Colombia,an unknown genetic diversity in the era of Big Data

Background

Latin America harbors some of the most biodiverse countries in the world, including Colombia. Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches in biodiversity studies. In this study, we used data mining methods to search in four main public databases of genetic sequences such as: NCBI Nucleotide and BioProject, Pathosystems Resource Integration Center, and Barcode of Life Data Systems databases. We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions. Additionally, we compared this data for Colombia with other countries of high biodiversity in Latin America, such as Brazil, Argentina, Costa Rica, Mexico, and Peru.

Results

In Nucleotide, we found that 66.84% of total records for Colombia have been published at the national level, and this data represents less than 5% of the total number of species reported for the country. In BioProject, 70.46% of records were generated by national institutions and the great majority of them is represented by microorganisms. In BOLD Systems, 26% of records have been submitted by national institutions, representing 258 species for Colombia. This number of species reported for Colombia span approximately 0.46% of the total biodiversity reported for the country (56,343 species). Finally, in PATRIC database, 13.25% of the reported sequences were contributed by national institutions. Colombia has a better biodiversity representation in public databases in comparison to other Latin American countries, like Costa Rica and Peru. Mexico and Argentina have the highest representation of species at the national level, despite Brazil and Colombia, which actually hold the first and second places in biodiversity worldwide.

Conclusions

Our findings show gaps in the representation of the Colombian biodiversity at the molecular and genetic levels in widely consulted public databases. National funding for high-throughput molecular research, NGS technologies costs, and access to genetic resources are limiting factors. This fact should be taken as an opportunity to foster the development of collaborative projects between research groups in the Latin American region to study the vast biodiversity of these countries using ‘omics’ technologies.

     

《昆明-蒙特利尔全球生物多样性框架》指引下中国生物多样性主流化实施路径探析

《昆明-蒙特利尔全球生物多样性框架》制定了未来一段时期全球范围内生物多样性保护的重要行动,包括将生物多样性及其多重价值纳入经济和社会活动的主流。中国作为联合国《生物多样性公约》(CBD)缔约方之一,在持续推进生物多样性主流化方面作出了不懈努力且成效显著。该文通过探讨解析生物多样性主流化的概念内涵,梳理总结我国生物多样性主流化的具体实践和阶段成效,对标《昆明-蒙特利尔全球生物多样性框架》目标,围绕政府、企业、公众不同行为主体,提出新时期我国全方位推进生物多样性主流化的4个主要实施路径:(1)引入统一的行动框架;(2)发挥政府治理的主导作用;(3)联动企业采取共同行动;(4)提高公众意识以促进其广泛参与,致力于将生物多样性融入各级政府部门政策机制及社会生产生活实践活动中,为完善生物多样性治理决策提供参考。     

Development by Design in Colombia: Making Mitigation Decisions Consistent with Conservation Outcomes

Mitigation policy and regulatory frameworks are consistent in their strong support for the mitigation hierarchy of: (1) avoiding impacts, (2) minimizing impacts, and then (3) offsetting/compensating for residual impacts. While mitigation frameworks require developers to avoid, minimize and restore biodiversity on-site before considering an offset for residual impacts, there is a lack of quantitative guidance for this decision-making process. What are the criteria for requiring impacts be avoided altogether? Here we examine how conservation planning can guide the application of the mitigation hierarchy to address this issue. In support of the Colombian government''s aim to improve siting and mitigation practices for planned development, we examined five pilot projects in landscapes expected to experience significant increases in mining, petroleum and/or infrastructure development. By blending landscape-level conservation planning with application of the mitigation hierarchy, we can proactively identify where proposed development and conservation priorities would be in conflict and where impacts should be avoided. The approach we outline here has been adopted by the Colombian Ministry of Environment and Sustainable Development to guide licensing decisions, avoid piecemeal licensing, and promote mitigation decisions that maintain landscape condition.     

