystals are blown inland from dried-up land during low tide . Excavations have, so far, produced no evidence of the existence of a pipeline to transport water from Kalalat to Berenike. Because the watering station is located in the active part of the wadi, where a direct water pipeline between Kalalat and Berenike could easily be damaged by erosive fl oodwaters, it seems more likely that the water was carried to Berenike by animal transport . Hitan Rayan and Shenshef are located in Wadi al-Rayan and Wadi Shenshef, respectively, at a distance of 8.5 km in a straight line from each other. Obviously, both settlements are located west of an outcrop of the impermeable bedrock, in very shallow sand. As a result, the underground water fl ow is pushed up and slowly running fresh surface water is present . Probably because the drainage basin of Wadi Shenshef is larger than that of Wadi al-Rayan, the amount of surface water in the latter is more substantial and has never been seen dried up over the last six years, as has been the case in Wadi al-Rayan. The long-term character of surface water is supported by the presence of bulrush near Hitan Rayan and common reed and Cyperus laevigatus near Shenshef.The function of Hitan Rayan is enigmatic. Shenshef was, most likely, a satellite settlement of Berenike and was occupied during the fifth to early sixth centuries AD. The settlement area of Hitan Rayan, which is mainly concentrated on the terraces on the north side of the wadi, comprises remnants of 141 separate structures and 31 burial cairns,raspberry container growing partly concentrated in a cemetery on a terrace at the east side of the settlement and partly at isolated locations on the mountains. An analysis based on variables, such as the method of wall construction in relation to roofi ng; the number of enclosed spaces in one building, varying from one to three; and the position of components such as ovens and storage vessels to each other, suggest that the settlement was primarily used for living . Despite the abundance of quartz veins in the rocks around Hitan Rayan, there is, with the exception of one locality close to the ruins, no indication of gold mining as is evidenced more to the southwest . The Hitan Rayan settlement might have been a gold exploration camp. Unlike Hitan Rayan, there is an obvious plan to the settlement of Shenshef. There, also, the buildings are Figure 1.7. Surface water in Wadi Shenshef near a narrow gorge westward of the settlement . See Color Plates section, page 204. of a better quality, due to the drystone construction with laminar-formed stones.

The ruins of houses are present over a distance of about 800 meters and occur on both elevated terraces of the wadi that become only occasionally flooded . In total, 332 structures are mapped, representing four distinct phases of construction. A comparison with Murray’s plan of the site, reflecting the situation in the 1920s, shows that in the last decades several buildings have been destroyed . In addition to the houses, there is an enclosure, and many partly clustered graves are scattered over the area. Finally, a large hilltop fort on the east side of the settlement stretches over two adjacent hilltops from which the Red Sea can be seen. Ceramic finds date this fort to the first century AD, possibly predating the settlement. Shenshef is not located along a major roadway or are quarries or mines present in the surroundings of Shenshef, which might have explained its former function. The quarries north and south of Shenshef follow aplite dikes and were only used for the production of local building material. It is also from this construction phase that some of the houses still have walls about 2.5 to 3 m high standing, with complete doorways, windows, and internal niches. The last Roman installation to be mentioned here is Qariya Mustafa ‘Amr Gama, located in Wadi Umm Athl . S. Sidebotham named the site in honor of the Ababda, who showed them the site, whereas the wadi itself bears the vernacular name of the leafless tamarix , which grows in this Figure 1.8. Shenshef with remains of buildings along both sides of the wadi, looking northwest . See Color Plates section, page 204. wadi at the site proper. This tree, which is also present near the former settlement of Khesm Umm Kabu, is sensitive to water shortage and its presence may be indicative of water accumulation or crack seepage. The site dates to the late fifth century, possibly early sixth century, and is, thus, contemporary with Hitan Rayan and Shenshef. A nearby shady rock pool contained a reasonable amount of water during a visit in early February 1998.Rainfall in the Eastern Desert is scanty, unpredictable, and concentrated in the winter period. Short, heavy showers may produce huge quantities of water, but these cloudbursts are quite rare and localized. After such heavy rains, silty, fl at depressions are filled for weeks or even months with water and can be used for cultivating plants that are adapted to this kind of water supply, such as sorghum . Especially in the Red Sea coastal strip, where a well-developed seed bank is present owing to the atmospheric humidity, which is responsible for a more regular water supply, such erratic cloudbursts will result in a considerable increase in the vegetation cover . In his description of the Eastern Desert, Theophrastus , states that it never rains except at intervals of four or five years, and then the rain comes down heavily and is soon over. According to Hobbs , rainfall is sometimes especially abundant in a particular year or even for several consecutive years.

There were fewer mites drowning in the wet felt in the spinetoram detection bio-assay on day one than seen in the initial field trial bio-assay on day one, indicating that the pesticide free leaf surface provided some sort of refuge for the mites. Spinetoram exposure at days one and three ultimately resulted in some mite mortality or mites drowned in the wet felt, but there were fewer overall mites dying and drowning on both sides of the leaf . Mite repellency was different from the control for both treated and untreated sides of the leaf, but on each subsequent bio-assay date, the level of significance dropped until on day 14, there was no statistical separation. Our data suggest that because fewer mites were repelled in the spinetoram detection trial on bio-assay days 7 and 10 and because of the pesticide free side of the leaf, more mites were alive, i.e. fewer picked up a toxic dose or drowned. It remains difficult with our bio-assay system to precisely separate whether or not mites received a toxic dose when repellency levels were high. Our studies were conducted with a conservative dilution rate of 2,843 L of water per ha while the majority of California avocados groves are grown on steep hillsides and utilize helicopter application using 468-935 L of applied water per ha. On these hillside groves, speed sprayers cannot be used and relatively few growers use drag hoses because of the high cost of labor in California. Application by helicopter may not provide complete coverage and many of the interior portions of the avocado tree remain untreated. With consideration of the following factors: helicopter application resulting in uneven distribution of pesticide on hillside avocado groves,square pot the conservative dilution rate used in our trial, our containment of mites on the pesticide treated arenas and providing a pesticide treated/ untreated leaf area, our data suggests that in a field setting, mites may not pick up a toxic dose of spinetoram.

Those mites that do not pick up a toxic dose will likely be repelled by the Thrips are common pests in most blueberry growing regions of the United States. These insects feed on the blueberry leaves, flowers and fruit and cause distorted, discolored, and stunted flush growth and poor development of fruiting wood for the subsequent crop . Many thrips preferentially feed on the styles and ovules, as well as the surrounding new green tissue, or ‘flush growth’ . Some studies have shown that thrips can feed on blueberry pollen and, under severe infestations, cause dimpling on the fruit, which can severely affect marketable yields . In Georgia and Mississippi, a 60% reduction in fruit set has been attributed to thrips injury in southern highbush blueberries . There is substantial variability in the thrips species complex that attacks blueberries across geographic regions of North America . The eastern flower thrips, Frankliniella tritici , and Scirtothrips ruthveni Shull infest northern highbush blueberries in New Jersey . Frankliniella vaccinii Morgan, Catinathrips vaccinophilus and Catinathrips kainos O’Neil are the main thrips species infesting lowbush blueberries in Canada and Maine . In contrast, the Florida flower thrips, F. bispinosa , and F. tritici are the most abundant thrips species in Florida and Georgia, respectively, where southern highbush and rabbiteye blueberries are grown . In the San Joaquin Valley of California, the southern highbush blueberry is a somewhat new host for citrus thrips, Scirtothrips citri . One of its more common native host plants in this area prior to the introduction of citrus was likely laurel sumac, Malosma laurina Abrams . In Florida however, S. citri have been reported on grapes but is rarely found on blueberries . Historically, lowbush varieties of blueberries could only be grown in regions too cold for citrus production. However, the development of heat-tolerant highbush varieties, which has enabled the development of a blueberry industry in the San Joaquin Valley , has also caused blueberries to be grown in a region where citrus and citrus thrips flourish. Other, less common thrips infesting blueberries include tobacco thrips, Frankliniella fusca , Frankliniella hawaiiensis and western flower thrips, Frankliniella occidentalis .

