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Systematic Conservation Assessment for Most of the Colombian Territory as a Strategy for Effective Biodiversity Conservation  [PDF]
Marcela Portocarrero-Aya, Germán Corzo, Angélica Diaz-Pulido, María Fernanda González, Magnolia Longo, Lina Mesa, Andrea Paz, Wilson Ramírez, Olga Lucía Hernández-Manrique
Natural Resources (NR) , 2014, DOI: 10.4236/nr.2014.516084
Abstract: Colombian ecosystems maintain key ecological processes that support thousands of species, including human beings. With the expansion of the country’s population, and the implementation of a government’s development plan based on an economy centred on extraction patterns, the conservation of these ecosystems is at serious risk. It is a priority to implement effective strategies that ensure the protection of the country’s biological diversity as well as the mitigation and prevention of threats and to contribute to its proper use. Colombia’s development strategies as well as its peoples’ wellbeing depend on the suitable condition of its natural assets. The identification of surrogates of conservation, the formulation of conservation goals, the prioritization of key areas and the formulation of conservation strategies based on the preservation, restoration and sustainable use of the territory and its biodiversity are proposed for 60% of the emerged land (~ 700,000 Km2). This research aims at giving proper guidelines to manage the territory and finding common points between development and biodiversity conservation, as well as to use this input for the development and implementation of a National Decision-making Support System (DSS) that will potentially have an impact on Colombia’s environmental policies and territorial planning schemes.
A New and Unified Nomenclature for Male Fertility Restorer (RF) Proteins in Higher Plants  [PDF]
Simeon O. Kotchoni,Jose C. Jimenez-Lopez,Emma W. Gachomo,Manfredo J. Seufferheld
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0015906
Abstract: The male fertility restorer (RF) proteins belong to extended protein families associated with the cytoplasmic male sterility in higher plants. Up till now, there is no devised nomenclature for naming the RF proteins. The systematic sequencing of new plant species in recent years has uncovered the existence of several novel RF genes and their encoded proteins. Their naming has been simply arbitrary and could not be adequately handled in the context of comparative functional genomics. We propose in this study a unified nomenclature for the RF extended protein families across all plant species. This new and unified nomenclature relies upon previously developed nomenclature for the first ever characterized RF gene, RF2A/ALDH2B2, a member of ALDH gene superfamily, and adheres to the guidelines issued by the ALDH Genome Nomenclature Committees. The proposed nomenclature reveals that RF gene superfamily encodes currently members of 51 families. This unified nomenclature accommodates functional RF genes and pseudogenes, and offers the flexibility needed to incorporate additional RFs as they become available in future. In addition, we provide a phylogenetic relationship between the RF extended families and use computational protein modeling to demonstrate the high divergence of RF functional specializations through specific structural features of selected members of RF superfamily.
Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges
Daniel P. Faith,Andrew M. Baker
Evolutionary Bioinformatics , 2006,
Abstract: Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.
Phylogenetic Patterns of Extinction Risk in the Eastern Arc Ecosystems, an African Biodiversity Hotspot  [PDF]
Kowiyou Yessoufou, Barnabas H. Daru, T. Jonathan Davies
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047082
Abstract: There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains – an important African biodiversity hotspot – and described the distribution of extinction risk across taxonomic ranks and phylogeny. We provide evidence for both taxonomic and phylogenetic selectivity in extinction risk. However, we found that selectivity varies with IUCN extinction risk category. Vulnerable species are more closely related than expected by chance, whereas endangered and critically endangered species are not significantly clustered on the phylogeny. We suggest that the general observation for taxonomic and phylogenetic selectivity (i.e. phylogenetic signal, the tendency of closely related species to share similar traits) in extinction risks is therefore largely driven by vulnerable species, and not necessarily the most highly threatened. We also used information on altitudinal distribution and climate to generate a predictive model of at-risk species richness, and found that greater threatened species richness is found at higher altitude, allowing for more informed conservation decision making. Our results indicate that evolutionary history can help predict plant susceptibility to extinction threats in the hyper-diverse but woefully-understudied Eastern Arc Mountains, and illustrate the contribution of phylogenetic approaches in conserving African floristic biodiversity where detailed ecological and evolutionary data are often lacking.
Global Biodiversity and Phylogenetic Evaluation of Remipedia (Crustacea)  [PDF]
Marco T. Neiber,Tamara R. Hartke,Torben Stemme,Alexandra Bergmann,Jes Rust,Thomas M. Iliffe,Stefan Koenemann
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019627
Abstract: Remipedia is one of the most recently discovered classes of crustaceans, first described in 1981 from anchialine caves in the Bahamas Archipelago. The class is divided into the order Enantiopoda, represented by two fossil species, and Nectiopoda, which contains all known extant remipedes. Since their discovery, the number of nectiopodan species has increased to 24, half of which were described during the last decade. Nectiopoda exhibit a disjunct global distribution pattern, with the highest abundance and diversity in the Caribbean region, and isolated species in the Canary Islands and in Western Australia. Our review of Remipedia provides an overview of their ecological characteristics, including a detailed list of all anchialine marine caves, from which species have been recorded. We discuss alternative hypotheses of the phylogenetic position of Remipedia within Arthropoda, and present first results of an ongoing molecular-phylogenetic analysis that do not support the monophyly of several nectiopodan taxa. We believe that a taxonomic revision of Remipedia is absolutely essential, and that a comprehensive revision should include a reappraisal of the fossil record.
