Non-cultivated Plants Research Articles

Diet of the Bobolink (Dolichonyx oryzivorus) in rice fields on its wintering grounds in Argentina

Winter diet of Bobolinks (Dolichonyx oryzivorus), a bird considered a pest of rice fields, is known to consist primarily of seeds. However, it is not yet possible to establish the extent to which non-rice plants and animal components contribute to its diet. To contribute to these issues, we studied the diet of the Bobolink found in rice fields on its wintering grounds in Santa Fe, Argentina, to provide information on (i) the composition of the diet and (ii) the relative importance of plant and animal components in the diet and of the different prey categories. We captured Bobolinks with mist nets and obtained samples of stomach contents by warm water and emetic-based regurgitation to determine the composition of the diet (n = 46 samples) and the importance of the different prey (n = 25 samples), mainly during March, just prior to northbound migration. We confirmed that the Bobolink’s diet in this region during this period is predominantly herbivorous (97%) and rice-based (55%), although it also consumes a large number of seeds of non-cultivated plants that represented 42% of the diet. Invertebrates, although of less importance than plant components (3%), had been consumed by 97% of captured individuais. Our results document the importance of non-cultivated plants and animal prey in the diet of Bobolinks in addition to rice.

Phytochemistry, pharmacology and perceived health uses of non-cultivated vegetable Cyphostemma adenocaule (Steud. ex A. Rich.) Desc. ex Wild and R.B. Drumm: A review

Abstract Vegetables have been one of the often recommended and cheap solution to the undernourishment/malnourishment challenge experienced worldwide. Beside the cultivated and exotic vegetables, there are greater number of non-cultivated and wild edible plants’ species. Documenting and revalorizing these neglected vegetables is a must and growing trend these days. The thrust of this study is to offer and give up-to-date knowledge cum perceive health uses of one of these edible plant species called Cyphostemma adenocaule (Steud. ex A. Rich.). This study clearly showed that C. adenocaule is a non-cultivated vegetable eaten by most countries in Africa. Empirical facts about the nutritional advantage inherent in this edible plant is scarce, more studies are needed to establish its functionality. There are enormous records of traditional uses of this wild vegetable though the biological and pharmacological evidences are very few, there is urgent need to justify this claims. Phytochemistry studies is scanting, showing twelve compounds mostly are ceanothane-type triterpenoids, have been isolated so far including some polysaccharide. This review tends to gather works till date on this plant so as to provide enough information for future research hence it is clear that the phytochemistry of this plant is yet to be explored fully.

A re-examination of Tuta absoluta parasitoids in South America for optimized biological control

We conducted a review of published information on Tuta absoluta parasitoids for the Neotropical region to (1) corroborate species records, (2) analyze associations including the T. absoluta, other insect and plant hosts and (3) identify research directions for enhancing their use as biological control agents. The literature review shows more than 50 species or morphospecies of Hymenoptera associated with T. absoluta, but less than a half (23) could be confirmed as parasitizing T. absoluta. Erroneous reports or invalid names of species, two new species records were found. Over a 100 pests and non-economically important insect and cultivated and non-cultivated plants directly or indirectly interact with T. absoluta in the region. Four T. absoluta parasitoid species include in their host range predatory insects or act as hyperparasitoids, a negative feature considered for a biological control agent. Five larval parasitoids have a narrow host range and could be considered for classical biological control programs in the areas of new invasion. Six Trichogrammatidae species are commercially used in various countries; of those, T. minutum and T. pretiosum are considered to be moderately generalist, being able to exploit several insect hosts. Apart from Apanteles gelechiidivoris and Pseudapanteles dignus, other native species have been the subject of field studies as biological control agents. The review presented here provides useful insights for identifying species that deserve further evaluation as T. absoluta biological control agents through augmentative or conservation strategies in South America, as well as for potential classical biological control programs in other continents.