Little is known about the biology, ecology and host plant selection of thrips in southern highbush blueberries, particularly in California and not all varieties are fed on equally by citrus thrips; i.e. there is a distinct varietal preference for some hybrids . Thrips preferences for tender, young flush foliage are well documented and determining the oviposition rates in the varieties of blueberries grown in California will begin to assist researchers in understanding thrips host plant preferences. Based on a survey of growers, the varieties of blueberry predominately planted in California’s SJV are Emerald, Jewel, Misty, O’Neal, Santa Fe and Star . The goal of this research was to determine if oviposition preferences differed between these varieties of blueberries using choice and no-choice oviposition tests and to document which varieties grown in the SJV of California are preferred. Citrus thrips were collected in Delano, Kern County, California from southern highbush blueberries varieties Star, Santa Fe, Jewel, Misty and O’Neal. Thrips were collected on blueberry canes by placing a brown paper bag over the flush growth and clipping the cane off into the bag with shears. This was done approximately 10 times per blueberry variety. The brown paper bags were carefully placed into a cooler with ice packs and brought to a greenhouse located at the University of California, Riverside, Agricultural Operations Field 16 in Riverside, California. Once in the greenhouse, the bags were opened, and canes gently placed on top of 40 potted Misty variety blueberry plants with a large amount of flush growth. The Misty variety was selected for rearing because growers reported it to be of intermediate preference to citrus thrips versus two preferred varieties versus two varieties that thrips appear to build up on to a lesser degree . The brown paper bags that transported the citrus thrips were gently placed on the greenhouse bench with the opening pointed toward the potted plants to entice any remaining thrips to leave the bags and move to the plant foliage. The thrips colony was established and maintained in the greenhouse for 1.3 years before used in the oviposition trials beginning on June 6, 2011 and were augmented with additional thrips in exactly the same manner as described above an additional three times over that 1.3 years.

All blueberry plants were grown in 2 L pots and were watered 3-4 days per week and fertilized as needed with azalea/camellia/ rhododendron acid fertilizer . The potted Misty plants were pruned in the citrus thrips colony greenhouse room and rotated out once only hardened leaves were present on the plants, at which point,blueberries in containers new flushing Misty plants were rotated into the colony cyclically with the flushing and pruning of the colony plants. Fall Creek Farm and Nursery, Lowell, Oregon, USA supplied all potted blueberry plants used for the colony and in oviposition trials. Varieties provided were Emerald, Jewel, Misty, O’Neal, Snowchaser and Star. Snowchaser was a fairly new variety at the time we obtained the plants and was used in our studies in lieu of Santa Fe , which was unavailable. Snowchaser has similar parentage to Santa Fe. Citrus volkameriana V. Ten. & Pasq. and laurel sumac plants were maintained in the same fashion as the blueberry plants but were fertilized with Miracle Grow All-Purpose plant fertilizer as needed. Plants used in the oviposition trials were held in a separate greenhouse from the citrus thrips colony . Potted blueberry with the varieties Emerald, Jewel, Misty, O’Neal, Snowchaser and Star, as well as, flushing citrus and laurel sumac potted plants were placed in random order on a greenhouse bench in 5 replicate blocks of the 8 plants . Two leaves from each plant that were flushing and nearly fully expanded were selected and clip-cages were clipped to the leaves while still attached to the plant such that the experimental arena was located on the abaxial surface of the leaf. Circular clip-cages consisted of two plastic rings covered on one side with a 1 cm thick foam pad enclosing a leaf surface area of 3.1 cm2 . The foam-plastic rings, one of which was covered by ultra fine nylon mesh, were connected by a coiled length of spring steel wire glued to the plastic which allowed the clip cages to attach to the leaf like a clothes pin without visibly damaging the leaves. Two adult female and two male citrus thrips of unknown age were carefully added to the clip cage and left in the cage for 5 days after which the leaf was excised from the plant, with the cage still attached, and was carefully transported to the laboratory. Once in the laboratory, leaves were thoroughly examined for any first instar larvae and adults. The leaves were then boiled in deionized water for 3 minutes in the microwave and stained with methyl red . Eggs were clearly visible using a binocular microscope with transmitted light. This experiment was repeated on two dates total and total counts of eggs and larvae combined were square root transformed pooled data were analyzed using a two-way ANOVA with count data and developmental stage as main treatment factors and means were separated by Tukey’s HSD test. The correlation coefficient between numbers of hatched larvae and eggs was also calculated. Five two L potted blueberry plants, one each of the Emerald, Jewel, O’Neal, Snowchaser and Star varieties were placed inside five replicate “No-thrips” screened bug dorms . Plants were arranged in a circle with the position of a variety randomized in the 5 bug dorms, ensuring that each variety occupied each position in the rotation. For example, positions one through five contained the varieties in order, Star, Jewel, Snowchaser, Emerald, and O’Neal and each subsequent cage’s plants rotated those varieties in that order one position clockwise. This arrangement was conducted twice on the same date . Each pot was reduced to one blueberry cane with approximately the same numbers of leaves , similar cane lengths and leaf flush and canes did not remain in contact with each other. The plants were placed in square foil pans to collect excess water or spilt water after plants were watered. Ten groups of approximately 60 male and 60 female citrus thrips each were collected from the colony the morning of the test and held in 15-dram plastic aspiration vials with a copper mesh screened lid. Adult thrips were of unknown age. The vials were then placed vertically into the center of the bug dorms and the lid removed to allow the thrips to escape. The plants were watered every third day, carefully through the mesh sleeve on the bug dorm door with an adjustable watering wand taking care to not fill the foil trays with water. Thrips were left with the plants for 14 days, after which time the cages were carefully opened, and a “No-thrips sleeve” open at one end was quickly placed over each plant and secured at the base of the cane with double-sided sticky tape. Once the sleeve was securely fastened to the cane, the cane was trimmed at the soil line. The sleeved canes were then transported to the laboratory where the adults were lightly shaken off into the sleeve and leaves quickly examined for remaining adults. If adults were found on the leaves, they were picked up with a paintbrush and added to the respective sleeve. The sleeves no longer containing the canes were placed in a freezer for 10 min and adults were counted. The canes were examined and any larvae found were counted. Once all live thrips were removed, the leaves were stripped from the respective third of each cane, boiled in deionized water for a minimum of 3 minutes in the microwave and stained with methyl red. Older leaf tissue had to be boiled for 5 minutes to clearly see eggs in the leaf. Subsequently, eggs were clearly visible using a binocular microscope using transmitted light. This experiment was replicated twice on one date and data were analyzed using a G-test of goodness-of-fit with plant, location on the plant , larval count and egg count as the main operators in the test.

As fruit grow, early feeding by avocado thrips becomes apparent as scabby or leathery brown scars that expand across the skin and is sometimes referred to as “alligator skin” . Avocado thrips damage is affected by practices that increase or decrease the abundance of succulent foliage during set and growth of young fruit. Thrips move to young fruit when leaves harden after the growth flush has finished and the most damage occurs when fruit are 5.1 to 15.2 mm long . Although Hass fruit are susceptible to feeding until they reach about 51 mm in length, thrips feeding rarely causes scars on fruit larger than about 19.1 mm. This scarring on young fruit may not become obvious until fruit enlarge. In severe cases, all fruit on a tree can have their entire fruit surface scarred by avocado thrips, causing some packinghouses to sell such fruit with the box marked “papacado.” The California Avocado Commission estimated a $50 million dollar crop lost in the 2006 due to avocado thrips scarring and the costs of control . Sticky card and beating tray sampling are research methods used for these two insects but are rarely used by growers or pest control advisors . Both PCAs and researchers monitor citrus thrips by counting the percent of fruit infested with immature thrips and the number of immature thrips per fruit is also indicative of the severity of the infestation. Thresholds in use in the San Joaquin Valley are 20% of Valencia oranges or 10% of navel oranges infested with immature thrips until the fruit reaches 20 mm in diameter or more. Avocado thrips are monitored by counting the number of immature thrips per leaf prior to fruit set or the number of thrips per fruit.

