Brazilian Agricultural Research Corporation

A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even in low technology laboratories. The amount of tissue required by this method is approximately 50-100 mg. The quantity and the quality of the DNA extracted by this method is high enough to perform hundreds of PCR-based reactions and also to be used in other DNA manipulation techniques such as restriction digestion, Southern blot and cloning.

Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.

BACKGROUND: Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. RESULTS: We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets' elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains. CONCLUSIONS: InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net .

Abstract Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy‐in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log‐normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait‐based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

The Gossypium genus is used to investigate emergent consequences of polyploidy in cotton species; comparative genomic analyses reveal a complex evolutionary history including interactions among subgenomes that result in genetic novelty in elite cottons and provide insight into the evolution of spinnable fibres. A phylogenetic and genomic study of plants of the cotton genus Gossypium provides insights into the role of polyploidy in the angiosperm evolution, and specifically, in the emergence of spinnable fibres in domesticated cottons. The authors show that an abrupt five- to sixfold ploidy increase about 60 million years ago, and allopolyploidy reuniting divergent genomes approximately 1–2 million years ago, conferred a roughly 30-fold duplication of ancestral flowering plant genes in the 'elite' cottons G. hirsutum and G. barbadense compared to their presumed progenitor G. raimondii. Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments1. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1–2 Myr ago2, conferred about 30–36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica3 among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum AtDt (in which ‘t’ indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.

Chitosan, a versatile hydrophilic polysaccharide derived from chitin, has a broad antimicrobial spectrum to which gram-negative, gram-positive bacteria and fungi are highly susceptible. In the current review, three possible and accepted antimicrobial mechanisms for chitosan are presented and briefly discussed. The activity dependence on polymeric molecular weight (MW) and degree of acetylation (DA) are described. The chitosan minimum inhibitory concentrations (MIC) are summarized according to recent data found in the literature. The potential to improve inhibitory growth of bacteria by using water soluble chitosan derivatives is also discussed. The data indicate that the effectiveness of chitosan varies and is dependent on species of target microorganisms.

