Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

What is ecological speciation

Wild and managed pollinators provide a wide range of benefits to society in terms of contributions to food security, farmer and beekeeper livelihoods, social and cultural values, as well as the maintenance of wider biodiversity and ecosystem stability. Pollinators face numerous threats, including changes in land-use and management intensity, climate change, pesticides and genetically modified crops, pollinator management and pathogens, and invasive alien species. There are well-documented declines in some wild and managed pollinators in several regions of the world. However, many effective policy and management responses can be implemented to safeguard pollinators and sustain pollination services.

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Safeguarding pollinators and their values to human well-being

A B S T R A C T Soil compaction influences all stages of crop growth, but in many low yield sugarcane fields critical levels and effects of soil compaction are ignored. Therefore, identifying localization and intensity of compaction are very relevant for descompactation of soil. In this context, this study aimed to apply three criteria for delineating zones for soil compaction management: soil layer where first appear values of soil penetration resistance considered critical for sugarcane growth; cone index for 0-40 cm layer, and depth of occurrence of maximum soil penetration resistance. Sampling was carried out in a grid with 113 points spaced at 100 m, georeferenced by means of a Global Positioning System receiver. Soil penetration resistance in eight layers of 5 cm depth, cone index and depth of occurrence of maximum penetration resistance were determined from data gathered by an automatic measuring penetrometer. Estimative of non-sampled values were obtained by means of kriging interpolation, which allowed drawing of contour maps and the definition of four regions in the field for site specific subsoiling . Palavras-chave: Saccharum ssp. resistencia do solo a penetracao geoestatistica penetrometro

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Revista Brasileira de Engenharia Agrícola e Ambiental

Traditional farming communities frequently maintain high levels of agrobiodiversity, so understanding their agricultural practices is a priority for biodiversity conservation. The cultural origin of agave spirits (mezcals) from west-central Mexico is in the southern part of the state of Jalisco where traditional farmers cultivate more than 20 landraces of Agave angustifolia Haw. in agroecosystems that include in situ management of wild populations. These systems, rooted in a 9000-year-old tradition of using agaves as food in Mesoamerica, are endangered by the expansion of commercial monoculture plantations of the blue agave variety ( A. tequilana Weber var. Azul), the only agave certifi ed for sale as tequila, the best-known mezcal. Using intersimple sequence repeats and Bayesian estimators of diversity and structure, we found that A. angustifolia traditional landraces had a genetic diversity ( H BT = 0.442) similar to its wild populations ( H BT = 0.428) and a higher genetic structure ( θ B = 0.405; θ B =0. 212). In contrast, the genetic diversity in the blue agave commercial system ( H B = 0.118) was 73% lower. Changes to agave spirits certifi cation laws to allow the conservation of current genetic, ecological and cultural diversity can play a key role in the preservation of the traditional agroecosystems.

Diversity and structure of landraces of Agave grown for spirits under traditional agriculture: A comparison with wild populations of A. angustifolia (Agavaceae) and commercial plantations of A. tequilana

Physalis is an American plant genus that includes species of economic importance for their edible fruit. Consumption of this fruit is a historic tradition in Mexico. Physalis philadelphica is one of the most abundant species, which can grow under wild, weedy or cultivated conditions. It presents high morphological variability in terms of vegetative and reproductive traits; however, no study has been made of its genetic diversity or the impact of human activity on its diversity and differentiation patterns. We determined genetic parameters in nine populations representing a management gradient, including three wild, three weedy and three cultivated populations, using 88 inter-simple sequence repeat markers. The diversity of the total gene pool was high (Ht = 0.292, HT
 B
  = 0.319) and did not decrease with the intensity degree of management. Reproductive system, life form and the wide distribution determined the genetic variation of the taxon. AMOVA revealed high variation within the total gene pool (44.3 %) and among populations (46.7 %). This was influenced by pollinator behavior, dispersal form, geographic discontinuity of the studied populations and human selection. Variation among population management categories was lower (9 %), indicating that this variable has little effect, most likely due to the broad gene pool of the taxon. However, analysis of genetic distance and Bayesian assignment distinguished two groups: cultivated and wild, with weedy populations interspersed between. This result suggests that selection for agricultural and morphological attributes of P. philadelphica contributes to this differentiation. Future studies could address the evolutionary dynamics of the wild–weedy–domesticated complex.