A review of Tuta absoluta (Lepidoptera: Gelechiidae) host plants and their impact on management strategies

Introduction. Tuta absoluta is one of the most harmful insect pests of tomato crops worldwide. While its host plants mainly include Solanaceae species, recent studies suggest that it can lay eggs and develop on a wider range of wild and cultivated plants. No complete list of host plants based on available scientific data exists. Such information is important for those who aim at performing integrated management strategies against this pest, especially when it comes to identify host reservoirs where the species can survive between harvests or avoid insecticide exposure. Literature. We identified cultivated and non-cultivated plant species belonging to Solanaceae, Amaranthaceae, Euphorbiaceae, Cucurbitaceae, Geraniaceae, Fabaceae, Asteraceae and Malvaceae that allow partial or complete egg-imago development. Among them, we found out that most non-Solanaceous plants serve as oviposition sites only (with no larval development possible), and a few of them allow partial life cycle (causing late instars to die prematurely). We also identified a strong cultivar-dependence in the most common cultivated plant species including tomato and potato. Conclusions. We discuss the potential of resistant and genetically modified tomato cultivars, plant chemical compounds and fertilization as components of integrated control strategies of T. absoluta.

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization.

RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.

Molecular Characterization of a Novel Begomovirus Infecting Malva (Gaya guerkeana K. Schum.)

The genus Begomovirus (family Geminirvidae) comprises circular single-stranded DNA viruses that infect both cultivated and non-cultivated hosts, being transmitted by the insect vector Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae). This study aimed to conduct the molecular characterization of a novel begomovirus infecting the non-cultivated plant Gaya guerkeana K. Schum. (Malvaceae). A leaf sample of G. guerkeana was collected in the State of Pernambuco, Brazil, in 2010. Viral genomic components were amplified via RCA, cloned, and commercially sequenced. The full-length DNA-A sequence was used for phylogenetic analysis and pairwise comparisons with other previously reported begomoviruses. The begomovirus DNA-A from G. guerkeana was most closely related to the Sida mottle Alagoas virus (SiMoAV, JX871386), having 84.8% nucleotide identity. Using the ≥ 91% identity criteria for DNA-A established by the Geminivirus Study Group of the International Committee on Taxonomy of Viruses, this isolate was considered a putative new begomovirus species, and the name Gaya yellow mosaic virus (GaYMV) is suggested. The GaYMV isolate grouped with SiMoAV and other begomoviruses infecting Sida spp. from the State of Alagoas, Brazil. This is the first report of a begomovirus infecting G. guerkeana, indicating that this non-cultivated plant can act as a reservoir/source of begomoviruses.

The changing face of farmers\u2019 home gardens: a diachronic analysis from Sillian (Eastern Tyrol, Austria)

BackgroundHome gardens are an integral part of many traditional land use systems around the world. They are subject to various conversion processes and undergo a variety of changes. We were interested if change is an ongoing process in farmers’ home gardens of Eastern Tyrol (Austria).MethodsIn Sillian, 16 farmers’ home gardens (FHGs) were studied. They had been studied in 1998 and were revisited in 2013 including again a botanical inventory of cultivated and non-cultivated plants, and structured interviews on appearance, management and plant use. In 2017, all the 16 gardens were visited again to verify whether any visible change on spatial configuration had occurred.ResultsThe home garden size had decreased between 1998 and 2013. A wider range of sizes was observed. The occurrence of plant taxa per garden was the same but an increase in the standard deviation of occurrence is seen. Plant diversity (occ./m2) increased between 1998 and 2013. Seventy-nine plant taxa were no longer cultivated in 2013, but 95 new plant taxa were being cultivated. The correlation between garden size and occurrence was not significant, i.e. small gardens might host many different plant taxa or large gardens might have fewer plant taxa. The occurrence for certain use categories was not significantly different between the years, except for the increase in the occurrence of plant taxa used as food and the food subcategory spice. The mean abundance of individuals for all plant taxa showed a significant decrease between the years. In 2013, an increase in standard deviation of abundance is seen. The variation in the different use categories expressed in abundance between the years was not significantly different, except for the decrease in the abundance of plant taxa used as food. Between 1998 and 2017, six home gardens showed a change of their spatial configuration (replacement by raised beds; merging with other structures; conversion to lawn). One FHG shows signs of abandonment.ConclusionsIn Sillian, gardens are by no way static agroecological units, but are dynamic and individual in their appearance, composition and function. Farmers’ home gardens in Sillian show a trend towards becoming more individual, i.e. conversion from being a product of a homogenous local cultural script of the community into an area where gardeners define more individually the role that farmers’ homegardens are expected to play for them or their family.