Potential conflict of interest: Listed at the end of the article for all authors. These recommendations have been approved by the American Association for the Study of Liver Diseases and the Infectious Diseases Society of America. Potential conflict of interest: Listed at the end of the article for all authors. All AASLD Practice Guidelines are updated annually. If you are viewing a Practice Guideline that is more than 12 months old, please visit www.aasld.org for an update in the material. Preamble The pace of hepatitis C virus (HCV) drug development in recent years has accelerated dramatically. For patients to benefit from these impressive advances, practitioners need access to the most up‐to‐date data and to advice from experienced experts. Such information and advice can be difficult to access readily given the diverse sources from which information is available and the sometimes lengthy time needed for publication of original articles and scholarly perspectives. Traditional practice guidelines for more established areas of medicine and care often take years to develop and bring to publication. In the new era in hepatitis C treatment, such a process would not be nimble or timely enough to address the needs of patients with HCV infection, practitioners caring for these patients, or payers approving therapies for use. A living document made available in a web‐based system, such as that used by the US Department of Health and Human Services for human immunodeficiency virus (HIV) treatment recommendations (http://aidsinfo.nih.gov/guidelines), was selected as the best model to provide timely recommendations for hepatitis C management. In 2013, the two major membership societies supporting liver and infectious disease specialists (American Association for the Study of Liver Diseases [AASLD] and Infectious Diseases Society of America [IDSA]) joined forces to develop guidance for the management of hepatitis C in this rapidly moving field. The International Antiviral Society‐USA, which has experience in developing treatment guidelines in HIV disease, was invited to join the effort as a collaborating partner responsible for managing the panel and the guidance development process. The goal of the hepatitis C guidance is to provide up‐to‐date recommendations for HCV care practitioners on the optimal screening, management, and treatment for adults with HCV infection in the United States, using a rigorous review process to evaluate the best available evidence. This review provides a condensed summary of recommendations from the guidance. The complete guidance, which is updated regularly, is available at www.hcvguidelines.org. Process This was conceived to be a living document that would reside online and undergo real‐time revisions as the field evolved. To lead the process, two cochairs selected by the governing boards of each founding society were joined by a fifth cochair representing the International Antiviral Society‐USA. These cochairs selected 10 panel members from each society. The panel members were chosen to represent expertise in the diagnosis, management, treatment, research, and patient care from the fields of hepatology and infectious diseases. At least 51% of the panelists could have no substantive industry support other than research advisory boards, data safety monitoring boards, or research funding that went to the member's employer. The panel first convened in person in October 2013. Panel members were divided into teams to review available data and to propose preliminary guidance in three areas: (1) testing and linkage to care, (2) initial treatment of HCV infection, and (3) retreatment of patients in whom prior HCV treatment had failed. The treatment section teams also reviewed data for special considerations in patients with hepatitis C, including those with HCV/HIV coinfection, with decompensated cirrhosis, and who had undergone liver transplantation. The teams and cochairs met regularly by conference call. All panel members reviewed and approved the final recommendations. Each society's governing board peer‐reviewed the final recommendations. The first version of the guidance was uploaded (www.hcvguidelines.org) on January 29, 2014. By September 2014, three additional sections were developed: (1) treatment of acute HCV infection, (2) monitoring during and after therapy, and (3) when and whom to treat. In October 2014, the panel reconvened in person to update recommendations to consider data on pending new treatments. The updated recommendations (and appropriate revisions of all current guidance) were uploaded on December 20, 2014. This report was prepared on May 20, 2015. Funding for the guidance itself was provided by the AASLD and the IDSA. No industry funding was solicited or accepted. The Centers for Disease Control and Prevention (CDC) provided separate funding for identifying and reviewing data pertaining to testing and linkage to care. Collecting, Evaluating, and Rating the Evidence The panel, comprising experts in the fields of hepatology and infectious diseases, used an evidence‐based approach to review available information for the guidance. Information sources considered were research published in peer‐reviewed journals or presented at major national or international research conferences; safety warnings from the US Food and Drug Administration (FDA), other regulatory agencies, or the manufacturer; drug interaction data; prescribing information from FDA‐approved products; and registration data for new products under FDA review. An initial search of the literature yielded 3939 unique citations on November 4, 2013. To be considered, articles needed to be published in English from 2010 to the present. Review studies, studies using mice or rats, and in vitro studies were excluded. Panel members monitor the literature and other sources regularly and update the guidance as new evidence warrants. Each recommendation is rated in terms of the level of evidence (depicted by Roman numeral I, II, or III) and the strength of the recommendation (depicted by letter A, B, or C) using a scale (Table 1) adapted from the American College of Cardiology and the American Heart Association Practice Guidelines.1 Table 1 - Rating by Classification and of Evidence Classification for which is evidence that a given or treatment is and for which is evidence a of the and of a or treatment of evidence is in of and and are established by evidence for which is evidence that a or treatment is not and or in be of Evidence from or from a studies, or C of studies, or of care such as for HCV with an or be The FDA has including or For additional and In those for which was a FDA‐approved panel members considered the evidence as to a for A and from the American College of Cardiology and the American Heart Association Practice Guidelines.1 HCV and to the to with HCV in the United States, are that are of those with infection is the first and HCV testing is in on prior and (Table In the HCV testing guidelines in with a recommendation to a HCV to all from of HCV have been This recommendation was by the of the to more than of HCV in the to for of all HCV with a than other A review that of with HCV infection would have been a testing would have been with the The of testing is to that of current Table - of for for HCV the years of and or including those who drug a in an Health care, and safety after or to to of or including who were that from a who for HCV infection a of or or an were HIV infection liver disease and hepatitis including and with the and the US Services a HCV is in in the and other on and that for HCV for HCV be using FDA‐approved such as testing for with or a A current HCV infection or infection that has or a FDA‐approved or testing with a level of or be used to HCV to HCV infection and management. for HCV also be in with a who are or who have been to HCV in the prior months these be An HCV is also needed to in after or for of and testing can be in the testing at www.hcvguidelines.org. All for HCV testing first be for using an FDA‐approved be by testing for HCV Evidence the optimal of testing in at for to HCV is the of testing on the of of the of HCV infection who and who have with who have at least HCV testing is in these HCV testing is for who and for who have with testing be to other at of HCV with HCV be to is of the of which lead to more of liver and the development of with HCV be for HIV and hepatitis as with hepatitis virus or HIV has been with of and additional from and and with and who have are more to have liver disease, which in who are or by a of or or or be to and and with HCV be disease and to to in of current hepatitis C and in treatment have on and patients have access to appropriate care. In the United States, is that of with HCV infection in to practitioners who are and to evaluate such patients and provide treatment is or is that all patients with current hepatitis C and a HCV be to and by a with expertise in the of liver disease and HCV those with or management, including of liver as by a who is prepared to provide management, including of therapy, is for all with current HCV and in to HCV hepatitis C treatment is in all patients and is by a as the of HCV for 12 or more after of is a for of HCV infection and has been to be in studies in more than of patients for at least who are of HCV infection experience including a in liver of in most and of in the and other of liver disease also An is with a more than in the of liver and a in the of and liver of HCV infection also and from including a to of with HCV with and other complete or in to of HCV These in disease to in patients an have of including and Evidence treatment for all those with than 12 to treatment is best in the of the disease and the development of the most of treatment be by at for the to all patients as is most appropriate to first those at of disease and those at for HCV or in whom treatment such of treatment for those in and is including patients with liver disease or or those with Table - of and Disease in HCV to the and for treatment to for or I, A I, or with I, or for treatment to for I, I, virus C liver disease C C to the strength and level of evidence with to of treatment in these Table - of HCV or in May who have with with on of to care who C at of HCV be on to and the of that in patients with the of an In a patients with or by were for more than The was in those who experienced an than in those treatment had or those who were and and for of of other studies benefit treatment is at prior to Antiviral treatment is for all patients with HCV infection, those with to If the to all patients as is most appropriate to those at of disease those with disease An of is in the for treatment, in the of treatment, and the need for more The of is of the most used to disease and In to in more need for therapy, with for and are to with cirrhosis, such as those with evidence of or or not additional the of patients testing to liver is the and when In the is and are patient and such as are to the of in patients with HCV infection such as and of the by and liver No is to have and the of each be The most approach to is to and liver of testing or liver is in to the of the of of HCV This section treatment of patients with hepatitis C who are to of and are approved by the FDA for HCV the initial for patients who are with HCV 1 has been by using are as and the of which to of drug the and For the of and has a interaction with the of and has a interaction with the and other that with the with HCV to have than patients with HCV with 1 HCV infection that be be as For HCV patients, are three of and and For the of and the of for those with those who not have The of is for who than to for those who or The safety of each of these are studies, than of patients treatment and were in with and HCV who were the had after treatment with and than those who not the in these patients, of the other for be for patients with HCV who are are in of for 12 of and for 12 or with or for 12 or for patients with a for the using available In patients with HCV and who have the of the other for is For HCV patients, are three of for 12 for 12 and with or for 12 for patients with for patients with HCV who are are in of for 12 of for 12 with or for 12 or is the for patients with HCV more data are treatment to in HCV patients with is for patients with HCV and for 12 treatment to is for patients with is the most difficult to with available for is the in the United on recent data from a than those with and for the of and for 12 is for the and monitoring of this a for 12 has been is not for patients with HCV and for 12 for and for for For the treatment of patients with HCV 4, three are of with or the in vitro and in of HCV 4, be data are for patients with HCV infection in of for 12 of and for 12 and for and for 12 with or for 12 or data are available to for patients with HCV or on is for patients with HCV or of for 12 and for 12 for patients who are of in of and a are in this and and In patients with cirrhosis, treatment with for than 12 of treatment, supporting the recommendation that HCV patients with of with given for 12 to of in patients with in whom a prior of and or had failed. 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Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral changes of individual animals and to the exclusion of species with long-range movements from areas with higher human impact. Global loss of vagility alters a key ecological trait of animals that affects not only population persistence but also ecosystem processes such as predator-prey interactions, nutrient cycling, and disease transmission.

