The draft genome of the C\u3csub\u3e3\u3c/sub\u3e panicoid grass species \u3ci\u3eDichanthelium oligosanthes\u3c/i\u3e

Background: Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C3 and C4 grasses. Results: We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C4 photosynthesis. Conclusions: The phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology

Association indices for quantifying social relationships: how to deal with missing observations of individuals or groups

Social network analysis has provided important insight into many population processes in wild animals. Constructing social networks requires quantifying the relationship between each pair of individuals in the population. Researchers often use association indices to convert observations into a measure of propensity for individuals to be seen together. At its simplest, this measure is just the probability of observing both individuals together given that one has been seen (the simple ratio index). However, this probability becomes more challenging to calculate if the detection rate for individuals is imperfect. We first evaluate the performance of existing association indices at estimating true association rates under scenarios where (1) only a proportion of all groups are observed (group location errors), (2) not all individuals are observed despite being present (individual location errors), and (3) a combination of the two. Commonly used methods aimed at dealing with incomplete observations perform poorly because they are based on arbitrary observation probabilities. We therefore derive complete indices that can be calibrated for the different types of incomplete observations to generate accurate estimates of association rates. These are provided in an R package that readily interfaces with existing routines. We conclude that using calibration data is an important step when constructing animal social networks, and that in their absence, researchers should use a simple estimator and explicitly consider the impact of this on their findings

Do-it-Yourself Aid: The Emergence of American Grassroots Development Organizations

The number of American-based international NGOs has increased tenfold since 1990. The growth is driven by GINGOs: grassroots international non-governmental organizations, or NGOs founded by amateurs with a personal tie to a developing country, and supported with volunteer labor and individual donations. The Americans who launch these organizations typically are middle-class college graduates, but have no training or professional experience in international development. Instead of being shaped by the norms of the professional aid field, these organizations are defined by the personal relationships and skills of the people who found them. They represent a countermovement to the trend of professionalization seen in aid organizations and the nonprofit sector broadly. This dissertation combines analysis of IRS records with fieldwork and interviews in Africa and the United States. I also create an original database of all known websites for international relief, development, and human rights organizations registered with the IRS in 2011, which is analyzed with topic modeling and content analysis of a random sample of 150 organizations. My findings show that globalization offers a tenuous opening for nonprofit organizations to bypass the isomorphic pressures of professionalization. And while supporting world society theory’s claims about the ways individual agency and rationalism shape international organization, I show that the expressive possibilities of nonprofit organizations are critical in understanding GINGOs’ emergence. I describe implications for development aid and for the American communities that support these groups

Grassroots Aid Survey: Key Findings on Small International Development Organizations

This report provides the first national survey data on the programs, finances, and challenges of small and mid-sized international development nonprofits. The data are drawn from the 2021 Grassroots Aid Survey, with a sample of 185 U.S.-based international development organizations with annual budgets of less than $1 million. We summarize key findings and offer a few conclusions for these nonprofits’ own work, the entities that support them, and for future research

NGOs and International Development: A Review of Thirty-Five Years of Scholarship

Since 1980, the number of non-governmental organizations (NGOs) in developing countries has exploded. Published research on NGOs has paralleled this growth, yet there exists scant synthesis of the literature. This article presents a synthesis, while also introducing a collaborative research platform, the NGO Knowledge Collective. We ask four questions: first, who studies NGOs, and how do they study them? Second, what issues, sectors and places are studied when NGOs are the focus? Third, what effect do NGO activities have on specific development outcomes? And fourth, what path should the NGO research agenda take? To answer these questions, we conduct a mixed-method systematic review of social science publications on NGOs, which includes computer-assisted content analysis of 3336 English-language journal articles (1980–2014), alongside a close, qualitative analysis of 300 randomly selected articles. We find, first, that interdisciplinary journals dominate NGO publishing, that research on NGOs is more qualitative than quantitative, and that practitioners publish, but Northern academics create most published knowledge. Second, we find the literature is framed around six overarching questions regarding: the nature of NGOs; their emergence and development; how they conduct their work; their impacts; how they relate to other actors; and how they contribute to the (re)production of cultural dynamics. Articles also focus disproportionately on the most populated and/or politically salient countries, and on the governance and health sectors. Third, we find that scholars generally report favorable effects of NGOs on health and governance outcomes. Fourth, we propose a research agenda calling for scholars to: address neglected sectors, geographies, and contextual conditions; increase author representativeness; improve research designs to include counterfactuals or comparison groups; and better share data and findings, including results from additional, focused NGO-related systematic reviews. Implementing this agenda will help reduce bias in decisions by donors, governments, and other development actors, which should improve development outcomes

The draft genome of the C\u3csub\u3e3\u3c/sub\u3e panicoid grass species \u3ci\u3eDichanthelium oligosanthes\u3c/i\u3e

Background: Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages represented by Setaria viridis and Sorghum bicolor occurred approximately 15 million years ago, which is significantly more recent than members of the Bambusoideae, Ehrhartoideae, and Pooideae subfamilies. D. oligosanthes is ideally placed within the panicoid clade for comparative studies of C3 and C4 grasses. Results: We report the assembly of the nuclear and chloroplast genomes of D. oligosanthes, from high-throughput short read sequencing data and a comparative transcriptomics analysis of the developing leaf of D. oligosanthes, S. viridis, and S. bicolor. Physiological and anatomical characterizations verified that D. oligosanthes utilizes the C3 pathway for carbon fixation and lacks Kranz anatomy. Expression profiles of transcription factors along developing leaves of D. oligosanthes and S. viridis were compared with previously published data from S. bicolor, Zea mays, and Oryza sativa to identify a small suite of transcription factors that likely acquired functions specifically related to C4 photosynthesis. Conclusions: The phylogenetic location of D. oligosanthes makes it an ideal C3 plant for comparative analysis of C4 evolution in the panicoid grasses. This genome will not only provide a better C3 species for comparisons with C4 panicoid grasses, but also highlights the power of using high-throughput sequencing to address questions in evolutionary biology

Oligogalactolipid production during cold challenge is conserved in early diverging lineages

Oligogalactolipid production is a response to severe cold in many land plant lineages. It occurs during times of membrane damage and can be reproduced in multiple species by cytosolic acidification. Severe cold, defined as a damaging cold beyond acclimation temperatures, has unique responses, but the signaling and evolution of these responses are not well understood. Production of oligogalactolipids, which is triggered by cytosolic acidification in Arabidopsis (Arabidopsis thaliana), contributes to survival in severe cold. Here, we investigated oligogalactolipid production in species from bryophytes to angiosperms. Production of oligogalactolipids differed within each clade, suggesting multiple evolutionary origins of severe cold tolerance. We also observed greater oligogalactolipid production in control samples instead of temperature challenged samples of some species. Further examination of representative species revealed a tight association between temperature, damage, and oligogalactolipid production that scaled with the cold tolerance of each species. Based on oligogalactolipid production and transcript changes, multiple angiosperm species share a signal of oligogalactolipid production initially described in Arabidopsis, cytosolic acidification. Together, these data suggest that oligogalactolipid production is a severe cold response that originated from an ancestral damage response that remains in many land plant lineages and that cytosolic acidification may be a common signaling mechanism for its activation

Additional file 4: of The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

PEPC amino acid sequences. (DOCX 35 kb