No firm economic threshold has yet been developed for avocado thrips but PCAs typically treat at 3-5 immature thrips per leaf prior to bloom in San Diego County due to restrictions on use of abamectin during bloom. The major documented citrus thrips predator is the phytoseiid mite, E. tularensis , although Jones and Morse questioned the importance of this predator. Avocado thrips are frequently preyed upon by Franklinothrips orizabensis Johansen and Chrysoperla carnea and is parasitized by the larval parasitoid Ceranisus menes . Franklinothrips vespiformis , black hunter thrips , and several banded-wing thrips also feed on avocado thrips . In many years,square pots natural enemies are unable to suppress avocado and citrus thrips populations below economic thresholds and chemical control is needed to reduce fruit scarring. By the time damage is noticed on ripening fruit, the thrips that caused the injury are often absent from the fruit. A variety of pesticides are registered for thrips control in different cropping systems . After a number of years of use, pesticides like dimethoate , formetante hydrochloride , cyfluthrin , and fenpropathrin resulted in failures in citrus thrips control in some regions, along with an increase in resistance confirmed with both laboratory and field bio-assays. Also, these materials are detrimental to natural enemies such as Aphytis melinus DeBach and other biological control agents important to citrus pest control. Since it was registered in 1998, spinosad has been the main material used for control of citrus thrips and a related and more effective material, spinetoram , was registered late in 2007 and will soon replace spinosad once MRL issues are resolved with export countries. Abamectin is the main material used for avocado thrips control with occasionally rotation with sabadilla . Resistance to sabadilla has been shown with avocado thrips and a similar pattern of resistance development with abamectin is of concern due to the persistence of this material in leaf tissue. To date, citrus thrips resistance to spinosad has not been documented but there is concern that resistance to it or spinetoram may appear soon. With a limited number of pesticides available for control and the frequency of resistance shown by thrips such as citrus thrips, it is wise to monitor population levels carefully, limit treatments to population levels of concern, and time treatments optimally .

Appropriate cultural practices and conservation of natural enemies should be practiced in concert with the use of pesticides only on an as-needed basis. Thus, the search continues for effective biological and chemical controls useful in citrus and avocado thrips management. For both species of thrips, some pupation occurs on the tree in cracks and in crevices, however, about three-fourths of avocado thrips drop as late second instars from trees to pupate in the upper layer of dry leaf litter . Propupae and pupae are rarely seen, move only if disturbed, and do not feed. This phenomenon of dropping down to the leaf-litter or soil surface for pupation may create the ideal interface for control using the entomopathogenic fungi B. bassiana. Adding coarse organic mulch beneath trees and maintaining a mulch layer may reduce survival of thrips that drop from trees to pupate below the tree, especially in avocados, because this is common practice by many growers as a method of Phytophthora management. The effectiveness of mulching to control thrips is uncertain and labor costs of adding mulch may not be justified solely for thrips control. However, applying coarse organic material such as composted yard waste beneath trees may help control weeds, and thrips reduction might be an additional benefit, particularly for blueberries. The deep mulch layer that is standard practice with blueberry culture in the San Joaquin Valley may also provide an ideal habitat for B. bassiana. It is possible that as citrus thrips are adapted to and evolved in a hot, dry climate, they may be more susceptible to B. bassiana, whereas avocado thrips has adapted to and evolved in a wet and cool climate and may be less susceptible to or even tolerant to B. bassiana. There is increasing pressure in the United States to move away from broadspectrum insecticides and focus on alternative methods of control, e.g., geneticallymodified crop plants expressing Bt toxins, use of entomopathogens, biorational insecticides. Implementation of such methods on avocado and citrus are difficult due to the relatively primitive methods available for thrips sampling, which are labor intensive and rely on experienced and intuitive pest control advisors. The goal of the work described here is to examine alternatives to traditional insecticides such as Bt proteins and entomopathogenic fungi to control avocado and citrus thrips, with the ultimate target of utilizing entomopathogens to aid in field control, evaluate the insecticides registered for avocado thrips management on the native predaceous mite Euseius hibisci, assess citrus thrips oviposition on blueberry varieties, and determine whether citrus thrips is actually a complex of species.

Citrus thrips, Scirtothrips citri , is a plant-feeding pest most widely recognized for the damage it causes to citrus and mango fruits and has been recognized as a major pest of California citrus since the 1890s . Recently, its known host range has broadened and they have become a significant pest of a relatively new crop planted in the San Joaquin Valley of California, highbush blueberries . Citrus thrips feed on blueberry foliage during the middle and late portions of the season causing distorted, discolored, and stunted flush growth and poor development of fruiting wood required to obtain the subsequent crop . High numbers of thrips on blueberries , coupled with repeated pesticide applications of the few effective and registered pesticides, poses a concern regarding pesticide resistance management . Currently, there are no integrated pest management plans available for control of citrus thrips in blueberry. This is primarily due to the recent nature of this crop-pest association. Avocado thrips, Scirtothrips perseae Nakahara, is a relatively new pest of avocados in California. It appeared in the state in 1996, and, at the time, was a species new to science . By 1998, crop damage reduced industry revenues by 12% . Avocado thrips adults can feed on over 11 plant species’, however, larvae have been found only on avocados in the field in both California and Mexico, suggesting that S. perseae has a highly restricted host range . Although it has little effect on tree health, avocado thrips feed directly on immature fruit , and obvious feeding scars cause severe downgrading and culling of damaged fruit . With a limited number of pesticides available for thrips control and the propensity with which economically important thrips develop insecticide resistance, it is wise to monitor population levels carefully,large plastic pots limit treatments to population levels of economic concern and time treatments optimally . Appropriate cultural practices and conservation of natural enemies should be practiced in concert with the use of pesticides only on an as-needed basis. Thus, continuing the search for effective biological and chemical controls useful in citrus and avocado thrips management is important. For both species of thrips, some pupation occurs on the tree in cracks and in crevices’, however, the majority of both species drop as late second instars from trees to pupate in the upper layer of the leaf litter under trees . Propupae and pupae are rarely seen, move only if disturbed, and do not feed. Thus, pupation in the upper layers of the soil surface may create the ideal interface for control using the entomopathogenic fungi Beauveria bassiana . Coarse organic mulch beneath trees and the maintenance of a mulch layer, a common practice by many growers as a method of Phytophthora spp. management in avocados , may reduce survival of thrips that drop from trees to pupate below the tree. The effectiveness of mulching to control thrips is uncertain and labor costs are required to add mulch may not be justified solely for thrips control. There is increasing pressure in the U.S. to move away from broad-spectrum insecticides and focus on alternative methods of control, e.g., genetically modified crop plants expressing Bacillus thuringiensis toxins , use of entomopathogens, and similar approaches. Applications of B. bassiana have been reported to decrease populations of thrips in greenhouse cucumbers, chrysanthemums, gerbera daisies, roses, and carnations .

Microbial insecticides containing δ-endotoxins from Bt have been used as alternatives to conventional chemical insecticides for almost 70 years . Bt produces insecticidal proteins during the sporulation phase as parasporal crystals. These crystals are primarily comprised of one or more proteins, i.e. Crystal and Cytolitic toxins, also called δ-endotoxins. From a practical perspective, Cry proteins are parasporal inclusion proteins from Bt that exhibit experimentally verifiable toxic effects to a target organism or have significant sequence similarity to a known Cry protein . Similarly, Cyt proteins are parasporal inclusion proteins from Bt that exhibit hemolytic activity or has obvious sequence similarity to a known Cyt protein. These toxins are highly specific to their target insect, are innocuous to humans, vertebrates and plants, are regarded as environmentally friendly, are completely biodegradable, and show little adverse effect on non-target species . The Cyt proteins are significantly different both in their structure and their biological activities from the Cryproteins. However, Cyt proteins have shown toxicity to non-dipterous insects . In fact, Cyt proteins in some cases can extend activity to other Bacillus spp. for mosquitoes that lack the proper receptor . Many studies with thrips involving Bt proteins have typically evaluated Cry toxins in transgenic crops targeted mainly toward lepidopterous pests and there are no published studies we know of representing the impact of Cyt proteins on thrips. Due to the synergism seen between these two Bt proteins and the method of thrips feeding, commonly described as ‘punch and suck’ , whereby leaf tissue is macerated prior to ingestion, we hypothesized that Cry or Cyt proteins could potentially be useful against thrips pests. The goal of this investigation was to determine if Cry or Cyt proteins or B. bassiana could be used effectively to manage citrus and avocado thrips. Field management of both thrips species is the ultimate goal with these biopesticides but field studies are laborious and expensive. Thus, we evaluated these materials in the laboratory to determine which were sufficiently efficacious to warrant follow-up field studies. Leaves of both avocado and citrus for all bio-assays were chosen in observably identical states; young and soft but fully expanded leaves were used as these are the type on which both species of thrips prefer to feed and large leaves were needed to fit in the Munger cell bio-assay units that confined the thrips on treated leaves . Briefly, Munger cells were constructed by using a Plexiglas sandwich; the middle cell layer was drilled with 3.2-cm diameter bit to provide a circular test arena .