The fall armyworm, Spodoptera frugiperda (J.E. Smith, 1797) (Lepidoptera: Noctuidae), is the most important noctuid pest in the Americas and has recently become an invasive pest in Africa. A detailed record of S. frugiperda's host plants is essential to better understand the biology and ecology of this pest, conduct future studies, and develop Integrated Pest Management programmes. In this study, we collected and systematically arranged the fragmented bibliographic information on S. frugiperda feeding records. Furthermore, we registered new records of host plants for S. frugiperda based on eight years of surveys in Brazil. The literature review and surveys resulted in a total of 353 S. frugiperda larval host plant records belonging to 76 plant families, principally Poaceae (106), Asteraceae (31) and Fabaceae (31). The literature search revealed 274 (77 % of total) bibliographic records, while 82 (23 %) are new records from surveys in Brazil. The new comprehensive and updated host plant list will improve our understanding of pest biology and management, as well as facilitate future studies on this pest.

The sequencing and analysis of the banana genome is reported; these results inform plant phylogenetic relationships and genome evolution, and provide a resource for future genetic improvement of this important crop species. Bananas (Musa spp.) are a staple food and a major source of income in many tropical and subtropical countries. This paper reports the sequencing and analysis of the banana genome. This is the first non-grass monocotyledon to have its genome sequenced, providing an important bridge for comparative genome analysis in plants. Global banana production is under threat from increasingly well-adapted pests and diseases, so the availability of the genome sequence is an important resource for future crop development and improvement. Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries1. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations2, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish)1. Pests and diseases have gradually become adapted, representing an imminent danger for global banana production3,4. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence.