STUDI ETNOBOTANI TUMBUHAN PANGAN YANG TIDAK DIBUDIDAYAKAN OLEH MASYARAKAT LOKAL SUB-ETNIS BATAK TOBA, DI DESA PEADUNGDUNG SUMATERA UTARA, INDONESIA

The Batak Toba sub-ethnic is an indegenous tribe in Sumatra Island, who has local knowledge of using plants as food (edible plants). This study aims to (1) document the non-cultivated plants used by Batak Toba sub-ethnic as edible plants; (2) compare the quantitative values of edible plants by Batak Toba sub-ethnic. The study was conducted with ethnobotany approach through surveys and parcifative observations. The interviews were conducted toward key informants (7 people) and the general respondents (30 people). The general respondents were grouped into 17-30 years old, 30-50 years old, more than 50 years old, which the numbers of each were 10 respondents. The data were analyzed qualitatively and quantitatively. The quantitative analysis was done by calculating the relative frequency of citation (RFC), and informant consensus factor (ICF). This research found a total of 44 species belonging to the 28 families and 40 genera have been used by Batak Toba sub-ethnic as edible plants. The edible plants have been used as vegetables (18 species), fruits (16 species), spices (6 species), and drinks (3 species). The mean of species known by respondents were 15.8 ± 5.18 (17-30 years old), 23.2 ± 3.58 (30-50 years old), 26.8 ± 4.66 (> 50 years old) and 36.85 ± 5.11 (key informants). The IFC values of edible plants were 0.943 (spices) - 0.968 (drinks). A total of nine species of foodstuffs have been known by all respondents (RFC = 1.0). The utilization of Calamus javensis and Arundina graminifolia, as foodstuffs are going to be further investigated as low-calorie of carbohydrate sources.

Complete genome sequences of two gemycircularviruses associated with non-cultivated plants in Brazil.

Gemycircularviruses (genus Gemycircularvirus, family Genomoviridae) are single-stranded DNA viruses that are spread around the world in association with several organisms and environments. In this work, we identified two gemycircularviruses associated with two non-cultivated plants in Brazil, Momordica charantia and Euphorbia heterophylla. Both viruses display the general genome structure of gemycircularviruses. The virus isolated from M. charantia showed the highest nucleotide sequence identity with Pteropus associated gemycircularvirus 5, and an atypical structure consisting of a hairpin embedded in the major stem-loop was observed in the intergenic region. The virus from E. heterophylla showed the highest nucleotide sequence identity with Odonata associated gemycircularvirus 1. Phylogenetic analysis groups the two new viruses together with other genomoviruses of the genus Gemycircularvirus.

Heterotrophic N2-fixation contributes to nitrogen economy of a common wetland sedge, Schoenoplectus californicus.

A survey of the ecological variability within 52 populations of Schoenoplectus californicus (C.A. Mey.) Soják across its distributional range revealed that it is commonly found in nitrogen (N) limited areas, but rarely in phosphorus limited soils. We explored the hypothesis that S. californicus supplements its nitrogen demand by bacterial N2-fixation processes associated with its roots and rhizomes. We estimated N2-fixation of diazotrophs associated with plant rhizomes and roots from several locations throughout the species’ range and conducted an experiment growing plants in zero, low, and high N additions. Nitrogenase activity in rhizomes and roots was measured using the acetylene reduction assay. The presence of diazotrophs was verified by the detection of the nifH gene. Nitrogenase activity was restricted to rhizomes and roots and it was two orders of magnitude higher in the latter plant organs (81 and 2032 nmol C2H4 g DW-1 d-1, respectively). Correspondingly, 40x more nifH gene copies were found on roots compared to rhizomes. The proportion of the nifH gene copies in total bacterial DNA was positively correlated with the nitrogenase activity. In the experiment, the contribution of fixed N to the plant N content ranged from 13.8% to 32.5% among clones from different locations. These are relatively high values for a non-cultivated plant and justify future research on the link between N-fixing bacteria and S. californicus production.