Two lot numbers of RMBD representing separately prepared batches of each diet were selected for analysis in order to assess for consistency of any ingredient contamination between the 2 batches. One canine and one feline veterinary prescription extensively hydrolyzed poultry feather-based diet were used as negative controls. Of the 9 species of animal DNA tested, 8 species, including pork, chicken, duck, rabbit, lamb, beef, salmon, and turkey, were detected in at least 1 sample of the canine and feline RMBD tested. Only kangaroo DNA was not detected in any of the RMBD. The 2 extensively hydrolyzed poultry feather-protein based diets contained either trace amounts of chicken DNA or no detectable DNA . In the canine RMBD, DNA of 1 or more animal species not indicated on the label was identified in 9 out of 9 diets, in either 1 or both of the tested batches . Of the 18 batches tested, 89% tested positive for unlisted animal-source DNA. An average of 4.4 unlisted proteins was detected in each diet. A total of 2 batches were found to contain DNA consistent with the stated label ingredients. The diet with the greatest number of unlisted proteins was a single batch , labeled as containing turkey and sardine. It contained a total of 6 unlisted proteins . The unlisted DNA most frequently detected was lamb . Discrepancy in the unlisted DNA between batches was noted in 78% of batches. In the feline RMBD, DNA of 1 or more animal species not indicated on the label was identified in 7 of 9 diets, in either 1 or both of the tested batches . Of the 18 batches tested, 61% were positive for unlisted animal-source DNA. An average of 2.6 unlisted proteins was detected in each diet. A total of 7 batches were found to contain DNA consistent with the stated label ingredients. The diet with the highest number of unlisted proteins was a single batch ,snap clamp labeled as containing chicken and salmon. It contained 5 unlisted proteins . The unlisted DNA most frequently detected was turkey .

Discrepancy between batches was noted in 56% of batches. All of the canine and feline RMBD included in the analysis were found to contain the proteins listed on their labels. sources of oil did not contain cod or sardine DNA as potential allergens. In general, plant- and animal-based oils are not considered allergenic when highly purified . The commercial RMBD tested were obtained in California due to the proximity to the testing facility . Since kangaroo meat is not used by any of the manufacturers in their RMBD, this finding serves as an additional negative control for this study to validate that no DNA of kangaroo origin was detected in the analysis, as would be expected. Analysis of the 2 extensively hydrolyzed poultry feather based diets revealed no detection of unlisted animal DNA. This is consistent with previous reports that contaminants are detected less commonly and in lower numbers in hydrolyzed diets . The extensive hydrolysis of poultry feather proteins into component amino acids or very short oligopeptides is intended to avoid inducing IgE-mediated mast cell activation that can occur with proteins 10 kDa in size or greater . Extensive hydrolysis to reduce poultry allergenicity has been validated in both serum IgE and feeding trials to show the clinical benefits for CAFR . These negative control diets were selected because of the rigorous quality control methods undertaken by the manufacturer to ensure cross-contamination does not occur before market release . While the canine diet did test positive for chicken DNA, the manufacturer does list the feathers of chicken, turkey, and duck as their sourced raw materials . The target gene of the analysis for chicken DNA, transforming growth factor beta 3, is a protein expressed in chicken feathers . Additionally, the manufacturer is aware that cross-contamination needs to be avoided in a therapeutic diet and has developed and clinically validated calibration curves to prevent contamination .

These calibration curves correspond to a known DNA level that was clinically tolerated based on Global Skin Scores in feeding trials in order to set a tolerance level for ancillary proteins known as the NPPI , which is strictly monitored in each diet prior to allowing market release . Based on the manufacturer’s quality control data, 72.3% of these extensively hydrolyzed diets contain DNA below the limit of detection , and 25.7% may have DNA above the LOD but below a safety threshold of 1.2 g/g . However, no diet released to market will exceed the established cut-offs of the NPPI based on the pre-established calibration curves . Therefore, trace copies of chicken DNA may be expected on PCR in some of the diets released to market, as was found in our study. The DNA in the feline extensively hydrolyzed diet in this study was below the LOD, and no animal DNA was detected in the assay. Based on the sensitivity of qPCR, it can be argued that these assays, being sensitive enough to detect as few as 10 copies of the target gene, are of greater sensitivity than that required to detect clinically meaningful contamination that would trigger CAFR. There is no established maximum tolerable level of a contaminating protein that may elicit a pruritic reaction in a food sensitized pet. In humans, soy protein concentration as low as 10 ppm may evoke a reaction in a soy-sensitized individual . Additionally, dose distribution has been demonstrated to vary between different food allergens in sensitized humans, showing that a tolerance range may exist for different food antigens themselves . The additional concern for CAFR pets is that, as opposed to most humans, pets are often fed a specific commercial diet with daily regularity, increasing their risk of chronic re-exposure to a food antigen contained therein. As a result, even small amounts of unknown allergens may lead to a cumulative reaction in a CAFR-affected pet and skew the clinical impression of their response to a particular ED.

These reactions may even be sporadic if there is significant variation of the protein constituents of the diet between batches. The need to validate food allergic threshold distributions in canine and feline CAFR is an important area for future research. Until such time, rigorous quality control using protein analysis methods such as qPCR or enzymelinked immunosorbent assay remains a sensitive method to confirm such contaminants are not detected in therapeutic diets fed for the purpose of the clinical diagnosis of CAFR. This remains the industry standard for quality control of commercially produced diets, including extensively hydrolyzed diets. In conclusion, this study confirms that commercial RMBD should not be considered appropriate for selection as ED in the diagnosis of CAFR as a result of their tendency to include unlisted protein ingredients, which can differ from batch to batch. A clinician should use caution when interpreting the results of an owner-directed ED trial using RMBD to exclude CAFR as a cause of their pet’s pruritic dermatopathy,growing blueberries and veterinarian-guided elimination diet oversight is still recommended. Until further evidence is presented, an elimination diet and provocation trial with a patient-appropriate prescription-based diet subjected to applicable quality control or a home-prepared novel protein diet remain the current diagnostic standard for CAFR.In vineyard production systems, canopy management practices are usually employed to control the source-sink balance and improve the cluster microclimate leading to an improved grape composition and resultant wines . Canopy density is usually controlled during the dormant season thought the winter pruning. Additional canopy management practices may be applied during berry development. Fruit-zone leaf removal and especially, shoot thinning have been widely used in order to increase the cluster exposure to solar radiation, reduce crop load as well as decreasing the pest pressures , increasing flavonoid content and diminishing herbaceous aromas . Nevertheless, when high air temperature and excessive radiation combine, detrimental effects on berry acidity and flavonoid content have been reported in warm climate regions . Leaf removal consists of removing basal leaves around the clusters in the east or north side during grape development increasing the cluster exposure to solar radiation. It is well known that an early leaf removal increased total soluble solids, anthocyanins, and flavonols . However, some authors reported increases in titratable acidity in Sangiovese and Teran cultivars while other authors found decreases in acidity with basal leaf removal on Tempranillo . Conversely, Sivilotti et al. reported a positive effect of leaf removal applied after flowering on Merlot grapevine by improving cluster integrity by reducing incidence of Botrytis, and lower herbaceous aromas without affecting yield and cluster mass. Contrariwise, Pastore et al. reported that defoliation at veraison reduced the anthocyanin content and increased the impact of sunburn. In fact, these authors found that leaf removal induced a general delay in the transcriptional ripening program, which was particularly apparent for structural and regulatory genes involved in the anthocyanin biosynthesis.