Conservation Planning for Offsetting the Impacts of Development: A Case Study of Biodiversity and Renewable Energy in the Mojave Desert

Balancing society’s competing needs of development and conservation requires careful consideration of tradeoffs. Renewable energy development and biodiversity conservation are often considered beneficial environmental goals. The direct footprint and disturbance of renewable energy, however, can displace species’ habitat and negatively impact populations and natural communities if sited without ecological consideration. Offsets have emerged as a potentially useful tool to mitigate residual impacts after trying to avoid, minimize, or restore affected sites. Yet the problem of efficiently designing a set of offset sites becomes increasingly complex where many species or many sites are involved. Spatial conservation prioritization tools are designed to handle this problem, but have seen little application to offset siting and analysis. To address this need we designed an offset siting support tool for the Desert Renewable Energy Conservation Plan (DRECP) of California, and present a case study of hypothetical impacts from solar development in the Western Mojave subsection. We compare two offset scenarios designed to mitigate a hypothetical 15,331 ha derived from proposed utility-scale solar energy development (USSED) projects. The first scenario prioritizes offsets based precisely on impacted features, while the second scenario offsets impacts to maximize biodiversity conservation gains in the region. The two methods only agree on 28% of their prioritized sites and differ in meeting species-specific offset goals. Differences between the two scenarios highlight the importance of clearly specifying choices and priorities for offset siting and mitigation in general. Similarly, the effects of background climate and land use change may lessen the durability or effectiveness of offsets if not considered. Our offset siting support tool was designed specifically for the DRECP area, but with minor code modification could work well in other offset analyses, and could provide continuing support for a potentially innovative mitigation solution to environmental impacts.     

Using microsatellites,isozymes and AFLPs to evaluate genetic diversity and redundancy in the cassava core collection and to assess the usefulness of DNA-based markers to maintain germplasm collections

The cassava core collection was selected to represent, with minimum repetitiveness, the potential genetic diversity of the crop. The core (630 accessions) was chosen from the base collection (over 5500 accessions) on the basis of diversity of origin (country and geographic), morphology, isozyme patterns and specific agronomic criteria. To asses the genetic diversity of the core, 521 accessions were typed with four microsatellite loci. Allele diversity and frequency, and size variance of dinucleotide repeats (Rst statistic) were estimated. Microsatellite allele numbers and frequencies varied among countries: Colombia and Brazil had the largest number of different alleles across all loci. Mexico also had a high number, ranking fifth after Peru, Costa Rica and Venezuela (which tied). Unique alleles were present in accessions from Brazil, Colombia, Guatemala, Venezuela and Paraguay. A small number (1.34%) of potential duplicates were identified through isozyme and AFLP profiles. Thus, the present results indicated that traditional markers have been highly effective at selecting unique genotypes for the core. Future selections of cassava germplasm sets can be aided by DNA-based markers to ensure genetically representative, non-redundant samples. This revised version was published online in June 2006 with corrections to the Cover Date.     

Biodiversity informatics in Eastern Africa: Status,drivers and barriers

This article uses content analysis to review policies and relevant documents that promote or hinder the generation and use of biodiversity data in Eastern Africa. The review found that all countries in the region are committed to international and regional conventions that emphasize the protection and conservation of biodiversity. Some of the other drivers for biodiversity informatics include countries’ national biodiversity related policies although there are few, which highlight the need for biodiversity data management systems. However, the existing policies are deficient in terms of policies for biodiversity data management. Suggestions to ensure the success of biodiversity informatics in East Africa include: (i) Avoiding overlaps but promoting complementarities within and/or between different institutions and stakeholders involved in biodiversity conservation; (ii) Putting in place clear, complete and simple policy documents pertaining to biodiversity data management.     