Distribution pattern of traditional ecological knowledge on plant utilization among major minority peoples in Guizhou, China

ABSTRACTIn this study, the traditional ecological knowledge (TEK) on non-cultivated plant utilization by the Miao and Buyi people in Guizhou, China, was investigated using semi-structured interviews and the joint plant and use (JPU) was used as an index of TEK. In addition, the regional TEK distribution patterns were depicted. The results showed that low-frequency JPUs accounted for a large proportion of the total TEK on non-cultivated plant utilization, implying a possible TEK loss. The TEK distribution pattern is similar to the 80/20 rule, indicating that most TEK is mastered by key informants who are important for regional TEK protection and inheritance. Different informants have different JPU amounts and diversities with specific relationships, and for the characteristic ethnic TEK, medicinal JPUs generally have a low frequency, while symbolic JPUs have a higher frequency. The results could provide references for regional sustainable development and biocultural diversity management.

Multipurpose plant utilization in ethnic areas of Guizhou, southwest China

In ethnic areas, plant utilization is an essential component of traditional ecological knowledge and an important intersection between biodiversity and cultural diversity. Multipurpose plants play an important role in diversity of plant utilization and can be used as an indicator of regional biocultural diversity. Different uses of the same multipurpose plant correspond to different gathering methods and have different impacts on plant resources. Although important in both daily life and scientific studies, multipurpose plants are rarely specifically studied. In this study, multipurpose plant utilization by Miao and Buyi people in Guizhou, China, was investigated using semi-structured interviews. Plant uses were classified into eight categories: food, medicine, timber, fuel, technological, recreation, ornamental and symbolic. Three indices, Joint Plant and Use (JPU), Joint Uses (JU), and Joint Index (JI), were proposed to analyze overall utilization for multipurpose plants and the relationships among their different uses. A total of 58 species of non-cultivated multipurpose plants and 140 corresponding JPUs were recorded. With the decrease in use number, the corresponding species number of multipurpose plants increased. Two-use plants were most common among multipurpose plants, and food–medicinal plants were most frequent among two-use plants. Moreover, medicinal use and food use have the highest JI value, representing the close relationship between these two uses. Multipurpose plants are essentially determined from the attributes of plants themselves. Trees tend to have more uses than herbaceous plants. Different uses of the same plant represent different cultural or economic values, which determine the importance of a specific use. Socio-economic conditions and policies also have impacts on multipurpose plant utilization. While socio-economic conditions, policies, and plant resources vary, people might choose among different uses; hence, some key multipurpose plants and their JPUs will reflect the variations. The JPU used in this study can be regarded as a basic biocultural diversity unit. Using JPU, JU or JI allows multipurpose plants and their uses to be analyzed quantitatively. Multipurpose plants should be valued in research and management and, for further research, it is important to establish a standard plant use categorization.

Fungal Disease Prevention in Seedlings of Rice (Oryza sativa) and Other Grasses by Growth-Promoting Seed-Associated Endophytic Bacteria from Invasive Phragmites australis.