Diversity and genetic structure of the husk tomato (Physalis philadelphica Lam.) in Western Mexico

Extensive monovarietal cultivation of Age tequilana Weber var. azul is threatening the diversity of the germplasm used in traditional Agave spirits production in west-central Mexico. To promote the preservation, use, and management of this germplasm, an ethnobotanical and morphological study was done in the center and south of the state of Jalisco, Mexico. The richness, distribution, and morphological variation of wild and cultivated Agave populations were characterized, and producers’ roles in germplasm maintenance and diversification were analyzed. Results indicated that: 1) A. angustifolia and A. rhodacantha are the primary gene pools used for selection; 2) Traditional landraces are differentiated morphological entities; and 3) In situ maintenance and increase of Agave germplasm diversity are the result of constant selection of wild germplasm, producer management of populations in the wild-domesticated gradient, and preservation of old landraces. Preservation of Agave germplasm diversity in west-central Mexico requires increased cultivation and valuation of traditional landraces.

In Situ Diversity and Maintenance of Traditional Agave Landraces Used in Spirits Production in West-Central Mexico

Over the last 30 years, cultivation of Agave tequilana Weber var blue for industrial production of tequila, has generated soil erosion, chemical pollution, displacement of traditional food crops and traditional Agave landraces used for preparing “mezcals” in the Appellation of Origin Tequila area. It is also associated with harmful cycles 8–10 years long of surplus-shortfall availability of raw material. Mezcal is the common traditional name given in Mexico to spirits like tequila, prepared with Agave tissue. We examined the traditional strategies of management of the Agave genetic resources for elaborating mezcal and tequila spirits by people of southern Jalisco, Mexico, analyzing the bases of their sustainable management, compared with management of the industrial tequila system. We found that mezcal spirits are prepared with different landraces of A. angustifolia Haw. and A. rhodacantha Trel. which are cultivated as living fences within the “milpa”, the traditional Mesoamerican multi-crop system. The whole system allows simultaneous production of agricultural, livestock and forest resources, permitting the adjustment of mezcal production to demand. Agave borders and terraces are laid out perpendicular to slopes to increase rainfall capture and filtration, and decrease soil erosion. The high species richness creates niche heterogeneity, substantially reducing pest and disease incidence. Genetic and morphological analyses indicated that traditional management and selection of A. angustifolia landraces have produced high genetic diversity (HBT = 0.438 ± 0.003) and structure (θB = 0.408) when compared with wild populations (HBT = 0.428 ± 0.015; θB = 0.212). Morphological differentiation is associated to artificial selection pressures. Differential precocity of Agave landraces and scaled planting favors continuous, year round spirit production. Growers directly market their mezcals, and a portion of the profits is reinvested in the parcel to ensure system continuity. The technological advantages of the traditional mezcal system could attenuate some challenges caused by the tequila industrial agriculture.

Ofelia Vargas-Ponce

Papers

Diversity and structure of landraces of Agave grown for spirits under traditional agriculture: A comparison with wild populations of A. angustifolia (Agavaceae) and commercial plantations of A. tequilana

Diversity and genetic structure of the husk tomato (Physalis philadelphica Lam.) in Western Mexico

In Situ Diversity and Maintenance of Traditional Agave Landraces Used in Spirits Production in West-Central Mexico

Sustainability of the traditional management of Agave genetic resources in the elaboration of mezcal and tequila spirits in western Mexico

Phenology, agronomic and nutritional potential of three wild husk tomato species (Physalis, Solanaceae) from Mexico