Great Apes and Biodiversity Offset Projects in Africa: The Case for National Offset Strategies

The development and private sectors are increasingly considering “biodiversity offsets” as a strategy to compensate for their negative impacts on biodiversity, including impacts on great apes and their habitats in Africa. In the absence of national offset policies in sub-Saharan Africa, offset design and implementation are guided by company internal standards, lending bank standards or international best practice principles. We examine four projects in Africa that are seeking to compensate for their negative impacts on great ape populations. Our assessment of these projects reveals that not all apply or implement best practices, and that there is little standardization in the methods used to measure losses and gains in species numbers. Even if they were to follow currently accepted best-practice principles, we find that these actions may still fail to contribute to conservation objectives over the long term. We advocate for an alternative approach in which biodiversity offset and compensation projects are designed and implemented as part of a National Offset Strategy that (1) takes into account the cumulative impacts of development in individual countries, (2) identifies priority offset sites, (3) promotes aggregated offsets, and (4) integrates biodiversity offset and compensation projects with national biodiversity conservation objectives. We also propose supplementary principles necessary for biodiversity offsets to contribute to great ape conservation in Africa. Caution should still be exercised, however, with regard to offsets until further field-based evidence of their effectiveness is available.     

Spatially Explicit Trends in the Global Conservation Status of Vertebrates

The world''s governments have committed to preventing the extinction of threatened species and improving their conservation status by 2020. However, biodiversity is not evenly distributed across space, and neither are the drivers of its decline, and so different regions face very different challenges. Here, we quantify the contribution of regions and countries towards recent global trends in vertebrate conservation status (as measured by the Red List Index), to guide action towards the 2020 target. We found that>50% of the global deterioration in the conservation status of birds, mammals and amphibians is concentrated in <1% of the surface area, 39/1098 ecoregions (4%) and eight/195 countries (4%) – Australia, China, Colombia, Ecuador, Indonesia, Malaysia, Mexico, and the United States. These countries hold a third of global diversity in these vertebrate groups, partially explaining why they concentrate most of the losses. Yet, other megadiverse countries – most notably Brazil (responsible for 10% of species but just 1% of deterioration), plus India and Madagascar – performed better in conserving their share of global vertebrate diversity. Very few countries, mostly island nations (e.g. Cook Islands, Fiji, Mauritius, Seychelles, and Tonga), have achieved net improvements. Per capita wealth does not explain these patterns, with two of the richest countries – United States and Australia – fairing conspicuously poorly. Different countries were affected by different combinations of threats. Reducing global rates of biodiversity loss will require investment in the regions and countries with the highest responsibility for the world''s biodiversity, focusing on conserving those species and areas most in peril and on reducing the drivers with the highest impacts.     

The Diversity of Flower Flies (Diptera: Syrphidae) in Colombia and Their Neotropical Distribution

In Colombia, like most Neotropical countries, faunistic studies on flower flies have been occasional and most of them have been primarily focused on taxonomy. Colombia is the second-most species-rich country in flower fly diversity in the Neotropics after Brazil, and has one of the highest numbers of species per unit area (2.49 per 10,000?km²), based on a review of literature and national collections. Including new data presented here, a total of 47 genera and 300 species are recorded in Colombia. The genera Scaeva Fabricius and Lycastrirhyncha Bigot, as well as 101 species are recorded here for the first time. The altitudinal range and the distribution of the flower fly genera in Colombia are presented. A preliminary comparison of the fauna of Colombia with that of other Neotropical countries is given. A historical perspective is also provided in order to illustrate how Colombian Syrphidae knowledge has progressed over the last 168?years. Information presented here will be useful for ongoing and future biodiversity research as well as conservation projects on Syrphidae in the Neotropical region.     

Global Diversity and Conservation Priorities in the Cactaceae

The purpose of this paper was to analyze the diversity patterns of Cactaceae at a global scale, to identify those countries where conservation actions should be performed. In order to do this, the species richness and the number of endemic species for 34 American countries were determined. With these data, the relationship between the total number of species or the number of endemic species and the area of the countries were analyzed. In addition, a complementarity analysis was conducted to determine the most important countries for cactus conservation. Results showed that Mexico had the highest number of total and endemic species followed by Argentina, Bolivia, Brazil, and Peru, among others. There was a significant positive relationship between both, the total and endemic species, and the area of the countries. Despite this fact, the cactus diversity in Mexico, Argentina, Peru, Bolivia, Chile, and Costa Rica was higher than expected according to their area. Further, these countries also presented the highest proportions of endemic species. The complementarity analysis indicated that 24 countries are necessary to preserve all cactus species. However, 94% of all species could be preserved with only 10 countries. Considering the diversity patterns and the complementarity analysis, three important groups for cactus conservation were identified: (1) Mexico, Argentina, Peru, Bolivia, Chile, and Costa Rica, (2) Paraguay and Cuba, and (3) Brazil and USA. Conservation efforts should be focused on these countries in order to preserve cactus diversity.     