Clearly, vineyard location, cultivar , timing of leaf removal , method , and degree of leaf removal , the growing season , among others, are all factors influencing how leaf removal affects grapevine berry composition and integrity. On the other hand, shoot thinning has been related to increased cluster and berry mass and the number of berries per cluster, with a reduction on yield . Conversely, Wang et al. observed that shoot thinning had relatively minor impacts on yield components because of a compensatory effect due to the lower cluster number with concomitant increase in cluster mass. Contrarily, shoot thinning practices on grapevine did not show a great impact on berry primary metabolism , however, secondary metabolites were affected by them . In fact, we recently reported an increase of two-fold in the flavonol content of Merlot berries when leaf or shoot removal was applied mainly by increasing the proportion of quercetin and kaempferol derivatives in detriment of the myricetin derivatives . Berry composition is dependent on a complex balance between compounds derived from primary and secondary metabolism. Between secondary metabolites, flavonoids play an important role in the quality and the antioxidant properties of grapes and are very responsive to environmental factors such as solar exposure . Anthocyanin compounds are responsive of the berry color, and flavonols act as a UV shields, contribute to the wine antioxidant capacity, color stability, and hue through copigmentation with anthocyanins . On the other hand, the methoxypyrazines are wine key odorants contributing to their herbaceous characteristics and have been related to unripe berries and poor-quality wines when these are not part of the wine typicity . Since they can be present in grape berry and wines at high levels, they may have an important sensorial impact on wine quality . Among methoxypyrazines, the 3-isobutyl-2- methoxypyrazine is considered the most relevant to wine flavor due to its correlation with the intensity of the bell pepper character of wines and its content at harvest seems to be dependent of the solar exposure . The differences found in the literature about the effect of manipulating the canopy architecture on the flavonoid and aromatic content due to different solar exposure of berries in warm climates opens an important field of research. Therefore, we aimed to find the optimal ranges of berry solar exposure estimated as percent of kaempferol for flavonoid synthesis up regulation and the thresholds for their degradation, and to evaluate how canopy management practices such as leaf removal, shoot thinning and a combination of both affect the grapevine yield components, berry composition, flavonoid profile, and herbaceous aromas.An experiment was performed in 2017 on 7-year Cabernet Sauvignon vines grafted onto 110 Richter root stock with NW-SE row orientation and a vine spacing of 2 m × 2.4 m in a commercial vineyard in Oakville, CA . Individual berries were sampled at harvest according to their position in the canopy and overexposure based on visual appearance. Each independent replicate was a sample of 75 berries collected from up to 50 plants each , these plants being potentially the same for all exposures. From each sample, 55 berries were used for must analyses and berry mass, and the remaining 20 berries were storedat −20°C for analyses of flavonoids. Thus, four observational treatments with four replicates consisted in two rows of 25 vines each were established: non-exposed berries collected from interior clusters ; exposed but free of signs of overexposure, collected from northeast exposed clusters ; exposed and with mild signs of sunburn, collected from southwest exposed clusters ; and exposed and with severe signs of sunburn with signs of damage collected from southwest exposed clusters .

The top three diseases that compose this data set are Bacterial Spot, Haunglongbing, and Yellow Leaf Curl. Bacterial Spot, which composes 10% of the data, is a bacterial disease that affects many crops by causing their leaves to develop yellow spots that turn brown in the middle. It also causes crops to develop black or brown spots of rot on their fruits. Haunglongbing composes 10% of the data set. This bacterial disease affects citrus trees causing their fruits to stay green and fall to the ground early before becoming ripe. This disease is common for citrus, but keep in mind that this data set only has images of this disease affecting Oranges. Yellow Leaf Curl composes 9.9% of the data set and is a Viral infection that only affects Tomatoes. “Yellow leaf curl virus is undoubtedly one of the most damaging pathogens of tomatoes, and it limits the production of tomatoes in many tropical and subtropical areas of the world. It is also a problem in many countries that have a Mediterranean climate, such as California. Thus, the spread of the virus throughout California must be considered a serious potential threat to the tomato industry” . Note that the total percentage of diseased images contributing to this data set is 72.2% because the other 27.8% of this data set is healthy crop images. See Table 2.4 for a comparison of the amount of diseased and healthy crop images in this data set. The crops that contributed to the diseased images are Apple, Bell Pepper, Cherry, Grape, Maize, Orange, Peach, Potato, Strawberry, Squash, and Tomato. The crops that contributed to the healthy images are Apple, Bell Pepper, Blueberry, Cherry, Grape, Maize, Peach, Potato, Raspberry, Strawberry, and Tomato. For a visual representation of what the diseased and healthy crop images look like, see Figure 2.1 for nine different crop images.

The crop images have their classification labels above them to identify the crop name and disease or healthy. The images in Figure 2.1 are crop images of classification labels Apple-Apple Scab, Apple-Healthy, Peach-Healthy, GrapeHealthy, Raspberry-Healthy, Soybean-Healthy, Grape-Black Rot, and Peach-Bacterial Spot. While the Transformer architecture has become the de-facto standard for natural language processing tasks,square plastic pot its applications to computer vision remain limited. This was the motivation for Dosovitskiy et al. to look into the implementations of the transformer model for image classification tasks, and the vision transformer was created. The transformer architecture for natural language processing tasks works similarly to a vision transformer. In natural language processing, sentences are broken down into words. Then each word is treated as a sub-token of the original sentence. Similarly, the vision transformer breaks down an image into smaller patches, each patch representing a small sub-section of the original image. To visually see how sentences are broken down into word tokens and images broken down into patches, see Figure 2.2 from. Keep in mind that the position of the image patch is very important. If the image patches are out of order, then the original image will also be out of order. The vision transformer is designed to start with an extra learnable class embedding that is equivilent to 0. Which represents the start of the image and sequence of patches to come. The extra learnable class embedding allows the model to learn embeddings specific to each classification label. “The pre-training function of vision transformer is based solely on the classification label given; therefore, the learnable class embedding is even more important to successfully pre-training the vision transformed model”. Without the learnable class embedding, the transformer will not understand the classification labels that are attached to each image.

To keep the order of the sequence of patches that make up the image, the patches are instilled with positional embeddings. “For the vision transformer, these positional embeddings are learned vectors with the same dimensionality as our patch embeddings. After creating the patch embeddings and pre-pending the classification label embedding, it is then summed with the positional embeddings”. Finally, the summed embeddings are shown to the transformer encoder. After the entirety of the image is shown to the transformer encoder, the model has then learned that image under the given classification label. For a more understandable visual example, see Figure 2.4 from . It visually demonstrates the architecture of how the image patches are linearly projected and linearly embedded, how the patches receive a learnable class embedding, and then finally showing the image to the transformer encoder and the model learning the given image for the given classification label. Dosovitskiy and et al. also found that “ViT attains excellent results when pre-trained at sufficient scale and transferred to tasks with fewer data points. When pre-trained on the public ImageNet-21k data set or the in-house JFT-300M data set, ViT approaches or beats state of the art on multiple image recognition benchmarks”. A vision transformer model that has been pre-trained on large data sets such as ImageNet-21k are able to help in making a model more effective [DBK21].This project will implement the vision transformer developed by Dosovitskiy et al. and mentioned in their paper. The framework of their ViT model will be used and accessed through the Hugging Face platform and their package transforms using Python. The vision transformer model comes pre-train on the ImageNet-21k, a benchmark data set consisting of 14 million images and 21k classes. The vision transformer model has been pre-trained on images with pixel size 224 × 224. Therefore, any data that is to be further trained on this model must also be of pixel size 224 × 224.“Data augmentation is the process of transforming images to create new ones for training machine learning models” . “Data augmentation increases the number of examples in the training set while also introducing more variety in what the model sees and learns from. Both these aspects make it more difficult for the model to memorize mappings while also encouraging the model to learn general patterns.