Non-cultivated plants carry microbial endophytes that may be used to enhance development and disease resistance of crop species where growth-promoting and protective microbes may have been lost. During seedling establishment, seedlings may be infected by several fungal pathogens that are seed or soil borne. Several species of Fusarium, Pythium and other water moulds cause seed rots during germination. Fusarium blights of seedlings are also very common and significantly affect seedling development. In the present study we screened nine endophytic bacteria isolated from the seeds of invasive Phragmites australis by inoculating onto rice, Bermuda grass (Cynodon dactylon), or annual bluegrass (Poa annua) seeds to evaluate plant growth promotion and protection from disease caused by Fusarium oxysporum. We found that three bacteria belonging to genus Pseudomonas spp. (SLB4-P. fluorescens, SLB6-Pseudomonas sp. and SY1-Pseudomonas sp.) promoted seedling development, including enhancement of root and shoot growth, and stimulation of root hair formation. These bacteria were also found to increase phosphate solubilization in in vitro experiments. Pseudomonas sp. (SY1) significantly protected grass seedlings from Fusarium infection. In co-culture experiments, strain SY1 strongly inhibited fungal pathogens with 85.71% growth inhibition of F. oxysporum, 86.33% growth inhibition of Curvularia sp. and 82.14% growth inhibition of Alternaria sp. Seedlings previously treated with bacteria were found much less infected by F. oxysporum in comparison to non-treated controls. On microscopic observation we found that bacteria appeared to degrade fungal mycelia actively. Metabolite products of strain SY1 in agar were also found to inhibit fungal growth on nutrient media. Pseudomonas sp. (SY1) was found to produce antifungal volatiles. Polymerase chain reaction (PCR) amplification using specific primers for pyrrolnitirin synthesis and HCN (hydrogen cyanide) production suggested presence of genes for both compounds in the genome of SY1. HCN was detected in cultures of SY1. We conclude that microbes from non-cultivated plants may provide disease protection and promote growth of crop plants.

Ethnobotanical study of medicinal plants from Ghana; confirmation of ethnobotanical uses, and review of biological and toxicological studies on medicinal plants used in Apra Hills Sacred Grove

The majority of human populations in developing countries rely on traditional medicines but the practice of traditional medicine is not the same across the world. In this study, the authors investigated traditional medicinal uses of plants by the communities living around Apra Hills Sacred Grove, in southern Ghana. A total of 75 households in three communities, namely, Akrampa, Apra and Loye, living in the study area were interviewed about the plants they used for the management of their common human ailments. Data collection was achieved after obtaining prior-informed consent, and using a semi-structured questionnaire. Botanical voucher specimens of the plants reported as being used were collected following standard ethnobotanical practice. A total of 31 species of plants belonging to16 families were reported as being used in the management and treatment of diseases. Approximately 65% of the plants were collected from degraded areas outside the protected area of the grove whereas 35% were obtained from inside the protected area of grove (wild). The majority (81%) of the plants reported were non-cultivated plants while 19% were semi-cultivated plants, and none were cultivated. Leaves formed a major component (57%) of the plant materials being used and most of the herbal remedies were prepared by boiling and the decoctions drunk. The results of the study have also confirmed the ethnobotanical uses of the plants as well as highlighted “new use reports”. The study has confirmed importance of degraded areas as a source of medicinal plants for indigenous communities and that a high proportion of non-cultivated plants is used for such medicines. Plants in need of further investigations based on a survey of the available literature on their ethnobotanical use, biological activity and toxicological studies have been highlighted.

Diversity and use of wild and non-cultivated edible plants in the Western Himalaya

BackgroundLocal people in the Himalayan region use a wide range of wild and non-cultivated edible plants (WNEPs) for food, spice, medicinal, and cultural purposes. However, their availability, use, status and contribution to livelihood security are poorly documented, and they have been generally overlooked in recent agro-biodiversity conservation and management programmes. The study aimed to investigate WNEP diversity and current status in a part of the Kailash Sacred Landscape—a transboundary landscape shared by Nepal, India and PR China—in terms of collection, use, management and conservation initiatives.MethodsMultiple methodologies and tools were used for data collection. A series of participatory tools (45 key informant interviews, 10 focus group discussions, a crop diversity fair, direct observation of species through a transect walk and rapid market assessments) was followed by a household survey (195 respondents) and complemented by a literature review.ResultsThe study recorded 99 WNEPs belonging to 59 families of which 96 were angiosperms, one gymnosperm and two pteridophytes. Species were used for food, spice, medicine, rituals and income generation. Thirty-five species had multiple uses, including these: 40 species were used for fruit and 31 for vegetables. WNEPs contribute significantly to daily food requirements, especially the vegetables. The use value of Dryopteris cochleata was found highest (0.98) among frequently used vegetable species. The values of informant consensus factor were found maximum for worms in the stomach (0.99) and minimum for skin disease treatment (0.67). Nearly 85% of households depended exclusively on WNEPs for at least more than a month per year. Results on the importance and use of different species, gender roles in WNEP activities and conservation approaches are presented.ConclusionsPeople living in the Kailash Sacred Landscape depend significantly on WNEPs, and this is especially critical in times of food shortage. The WNEPs have considerable potential as an important supplement to cultivated food crops. Farmers prioritise species with multiple use values and popular vegetables. However, there are numerous challenges and interventions needed to ensure conservation and management of species and their continued availability to support food security and local livelihoods.