The El Niño southern oscillation and malaria epidemics in South America

A better understanding of the relationship between the El Ni?o Southern Oscillation (ENSO), the climatic anomalies it engenders, and malaria epidemics could help mitigate the world-wide increase in incidence of this mosquito-transmitted disease. The purpose of this paper is to assess the possibility of using ENSO forecasts for improving malaria control. This paper analyses the relationship between ENSO events and malaria epidemics in a number of South American countries (Colombia, Ecuador, French Guiana, Guyana, Peru, Suriname, and Venezuela). A statistically significant relationship was found between El Ni?o and malaria epidemics in Colombia, Guyana, Peru, and Venezuela. We demonstrate that flooding engenders malaria epidemics in the dry coastal region of northern Peru, while droughts favor the development of epidemics in Colombia and Guyana, and epidemics lag a drought by 1 year in Venezuela. In Brazil, French Guiana, and Ecuador, where we did not detect an ENSO/malaria signal, non-climatic factors such as insecticide sprayings, variation in availability of anti-malaria drugs, and population migration are likely to play a stronger role in malaria epidemics than ENSO-generated climatic anomalies. In some South American countries, El Ni?o forecasts show strong potential for informing public health efforts to control malaria.     

Female sterilization in Latin America: cross-national perspectives

Fertility levels have dropped substantially in Latin America in recent decades, fuelled by increased contraceptive use and notably a method mix skewed towards female sterilization. This study examined choice of female sterilization in four Latin American countries: Brazil, Colombia, the Dominican Republic and Peru. Data were drawn from national Demographic and Health Surveys conducted in 1995--1996. Discrete-time hazard models were used on the five-year calendar modules of women's reproductive histories to consider the effects of a number of sociodemographic and contextual determinants as they pertained to status at the moment of the event. The results revealed that the likelihood of a woman's having undergone contraceptive sterilization was increasing over time in Brazil and Peru, suggesting that the potential for future growth of this method remains strong. A consistent pattern of increased probability of sterilization with higher education was seen across all countries, seemingly dispelling certain controversial claims that the procedure may have been disproportionately performed on the poor. At the same time, the multilevel analytical approach pointed to significant cluster-level random effects, suggesting that there were additional unmeasured contextual influences on women's propensity to choose sterilization.     

Intraspecific variation of cuticular hydrocarbon profiles in the Anastrepha fraterculus (Diptera: Tephritidae) species complex

The goal of this study was to define whether cuticular hydrocarbons (CHs) could be used for taxonomic determination of putative species hidden in the Anastrepha fraterculus cryptic species complex, widespread from Argentina to Mexico. Recently, increasing evidence of phenotypic and genetic variability has resulted in the characterization of eight morphotypes within this complex. The CH profiles of six A. fraterculus populations from Argentina, Brazil, Peru, Colombia and Mexico were analysed in this study by two‐dimensional gas chromatography coupled with mass spectrometry. In parallel, multiple factorial analyses were used to elucidate population structures. Vector populations segregated into four distinct groups. The analysis demonstrated that the studied populations from Peru, Argentina and southern Brazil (Vacaria) might be classified in accordance with the earlier division of the A. fraterculus complex into Peruvian, and Brazilian‐1 cryptic species, using the specific CH profiles. Population from south‐eastern Brazil (Piracicaba) formed separated group. Mexican and Andean (Colombian) putative species had similar CH signatures, when compared to each other.     