Protecting plants from the inside out Some soils show a remarkable ability to suppress disease caused by plant pathogens, an ability that is attributed to plant-associated microbiota. Carrión et al. investigated the role of endophytes, the intimate microbial community found within roots, in fungal disease suppression (see the Perspective by Tringe). The wilt fungus Rhizoctonia solani infects sugar beets, whereupon transcriptional analysis shows that several bacterial endophyte species activate biosynthetic gene clusters to cause disease suppression. These organisms produce antifungal effectors, including enzymes that can digest fungal cell walls, and secondary metabolites, including phenazines, polyketides, and siderophores, which may contribute to the antifungal phenotype. Science , this issue p. 606 ; see also p. 568

Aluminum (Al) toxicity in acid soils is a significant limitation to crop production worldwide, as approximately 50% of the world's potentially arable soil is acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring resistance to Al toxicity has been a focus of intense research interest in the decade since the last article on crop acid soil tolerance was published in this journal. An impressive amount of progress has been made during that time that has greatly increased our understanding of the diversity of Al resistance genes and mechanisms, how resistance gene expression is regulated and triggered by Al and Al-induced signals, and how the proteins encoded by these genes function and are regulated. This review examines the state of our understanding of the physiological, genetic, and molecular bases for crop Al tolerance, looking at the novel Al resistance genes and mechanisms that have been identified over the past ten years. Additionally, it examines how the integration of molecular and genetic analyses of crop Al resistance is starting to be exploited for the improvement of crop plants grown on acid soils via both molecular-assisted breeding and biotechnology approaches.

Abstract The classification of the legume family proposed here addresses the long‐known non‐monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near‐complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well‐supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community‐endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade‐based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Liu, J., V. Hull, M. Batistella, R. DeFries, T. Dietz, F. Fu, T. W. Hertel, R. C. Izaurralde, E. F. Lambin, S. Li, L. A. Martinelli, W. J. McConnell, E. F. Moran, R. Naylor, Z. Ouyang, K. R. Polenske, A. Reenberg, G. de Miranda Rocha, C. S. Simmons, P. H. Verburg, P. M. Vitousek, F. Zhang, and C. Zhu. 2013. Framing sustainability in a telecoupled world. Ecology and Society 18(2): 26. https://doi.org/10.5751/ES-05873-180226

David Bertioli and colleagues report the genomes of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut, Arachis hypogaea. Their analyses are a first step in understanding the evolution of the peanut's tetraploid genome. Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.

Amazon deforestation has been measured by remote sensing for three decades. In comparison, selective logging has been mostly invisible to satellites. We developed a large-scale, high-resolution, automated remote-sensing analysis of selective logging in the top five timber-producing states of the Brazilian Amazon. Logged areas ranged from 12,075 to 19,823 square kilometers per year (+/-14%) between 1999 and 2002, equivalent to 60 to 123% of previously reported deforestation area. Up to 1200 square kilometers per year of logging were observed on conservation lands. Each year, 27 million to 50 million cubic meters of wood were extracted, and a gross flux of approximately 0.1 billion metric tons of carbon was destined for release to the atmosphere by logging.

Association mapping is a method for detection of gene effects based on linkage disequilibrium (LD) that complements QTL analysis in the development of tools for molecular plant breeding. In this study, association mapping was performed on a selected sample of 95 cultivars of soft winter wheat. Population structure was estimated on the basis of 36 unlinked simple-sequence repeat (SSR) markers. The extent of LD was estimated on chromosomes 2D and part of 5A, relative to the LD observed among unlinked markers. Consistent LD on chromosome 2D was <1 cM, whereas in the centromeric region of 5A, LD extended for approximately 5 cM. Association of 62 SSR loci on chromosomes 2D, 5A, and 5B with kernel morphology and milling quality was analyzed through a mixed-effects model, where subpopulation was considered as a random factor and the marker tested was considered as a fixed factor. Permutations were used to adjust the threshold of significance for multiple testing within chromosomes. In agreement with previous QTL analysis, significant markers for kernel size were detected on the three chromosomes tested, and alleles potentially useful for selection were identified. Our results demonstrated that association mapping could complement and enhance previous QTL information for marker-assisted selection.