Data augmentation can be a good substitute when resources are constrained” because it artificially creates more of your data when it is not possible to get more data.In the case of this project, the function being used to perform the data augmentations isset transfrom from the Hugging Face Datasets package in Python. This function performs data transformations only when the model training begins. Therefore, transformations can be done on the fly and save on computational resources. Then at each epoch, the transformations are applied to every image given to the model, so the amount of training data stays constant, but variation is added to the original data through transformations. This does not increase the number of training images as other data augmentation packages would, this artificially augments with transformations and variation .Data augmentation is an important step when training machine learning models because they can perform very powerfully if the given data sets for training are too small to train with. These models can start to over-fit, which is a problem because then the model will memorize mappings between the inputs and expected outputs. There are 54,306images in this data set, which may seem like a lot of images,square pot but for a machine learning model, it is not that much. That is why data augmentation is being implemented as a step to reduce possible model over fitting.See Table 3.1, for training results of the pre-trained ViT Image classification model trained on the Plant Village data set. The table displays the model’s Training Loss, Validation Loss, Precision, Recall, model F1 score, and model Accuracy over the 10 epochs. Model training loss indicates how well the model is fitting the training data. Model validation loss indicates how well the model fits new data. The best model that was chosen was epoch 10, which is bold in Table 3.1. The model from epoch 10 has a training loss of 0.088 with a validation loss of 0.073, the lowest pair out of all the epochs. For this model, Precision, Recall, the model F1 Score, and Accuracy all have the value of 1.00. These results indicate that the model has a high positive identification rate. The model seems to have reached a convergence in values between epochs 8 to 10. The training results for epoch 10 showed that the Evaluation of Samples per Second for the model is 50.29. This indicates that number of samples the machine learning model can process and make predictions of in one second is 50.29. Also, the Evaluation Steps per Second is 1.58, which indicates the number of iterations that the machine learning model can complete in one second. Model testing was done with the 15% of the data that was reserved for testing and never shown to the model during training. See Table 3.2, in order to see the overall testing results of the model in a table. The model has an Accuracy of 99%. Meaning the model has the ability to guess the classification label 99% of the time correctly. Total Time in Seconds is the amount of time it took for the image classification model to be tested with the test data set, which is 1460.88 seconds also 24.34 minutes. Samples per Second is 1.15, which is the amount of data samples or instances that the image classification model can process and make predictions on in one second. Latency in Seconds is 0.86, which refers to the amount of time it takes for a single prediction to be made by the image classification model in oneIn order to see how the image classification model can classify an image, see Figure 3.2 and Table 3.3.

Figure 3.2 shows an example image of which the image classification model was tested on. The image has its true classification label above it, which is Apple-Apple Scab. Table 3.3 has the scores and labels of five different classification label predictions for what it thinks the image in Figure 3.2 could be. The score is on a scale from 0 to 1, with 1 meaning 100% confidence in the classification label that the model is predicting. The value of the score is split across the five predictions, meaning when we add up all of the score values for all five predictions, the value will add up to 1. The model’s top prediction with a score of 0.91% is the classification label Apple-Apple Scab, which is the true classification label of the image in Figure 3.2.The overall performance of the pre-trained ViT image classification model with data augmentation shows good promise. The best epoch provided that F1, Accuracy, Precision, and Recall, were all equal to 1.0. This is not the best situation but shows there is room for improvement. Given the previous epochs from 1 to 8, has values for their F1 Score and Accuracy. It shows that there is possible room to improve the model with more fine-tuning and possibly an early stop in training to not have the model over-train to get the result of 1.0 for F1 Score and Accuracy. Another possible reason for the result could be the large imbalance of images between classification labels and that the Plant Village data set is considered to be a small data set. These types of results are good but not realistic for model prediction power. Even though these values are incredibly high, the training and validation loss is still fairly low and slowly converging to 0. This means that the model is learning over time, which is a good sign and shows room for improvement. A possible future improvement for this project would be to find another data set with more specific plant disease information to train the model on. Efforts will be made to look for data that includes more plant pests. That variation would be beneficial because the data set for this project mainly contains crop disease images. The disease Spider Mite, is labeled as a disease in this data set but in reality, is not a disease. It is the only classification label that has pest-inflected crop images in this data set. Having more data on crop pests would be beneficial because crop pests also cause a significant amount of crop loss and damage as well.

The enzyme UFGT catalyzes the final step of anthocyanin biosynthesis, therefore UFGT has been considered by many authors to be a critical enzyme in anthocyanin biosynthesis . Temporary stimulation of gene transcription is believed to be related to a decrease in S-ABA concentration over time. In ‘Crimson Seedless’ grapes, a constant decrease in S-ABA levels with a half-life time of 14.7 days was observed in treated grape berries . The natural decrease in ABA concentration, along with the decrease in S-ABA levels, may, therefore, lead to decreased activity of some genes, depending on the S-ABA concentration in the plant. Expression of the UFGT gene increased considerably 7 days after S-ABA application in ‘Crimson Seedless’ grapes but decreased 3 weeks after treatment, becoming similar to the control . In “Cabernet Sauvignon” grapes treated with ±cis, trans-ABA, expression analysis of anthocyanin biosynthetic genes revealed that the maximum expression levels were only reached 10–17 days after application and that they then rapidly decreased . ABA cis– and trans-isomers differ in the orientation of the carboxyl group at carbon 2. Only the ABA cis-isomer is biologically active, and it accounts for almost all of the ABA produced in plant tissues. However, unlike the S and R enantiomers, the cis– and trans-isomers can be interconverted in plant tissue . Most of the studies on S-ABA involved V. vinifera cultivars were done in temperate zones and testing a single application . In this study, we evaluated the response of a new V. vinifera × V. labrusca hybrid grape cultivar grown in a subtropical area to multiple S-ABA applications. This hybrid often shows lack of color development; therefore,25 liter round pot our results confirm the effectiveness of S-ABA to improve the color of ripening berries, even under warm climate conditions.

The application of S-ABA to berries of the seedless grape Selection 21 increased the total anthocyanin concentration, changed the proportion of individual anthocyanins, improved their color attributes, and increased the expression of transcription factors and anthocyanin biosynthetic genes. Two applications of 400 mg/L S-ABA, at 7 and 21 DAV, resulted in the best results in terms of color increment and total anthocyanin concentration, favored the accumulation of trihydroxylated anthocyanins, and increased the expression of transcription factors and of the genes F3H and UFGT. These results not only show that S-ABA is a valuable tool for improving the color of red grapes in warm areas, where color deficiency is frequently observed, but also suggest that S-ABA may be useful in grape breeding programs by permitting the selection and release of new cultivars with natural poor color, but other desirable characteristics such as high yield and resistance to common diseases. The iCT in Hemodialysis Centers initiative is governed by a Steering Committee consisting of a health professional , a new Faculty member , a health care administrator , 2 patients , and a health researcher . The Steering Committee takes overall responsibility for all aspects of the initiative, including the workshop. Aligned with the vision of CIHR’s SPOR, the grant activities are undertaken in full partnership with persons on hemodialysis , as well as health care providers and health administrators.Guided by their priorities in every stage of the research process, needed and meaningful clinical trials in hemodialysis can be implemented for successful knowledge translation and uptake in care settings.As many clinical decisions in hemodialysis care are made at the program/unit level , rather than from individual clinician-patient discussions, the trials in this initiative use cluster-randomization of entire hemodialysis units to assess the benefits and risks of intervention. With these considerations, pragmatic trials can test the effectiveness of promising interventions in real-world hemodialysis settings and broad patient groups.

Furthermore, critically needed trials can be conducted with the same quality as traditional trials with individual randomization, but with less time and at a fraction of the cost. The knowledge gained from these new trials is ultimately expected to improve the health and care of those undergoing hemodialysis. A key objective of the iCT in Hemodialysis Centers initiative is to support the development of at least 2 new promising interventions so that by the end of the 4-year grant period , they are ready for large-scale trial implementation in hemodialysis centers. With the involvement of patients, health care providers, and health care administrators, trial planning will be advanced in a manner that builds consensus on research priorities and considers the challenges to implementing different trial concepts. To fulfill this objective, a stakeholder engagement and research development workshop was held in Toronto, Ontario on June 2 and 3, 2018. The workshop emcee was Dr Amit Garg, nephrologist, Program Lead of the ICES Kidney, Dialysis and Transplantation Ontario provincial program , and the nominated principal investigator of the funded iCT CIHR SPOR grant. Through structured presentations, facilitated group discussions, and expert panel feedback , workshop attendees shared knowledge and opportunities to develop and collaborate on innovative, pragmatic, cluster-randomized registry trials embedded in hemodialysis care.In the last decade there has been a rise in adoption of sustainable soil management practices that reduce soil erosion and bolster soil organic matter to counter the impacts of climate change on agricultural soils . Traditionally, vineyard rows were kept bare, with the use of herbicides and tillage. However, there is disagreement on the utility of this practice due to the detrimental effects of tillage on air quality and soil physical, chemical, and biological properties . Thus, the adoption of cover crops and reduced tillage is considered a sustainable alternative to traditional management of vineyard floors . Furthermore, environmental regulations and public perception serve as additional incentive to adopt climate-smart practices . The benefits of cover crops on the properties of soils are well documented.