Seasonal abundance of Thyanta perditor (F.) (Heteroptera: Pentatomidae) and its preference among cultivated and non-cultivated plants

Results of field studies with the red-shouldered stink bug Thyanta perditor (F.) demonstrated that nymphs and adults are highly abundant in late summer (March) on maturing soybean [ Glycine max (L.) Merrill] plants, and on maturing plants of the weed black jack ( Bidens pilosa L.) in the northern area of the state of Rio Grande do Sul, Brazil. Since soybean is harvested in March, populations decreased sharply in April and resurged somewhat in May. After this month, stink bugs were not observed until late spring in November when adults on maturing wheat plants were captured. Laboratory tests comparing the bug preference for seedlings of cultivated plants indicated that soybean and maize ( Zea mays L.) were preferred hosts compared to wheat ( Triticum aestivum L.) and barley ( Hordeum vulgare L.). For non-cultivated plants (weeds), seedlings of milkweed ( Euphorbia heterophylla L.) and of flax-leaf fleabane ( Conyza bonariensis L.) were preferred over those of signal grass [ Brachiaria plantaginea (Link)] and black jack. Seedlings of non-cultivated plants were preferred over cultivated ones, in particular milkweed and black jack. Resultados de estudos em campo com o percevejo Thyanta perditor (F.) demonstraram que ninfas e adultos foram mais abundantes no final do verao (marco) em soja [ Glycine max (L.) Merrill] em fase de maturacao e em picao-preto ( Bidens pilosa L.) em Passo Fundo, no norte do Rio Grande do Sul, Brasil. Apos a colheita da soja em marco, as populacoes diminuiram em abril e reapareceram em maio. Apos maio, nao foram constatados percevejos ate o final da primavera em novembro, quando foram capturados adultos no trigo em maturacao. Testes em laboratorio indicaram que plântulas de soja e milho ( Zea mays L.) foram hospedeiros preferidos em comparacao ao trigo ( Triticum aestivum L.) e cevada ( Hordeum vulgare L.). Plântulas de ervas daninhas, como o leiteiro ( Euphorbia heterophylla L.) e a buva ( Conyza bonariensis L.) foram preferidas em relacao as plântulas de capim-papua [ Brachiaria plantaginea (Link)] e picao-preto. Em geral, plântulas de especies nao cultivadas foram preferidas comparado com plântulas de especies cultivadas, em especial o leiteiro e o picao-preto.

AGROMYZID (DIPTERA) SPECIES AND THEIR PARASITOIDS IN BATMAN PROVINCE, TURKEY

This study was carried out during 2010 and 2012 in province of Batman, Turkey, for surveying the agromyzid fauna. The specimens were collected by rearing of the mine-infested leaves of different cultivated and non-cultivated host plants. Seven species belonging to three genera of the subfamily of Agromyzinae and two species belonging to one genera of subfamily of Phytomyzinae were collected. These species; Agromyza albitarsis, Chromatomyia horticola, Liriomyza bryoniae, Liriomyza cicerina, Liriomyza huidobrensis, Liriomyza strigata, Liriomyza trifolii, Phytomyza affinis and Phytomyza orobanchia. In this study, such as parasitoids were determined 5 species of which were 3 species belonging to family of Braconidae and 1 species belonging to of family of Eulophidae and Aphidiidae. Among them, Diglyphus isaea Walker was the most widespreading species.

From Songlines to genomes: Prehistoric assisted migration of a rain forest tree by Australian Aboriginal people.