The impact of biomass crop cultivation on temperate biodiversity

The urgency for mitigation actions in response to climate change has stimulated policy makers to encourage the rapid expansion of bioenergy, resulting in major land‐use changes over short timescales. Despite the potential impacts on biodiversity and the environment, scientific concerns about large‐scale bioenergy production have only recently been given adequate attention. Environmental standards or legislative provisions in the majority of countries are still lagging behind the rapid development of energy crops. Ranging from the field to the regional scale, this review (i) summarizes the current knowledge about the impact of biomass crops on biodiversity in temperate regions, (ii) identifies knowledge gaps and (iii) drafts guidelines for a sustainable biomass crop production with respect to biodiversity conservation. The majority of studies report positive effects on biodiversity at the field scale but impacts strongly depend on the management, age, size and heterogeneity of the biomass plantations. At the regional scale, significant uncertainties exist and there is a major concern that extensive commercial production could have negative effects on biodiversity, in particular in areas of high nature‐conservation value. However, integration of biomass crops into agricultural landscapes could stimulate rural economy, thus counteracting negative impacts of farm abandonment or supporting restoration of degraded land, resulting in improved biodiversity values. Given the extent of landconversion necessary to reach the bioenergy targets, the spatial layout and distribution of biomass plantations will determine impacts. To ensure sustainable biomass crop production, biodiversity would therefore have to become an essential part of risk assessment measures in all those countries which have not yet committed to making it an obligatory part of strategic landscape planning. Integrated environmental and economic research is necessary to formulate standards that help support long‐term economic and ecological sustainability of biomass production and avoid costly mistakes in our attempts to mitigate climate change.     

Priorities for biodiversity monitoring in Europe: A review of supranational policies and a novel scheme for integrative prioritization

Trends and status of species and habitats need to be measured to assess whether global biodiversity policy targets have been achieved. However, it is impossible to monitor all species and habitats with a justifiable effort. Therefore, it is critical to prioritize the monitoring of specific biodiversity components. Priorities must be linked to key nature conservation policies to ensure that monitoring efforts are relevant to policy needs, achieve maximum impact, and obtain governmental support. Here we discuss priority setting in biodiversity monitoring in view of monitoring obligations and priorities in supranational biodiversity legislation and policies in Europe and assess overlaps in priorities among policies. While most supranational biodiversity regulations require monitoring of biodiversity, obligations are legally enforceable only for the Nature Directives, the Water Framework Directive, and the Marine Strategy Framework Directive of the European Union. Of the assessed international conventions and other relevant policy instruments about 50% explicitly designate priority species and most focus on vertebrates. Lower emphasis is given to habitats and geographical priorities are even less pronounced. Also, an overarching system for monitoring prioritization is still missing. Our prioritization system is based on three main criteria: (1) legal requirement for reporting, (2) wording used to define priority or importance, and (3) inclusion in lists that indicate importance of monitoring due to e.g. threats or relevance of a region for a species. Our system contains five main priority levels, within which an additional division differentiates priorities according to national/European responsibility criteria. Based on this system, we provide recommendations for allocating species and habitats enlisted by the reviewed policy tools to explicit non-overlapping priority levels. Our approach will facilitate synergies between monitoring activities for different policy needs, and contribute to alleviate the notorious resource shortage for biodiversity monitoring.     

Considerable qualitative variability in local-level biodiversity surveys in Finland: A challenge for biodiversity offsetting

High-quality biodiversity monitoring is crucial in the era of rapid global biodiversity loss and for the evaluation of conservation outcomes at different spatial scales. Biodiversity offsets are conservation actions that aim to an outcome of no net loss of biodiversity by compensating for the negative impacts from development projects. Successful use of offsets requires that the biodiversity gains and losses between offset and development areas are adequately and comparably measured. Numerous local-level biodiversity surveys are conducted to estimate the biodiversity values of potential development areas in Finland every year. These surveys are done for local planning purposes, and their results are almost never published. We studied Finnish biodiversity surveys to assess their adequacy with regards to biodiversity offsetting. Our data included all biodiversity surveys (n = 206) documented in the region of Southwest Finland during the time period of 1997–2014. We analysed the surveys based on Finnish nature legislation and biodiversity related criteria gathered from other offset and conservation programs. We found the surveys to be inadequate in their assessment of nature values and spatial considerations for offset purposes. We used cluster analysis to study the differences between surveys based on the inventoried nature values and found surveys were clustered into 3 different groups. The characteristics of surveys also varied between individual surveyors. Our results show that the current execution of biodiversity surveys is not compatible enough with the quality of surveys needed for biodiversity offsets. Surveys must be standardized to ensure their comparability and sufficient measurement of biodiversity with ecologically and geographically important features.     