They can increase soil organic matter , improve water infiltration and aggregate stability, reduce soil erosion and greenhouse gas emissions , and increase vineyard biodiversity . Nevertheless, the adoption of cover crops in vineyards is limited by the concern of excessive competition between the cover crop and grapevine for water and nutrients . Many studies have sought to quantify the effects of cover cropping on the grapevine, yet the influence of cover crop adoption on grapevine physiology and production remains elusive. There is agreement in literature that cover crops may reduce vegetative growth, with more pronounced yield losses in warmer regions. However some studies have found no effect . Grapevine physiological responses to cover cropping were also documented, and minimal effects on leaf gas exchange have been found. The presence of a cover crop is generally reported to detrimentally affect grapevine water status . Despite wide acceptance of this particular effect, results are inconsistent as some studies have shown that cover crops may improve early season water status, yet others have concluded that cover cropped vineyards do not display better water status compared to those with bare soil . Ultimately, previous works agree that changes in grapevine physiological response to cover crop adoption are largely driven by the climatic conditions and irrigation regime at a given site . Likewise, it was assumed that the competition between the grapevine and cover crop for water and nutrients resulted in yield decreases, but this effect was also not consistent . Yield reductions and/or no effect on yield are the most common results from such work. However, cover crop species appears to be a more influential factor than merely the presence of a cover crop. Yield increases have even been reported in some vineyards planted with annual species such as oats or legumes . Consequently, any changes to berry composition as a result of cover crop adoption is closely associated with changes in yield, such as smaller berry size and purportedly greater content berry flavonoids . The adoption of reduced or no-till management preserves SOM, reduces soil erosion, improves soil structure, and is considered integral to reducing GHG emissions from the agriculture sector . The influence of tillage on soil properties, while not entirely understood, is more studied than the impact on crops themselves, particularly in permanent cropping systems such as vineyards. However,25 liter pot few reports have investigated the influence of tillage on grapevine physiology under the presence of a cover crop. While differences in leaf gas exchange have been reported between grapevines grown under conventional tillage compared to those under permanent cover crops, there is little evidence of tillage having a direct influence on grapevine stomatal conductance and net photosynthesis . Although no-till practices are often promoted for their positive influence on soil infiltration and conservation of soil water, few studies have found that this effect translated to ameliorated plant water status in grapevine . Previous works indicated that vegetative growth is greater under conventional tillage while yield reductions are typically associated with no-till management, despite research that indicated no effect on production . Furthermore, while some studies have reported increased berry skin anthocyanin content under no-till management, overall there is limited impact of tillage on berry composition . Cover cropping and reduced tillage management are two practices that directly alter the growing environment of the grapevines. Thus, the selection of appropriate vineyard floor management practices is critical in order to maximize benefits to the soil while minimizing the impact on grapevine function and productivity.

This selection involves decisions in space , type , and time including perennial vs. annual species selection and timing of termination . Factors such as cultivar, vineyard age, macroclimate, soil physiochemical characteristics, and the overall goals for the use of the selected cover crop and tillage system must also be considered. These elements have been shown to contribute to the effect of the practices on grapevine functioning and production . The objective of this work was to investigate the effects of cover cropping and tillage on whole grapevine physiology in two contrasting production regions in California, USA. Specifically, we studied the interactive effects of tillage and cover crops on grapevine water status, leaf gas exchange, components of yield, berry composition and resulting water footprint in two contrasting production regions of California during arid seasons. At both experimental sites, the experiments were arranged as a split-plot 3 × 2 factorial arrangement of treatments with four and three replications . Each treatment-replicate consisted of 15 grapevines. Three grapevines in the middle of each replicate were used for measurements and the distal plants on either end served as buffer plants. Treatments included tillage as the main plot [conventional tillage and no-till ] and the sub-plot was randomly applied within the main plots as i) Perennial grass ; ii) Annual grass ; iii) Resident vegetation . The cover crop seed was drilled in a 1.5 m wide strip according to seed manufacturer’s recommended rate prior to receiving fall/winter rains in 2019 and 2020 at a rate of 605 kg/ha and 84 kg/ha for the perennial grass and annual grass treatments, respectively. Resident vegetation was allowed to grow within the 1.5 m strip and mowed at the vineyard manager’s discretion. All other cultural practices were conducted according to University of California Cooperative Extension guidelines .At harvest, fifty berries were randomly collected from the three middle grapevines within each replicate and immediately processed. Berries were weighed and gently pressed by hand to squeeze the juice. Total soluble solids were determined using a temperature compensating digital refractometer . Must pH and titratable acidity were determined with an autotritrator . TA was determined by titrating with 0.1 N sodium hydroxide to an end point of 8.3 pH and reported as g/L of tartaric acid. Berry skin anthocyanin content was determined at harvest from 20 berries randomly collected from each treatment-replicate. Berries were gently peeled, skins were freeze-dried . Freeze-dried tissue was ground with a tissue lyser . Fifty milligrams of the resultant powder was extracted in methanol: water: 7 M hydrochloric acid to determine anthocyanin content. Extracts were filtered using a 0.45 µm filter and analyzed using an Agilent 1260 series reversed-phase high performance liquid chromatography system coupled to a diode array detector. Separation was performed on a reversed-phase C18 column LiChrospher 100, 250 mm × 4 mm with a 5 µm particle size and a 4 mm guard column of the same material at 25 ℃ with elution at 0.5 mL per minute. The mobile phase consisted of a constant 5% of acetic acid and the following gradient of acetonitrile in water: 0 min 8%, at 25 min 12.2%, at 35 min 16.9%, at 70 min 35.7%, 65% between 70–75 min, and 8% between 80–90 min.

The domestication of cultivated strawberry has followed a path different from that of other horticulturally important species, many of which were domesticated over millennia and traced to early civilizations, e.g., apple , olive , and wine grape . Although the octoploid progenitors were cultivated before the emergence of F.  ananassa, the full extent of their cultivation is unclear and neither appears to have been intensely domesticated; e.g., Hardigan et al. did not observe changes in the genetic structure between land races and wild ecotypes of F. chiloensis, a species cultivated in Chile for at least 1,000 years . With less than 300 years of breeding, pedigrees for thousands of F. ananassa individuals have been recorded, albeit in disparate sources. To delve more deeply into the domestication history of cultivated strawberry, we assembled pedigree records from hundreds of sources and reconstructed the genealogy as deeply as possible. One of our initial motives for reconstructing the genealogy of cultivated strawberry was to identify historically important and genetically prominent ancestors of domesticated populations, in large part to guide the selection of individuals for whole-genome shotgun sequencing and DNA variant discovery, inform the development of single-nucleotide polymorphism genotyping platforms populated with octoploid genome-anchored subgenome-specific assays, and identify individuals for inclusion in genome-wide studies of biodiversity and population structure . The genetic relationships and genetic contributions of ancestors uncovered in the genealogy study described here guided the selection of individuals for downstream genomic studies that shed light on genetic variation and the genetic structure of domesticated populations worldwide .

Our other early motive for reconstructing the genealogy of strawberry was to support the curation and stewardship of a historically and commercially important germplasm collection preserved at the University of California, Davis ,black plastic plant pots with accessions tracing to the early origins of the strawberry breeding program at the University of California, Berkeley , in the 1920s . We sought to develop a complete picture of genetic relationships among living and extinct individuals in the California and worldwide populations, in part to assess how extinct individuals relate to living individuals preserved in public germplasm collections. Because 80% or more of the individuals we documented in the genealogy appear to be extinct, they could only be connected to living individuals through their pedigrees. One of the ways we explored ancestral interconnections between extinct and living individuals was through multivariate analyses of a combined pedigree–genomic relationship matrix estimated from genotyped and ungenotyped individuals . The holdings and history of the UCD Strawberry Germplasm Collection were shrouded in mystery when our study was initiated in 2015. The immediate challenge we faced in reconstructing the genealogy was the absence of pedigree records for 96% of the 1,287 accessions preserved in the collection, which is hereafter identified as the “California” population. To solve this problem, authenticate pedigrees, and fully reconstruct the genealogy of the California population, we applied an exclusion analysis in combination with high-density SNP genotyping . Here, we demonstrate the exceptional accuracy of diploid paternity analysis methods when applied to individuals in an allooctoploid organism genotyped with subgenome-specific SNPs on high-density arrays .