BackgroundPrehistoric human activities have contributed to the dispersal of many culturally important plants. The study of these traditional interactions can alter the way we perceive the natural distribution and dynamics of species and communities. Comprehensive research on native crops combining evolutionary and anthropological data is revealing how ancient human populations influenced their distribution. Although traditional diets also included a suite of non-cultivated plants that in some cases necessitated the development of culturally important technical advances such as the treatment of toxic seed, empirical evidence for their deliberate dispersal by prehistoric peoples remains limited. Here we integrate historic and biocultural research involving Aboriginal people, with chloroplast and nuclear genomic data to demonstrate Aboriginal-mediated dispersal of a non-cultivated rainforest tree.ResultsWe assembled new anthropological evidence of use and deliberate dispersal of Castanospermum australe (Fabaceae), a non-cultivated culturally important riparian tree that produces toxic but highly nutritious water-dispersed seed. We validated cultural evidence of recent human-mediated dispersal by revealing genomic homogeneity across extensively dissected habitat, multiple catchments and uneven topography in the southern range of this species. We excluded the potential contribution of other dispersal mechanisms based on the absence of suitable vectors and current distributional patterns at higher elevations and away from water courses, and by analyzing a comparative sample from northern Australia.ConclusionsInnovative studies integrating evolutionary and anthropological data will continue to reveal the unexpected impact that prehistoric people have had on current vegetation patterns. A better understanding of how traditional practices shaped species’ distribution and assembly will directly inform cultural heritage management strategies, challenge “natural” species distribution assumptions, and provide innovative baseline data for pro-active biodiversity management.

Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae

BackgroundGeminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species. As a result, determining the nomenclature and taxonomically classifying geminiviruses turned into complex tasks. In addition, the gene responsible for viral replication (particularly, the viruses belonging to the genus Mastrevirus) may be spliced due to the use of the transcriptional/splicing machinery in the host cells. However, the current tools have limitations concerning the identification of introns.ResultsThis study proposes a new method, designated Fangorn Forest (F2), based on machine learning approaches to classify genera using an ab initio approach, i.e., using only the genomic sequence, as well as to predict and classify genes in the family Geminiviridae. In this investigation, nine genera of the family Geminiviridae and their related satellite DNAs were selected. We obtained two training sets, one for genus classification, containing attributes extracted from the complete genome of geminiviruses, while the other was made up to classify geminivirus genes, containing attributes extracted from ORFs taken from the complete genomes cited above. Three ML algorithms were applied on those datasets to build the predictive models: support vector machines, using the sequential minimal optimization training approach, random forest (RF), and multilayer perceptron. RF demonstrated a very high predictive power, achieving 0.966, 0.964, and 0.995 of precision, recall, and area under the curve (AUC), respectively, for genus classification. For gene classification, RF could reach 0.983, 0.983, and 0.998 of precision, recall, and AUC, respectively.ConclusionsTherefore, Fangorn Forest is proven to be an efficient method for classifying genera of the family Geminiviridae with high precision and effective gene prediction and classification. The method is freely accessible at www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp.

A preliminary investigation of seed dispersal by elephants (<em>Elephas maximus maximus</em>) in Kumaragala Forest Reserve, Matale District, Sri Lanka

Elephants are capable of dispersing seeds in the wild and hence, have the potential to affect the vegetation dynamics of forests. Only few studies have been conducted in Sri Lanka to study the seed dispersal capability of wild elephants. Thus, this study was initiated to determine the diversity of plant species that are dispersed by the elephants in Kumaragala forest reserve, Central Sri Lanka. Dung piles were searched twice a month and three dung boli were collected randomly from each dung pile. Visible seeds were identified by comparing with a reference seed collection. A total of 84 dung piles were recorded from September 2014 to February 2015. Fifty three dung piles out of 84 (63.1%) contained seeds or seedlings of one or more plant species. Most of the dung piles were found in relatively undisturbed areas of the study site. Twenty two plant species; 15 cultivated (68.2%) and seven non-cultivated (31.8%) plants belonging to nine families were identified from dung boli. Careya arborea, Megathyrsus maximus and Mimosa pudica were the most commonly noted seedlings. The findings of this study prove that elephants assist in dispersing seeds of some plant species in Kumaragala forest reserve area.