Brazil cannot risk its environmental leadership

Brazil is an international environmental leader that has led important negotiations to set sustainable development targets over the last decade. However, in terms of national policies, Brazil is consistently making decisions that go against the global policies it ratifies. For instance, Brazilian governors have recently revised the Brazilian Forest Act ‐ its main environmental legislation on private land, reduced the area covered by some protected areas and allowed the creation of new hydropower plants on undisturbed Amazonian rivers, and have plans to open indigenous reserves to mining. Among other consequences, these controversial actions made by national leaders may increase CO₂ emissions and propel a massive loss of species, with irreversible consequences to the provision of ecosystem services and goods. In this paper, I present inconsistent actions made by policy and decision makers in Brazil and argue for a more focused environmental decision in Brazil, which matches the country's international position as a leader and that could help Brazil to achieve the status of a biodiversity superpower.     

Cultivation of red seaweeds: a Latin American perspective

The Latin American seaweed industry plays an important role at a global scale as 17 % of all seaweeds and 37 % of red seaweeds for the phycocolloid industry comes from this region. Increased market demand for algal raw materials has stimulated research and development into new cultivation technologies, particularly in those countries with economically important seaweed industries such as Argentina, Brazil, Chile, México, and Peru. The marine area of Latin America includes almost 59,591 km² of coastline ranging in latitude from 30ºN to 55ºS and encompasses four different oceanic domains: Temperate Northern Pacific, Tropical Eastern Pacific, Temperate South America, and Tropical Atlantic. Commercial cultivation of red seaweed in Latin America has been basically centered in the production of Gracilaria chilensis in Chile. Attempts have been made to establish seaweed commercial cultivation in other countries, going from experimental research-oriented studies to pilot community/enterprise based cultivation trials. Some genera such as Kappaphycus and Eucheuma have been studied in Brazil and Mexico, Gracilaria species in Argentina and Brazil, Gracilariopsis in Peru and Venezuela, and Chondracanthus chamissoi in Peru and Chile. In this short review, we address the Latin America perspective on the status and future progress for the cultivation of red seaweeds and their sustainable commercial development, and discuss on the main common problems. Particular emphasis is given to the needs for comprehensive knowledge necessary for the management and cultivation of some of the most valuable red seaweed resources in Latin America.     

Toward a forest biomass reference measurement system for remote sensing applications

Forests contribute to climate change mitigation through carbon storage and uptake, but the extent to which this carbon pool varies in space and time is still poorly known. Several Earth Observation missions have been specifically designed to address this issue, for example, NASA's GEDI, NASA-ISRO's NISAR and ESA's BIOMASS. Yet, all these missions' products require independent and consistent validation. A permanent, global, in situ, site-based forest biomass reference measurement system relying on ground data of the highest possible quality is therefore needed. Here, we have assembled a list of almost 200 high-quality sites through an in-depth review of the literature and expert knowledge. In this study, we explore how representative these sites are in terms of their coverage of environmental conditions, geographical space and biomass-related forest structure, compared to those experienced by forests worldwide. This work also aims at identifying which sites are the most representative, and where to invest to improve the representativeness of the proposed system. We show that the environmental coverage of the system does not seem to improve after at least the 175 most representative sites are included, but geographical and structural coverages continue to improve as more sites are added. We highlight the areas of poor environmental, geographical, or structural coverage, including, but not limited to, Canada, the western half of the USA, Mexico, Patagonia, Angola, Zambia, eastern Russia, and tropical and subtropical highlands (e.g. in Colombia, the Himalayas, Borneo, Papua). For the proposed system to succeed, we stress that (1) data must be collected and processed applying the same standards across all countries and continents; (2) system establishment and management must be inclusive and equitable, with careful consideration of working conditions; and (3) training and site partner involvement in downstream activities should be mandatory.