Several thousand SNP markers common to the three arrays were integrated to develop a SNP profile database for the parentage analyses described here. SNPs on the 50-K and 850-K arrays are uniformly distributed across the octoploid genome and informative in octoploid populations worldwide . The 50-K SNP array harbors 1 SNP/16,200 bp, whereas the 850-K array harbors 1 SNP/953 bp, telomere-to-telomere across the 0.81-Gb octoploid genome. The genealogies of domesticated plants, especially those with long-lived individuals, overlapping generations, and extensive migration and admixture, can be challenging to visualize and comprehend . We used Helium to visualize smaller targeted pedigrees; however, the strawberry pedigree networks we constructed and investigated were too large and mathematically complex to be effectively visualized and analyzed with Helium and other traditional hierarchical pedigree visualization approaches. Hierarchical methods often produce comprehensible insights and graphs when applied to pedigrees of individuals or small groups but yield exceedingly complex,labyrinthine graphs that are difficult to interpret when the genealogy contains a large number of individuals and lineages. We turned to social network analysis to explore alternative approaches to search for patterns and extract information from the complex genealogy of strawberry. The pedigree networks of plants and animals share many of the features of social networks with nodes connected to one another through edges relationships. We used SNA methods, in combination with classic population genetic methods, to analyze the genealogy and develop deeper insights into the domestication history of strawberry . SNA approaches have been applied in diverse fields of study but have apparently not been applied to the problem of analyzing and characterizing pedigree networks . With SNA, narrative data are translated into relational data and summary statistics and visualized as sociograms . Here, we report insights gained from genealogical studies of domesticated strawberry populations worldwide.

Our studies shed light on the complex wild ancestry of F. ananassa, the diversity of founders of domesticated populations of cultivated strawberry that have emerged over the past 300 years, and genetic relationships among extinct and extant ancestors in demographically unique domesticated populations tracing to the earliest ancestors and interspecific hybrids .To develop a SNP profile database for DNA forensic and population genetic analyses , we recalled and reanalyzed SNP marker genotypes for 1,495 individuals, including 1,235 UCD and 260 USDA accessions previously genotyped by Hardigan et al. with the iStraw35 SNP array . SNP marker genotypes were automatically called with the Affymetrix Axiom Analysis Suite . DNA samples with > 6% missing data were dropped from our analyses. This yielded 14,650 high-confidence codominant SNP markers for paternity–maternity analyses. While SNP markers are codominant by definition, a certain percentage of the SNP markers assayed in a population produce genotypic clusters lacking one of the homozygous genotypic clusters. These so-called no minor homozygote SNP markers were excluded from our analyses.For a second DNA forensic analysis, 1,561 UCD individuals were genotyped with 50-K or 850-K SNP arrays . This study population included 560 hybrid offspring from crosses among 27 elite UCD parents, the F.  ananassa cultivar “Puget Reliance,” and the F. chiloensis subsp. lucida ecotypes “Del Norte” and “Oso Flaco.” Hardigan et al. included 16,554 SNP markers from the iStraw35 and iStraw90 SNP arrays on the 850-K SNP array. To build a SNP profile database for the second paternity–maternity analysis, we identified 2,615 SNP markers that were common to the three arrays and produced well-separated codominant genotypic clusters with high confidence scores . We subdivided the global population into “California” and “Cosmopolitan” populations, in addition to continent-, region-, or country-specific populations, for different statistical analyses. These subdivisions are documented in the pedigree database . The California population included 100% of the UCD individuals from the global population, in addition to 262 non-California individuals that were ascendants of UCD individuals. The Cosmopolitan population included 100% of the non-California individuals ,black plastic planting pots in addition to 160 California individuals that were ascendants of non-California individuals. We subdivided individuals in the US population into Midwestern, Northeastern, Southern, and Western US populations. The Western US population included only those UCD individuals that were ascendants in the pedigrees of Western US individuals. The country-specific subdivisions were Australia, China, Japan, South Korea, Belgium, Czechoslovakia, Denmark, England, Finland, France, Germany, Israel, Italy, the Netherlands, Norway, Poland, Russia, Scotland, Spain, Sweden, and Canada.DTR and TTR statistics were estimated from equations and using custom R code that we developed and provided as supplemental material . DTR estimates for PO duos and TTR estimates for PPO trios were compared to empirically estimate statistical thresholds to exclude parents. With a perfect dataset , TTR ¼ 0 when both parents in a trio are correctly identified. When estimated from a real-world dataset , TTR ¼ 0 even when both parents in the trio are correctly identified. However, TTR estimates for correctly identified parents are typically exceedingly small and approach zero when genotyping errors are small and DNA profiles are informative . The probability of a type I error depends on the genetic relatedness of individuals in the DNA profile database and the number, informativeness, and genotyping error rates of the DNA markers . A false-positive error occurs when an individual that is not a parent is declared to be a parent , whereas a false negative error occurs when an individual that is a parent is excluded . DTR and TTR thresholds for excluding parents were empirically estimated by bootstrapping .

We drew 50,000 bootstrap samples from a population of 1,002 individuals with known pedigrees by replacing one or both parents in the known PPO trio with a randomly selected individual from the population. We built empirical DTR and TTR distributions from the 50,000 estimates and ascertained the statistical thresholds needed to accurately identify parents, exclude non-parents, and minimize false-positive errors. The bootstrap estimated DTR threshold of DTR  0:0016 yielded a false-positive probability of zero and a false-negative probability of 5%, whereas the bootstrap-estimated TTR threshold of TTR  0:01 yielded false-positive and false-negative probabilities of zero. Thesethresholds were estimated by summing transgression scores summed over 14,650 SNP marker loci. To increase the computational speed and efficiency, DTR statistics were estimated for every PO combination, whereas TTR statistics were only estimated for PPO combinations where the DTR estimates for both parents were less than the empirical threshold . This was done because the number of PPO combinations was prohibitively large and most PPO combinations could be unequivocally excluded using DTR estimates.We reconstructed the genealogy of cultivated strawberry as deeply as possible from wild founders to modern cultivars . To build the database, pedigree records for 8,851 individuals were assembled from more than 800 documents, including scientific and popular press articles, laboratory notebooks, garden catalogs, cultivar releases, plant patent databases, and germplasm repository databases . The database holds pedigree records and passport data for 2,656 F. ananassa cultivars, of which approximately 310 were private sector cultivars with pedigree records in public patent databases . The parents of the private sector cultivars, however, were nearly always identified by cryptic alphanumeric codes, and thus could not be integrated into the “giant component” of the sociogram . Our computer forensic search did not recover pedigree records for 220 individuals in the California population; however,we suspected that their parents might be present in the SNP profile database. Using duo and trio exclusion analyses, we identified both parents for 214 of these individuals and one parent each for the other six individuals. Hence, using a combination of computer and DNA forensic approaches, 2,222 out of 2,470 possible parents of 1,235 individuals in the California population were identified and documented in the pedigree database . The parents declared in pedigree records , identified by DNA forensic methods , or both are documented in the pedigree database . Despite their historic and economic importance, the pedigrees of individuals preserved in the UCD Strawberry Germplasm Collection had not been previously documented. Besides reconstructing the genealogy of the California population, previously undocumented pedigrees of extinct and extant individuals were discovered in the laboratory notebooks of Harold E. Thomas, Royce S. Bringhurst, and others , and integrated into the pedigree database . To further validate the accuracy of DNA forensic approaches for parent identification in strawberry, we applied an exclusion analysis to a population of 560 hybrid individuals developed from crosses among 30 UCD individuals . The pedigrees of the parents and hybrids were known. The parents and hybrids and 1,561 additional UCD individuals were genotyped with 50-K or 850-K SNP arrays . The 50-K array was developed with SNP markers from the 850-K array , which included a subset of 16,554 legacy SNP markers from the iStraw35 and iStraw90 arrays . We developed an integrated SNP profile database using 2,615 SNP markers common to the three arrays. Using PPO trios, we discovered that the SNP profile for one of the parents was a mismatch, whereas the SNP profiles of the other 29 parents perfectly matched their pedigree records. We discovered that the parent stated for 11C151P008 was correct, but that the DNA sample and associated SNP marker profile were incorrect. Hence, the DNA sample mismatch was traced by trio exclusion analysis to a single easily corrected laboratory error. This analysis empirically demonstrated the utility of exclusion analysis for authenticating pedigrees and curating germplasm collections, and showed that parents can be accurately identified with substantially smaller numbers of DNA markers than those applied in our initial study.