Phylogenetic nomenclature and evolution of mannose-binding lectin (MBL2) haplotypes
Angelica BW Boldt, Iara J Messias-Reason, Diogo Meyer, Carlos G Schrago, Florian Lang, Bertrand Lell, Klaus Dietz, Peter G Kremsner, Maria Petzl-Erler, Jürgen FJ Kun
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-38
Abstract: In this work, we applied the same method in 288 and 470 chromosomes from Gabonese and European adults, respectively, and found three new haplotypes in the last group. We propose a phylogenetic nomenclature to standardize MBL2 studies and found two major phylogenetic branches due to six strongly linked polymorphisms associated with high MBL production. They presented high Fst values and were imbedded in regions with high nucleotide diversity and significant Tajima's D values. Compared to others using small sample sizes and unphased genotypic data, we found differences in haplotyping, frequency estimation, Fu and Li's D* and Fst results.Using extensive testing for selective neutrality, we confirmed that stochastic evolutionary factors have had a major role in shaping this polymorphic gene worldwide.MBL (mannose-binding lectin) is an important component of innate immunity and a central recognition molecule of the lectin pathway of complement, which probably represents the most ancient pathway of complement activation [1]. It binds to an array of carbohydrates such as D-mannose and N-acetyl-D-glucosamine on the surface of pathogens and directly opsonizes the microorganism for phagocytosis or activates the complement system via interaction with MBL-associated serine proteases (MASP-1, -2, -3 and Map19). Complement activation kills the pathogen by the membrane-attack complex or by complement-mediated phagocytosis through increased deposition of opsonic C3 fragments. MBL is also able to recognize altered self structures present on apoptotic cells, promoting their clearance, and to modulate the release of various pro-inflammatory cytokines [2,3].The MBL2 genetic polymorphism is responsible for the very common and widespread variation of circulating levels of MBL oligomers and of functional activity of the protein in the human species. This variation is mainly caused by three single nucleotide polymorphisms (SNPs) in the first exon of the gene: MBL2*D (Arg52Cys), *B (Gly54As
Jiufeng Protected Area Biodiversity Threats Assessment  [cached]
Antoine Sambou,Shenggao Cheng,Lei Huang,Charles Nounagnon Gangnibo
Journal of Agricultural Science , 2010, DOI: 10.5539/jas.v2n3p108
Abstract: Located in the East of Wuhan City, Jiufeng Protected area is endowed with a rich biodiversity in diversity landscape (Metasequoia forests, forest ponds, pine forest, Wetland pine, fir, cedar forest, Liquidambar forests, oak forests massoniana and lobular, Lin and mushroom). The objectives of this study were to assess and understand the biodiversity threats, evaluate activities, help prioritize and anticipate what threats might become more severe in the future. Threat assessment was based on a review of peer articles and secondary data sources such as key informant interviews. Interviews with local and provincial authorities and visits in the field were held to gather information on Jiufeng protected area resources and biodiversity threats. This research was carried out on June 2009. The Interviews, the literature review and field report showed that the biodiversity is threatened by a variety of human activities and natural factors such as climate change and invasive alien species. These threats can cause the biodiversity loss. In Jiufeng Protected Area, human activities such as land use and land cover change, industrialization and pollution, tourism and recreation constitute threats for biodiversity.
Oxidative Sequence: a Chemical Principle in Support of priority Sequence Rule in Systematic Nomenclature of Organic Functional Groups
American Journal of Chemistry , 2012, DOI: 10.5923/j.chemistry.20120201.03
Abstract: A chemical principle supporting the priority sequence rule in the systematic nomenclature of organic compounds was sought for. The positions of functional groups containing carbon, hydrogen and oxygen in the priority sequence were examined for possible chemical criteria that could be used to buttress the positions of the functions. Oxidative sequence emerged as possible chemical criteria. This chemical principle was applied to other functions containing nitrogen as well and the result was highly positive. However the position of -C≡C- was not favored, this is commented upon. In general oxidative sequence supports the priority sequence and provides a fast means of deciding which function has higher priority instead of resorting to rote learning.
Biodiversity  [cached]
Editorial Office
Koers : Bulletin for Christian Scholarship , 2006, DOI: 10.4102/koers.v71i2-4.252
Abstract: The origin of life and the development of biodiversity
Mutualism Disruption Threatens Global Plant Biodiversity: A Systematic Review  [PDF]
Clare E. Aslan, Erika S. Zavaleta, Bernie Tershy, Donald Croll
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0066993
Abstract: Background As global environmental change accelerates, biodiversity losses can disrupt interspecific interactions. Extinctions of mutualist partners can create “widow” species, which may face reduced ecological fitness. Hypothetically, such mutualism disruptions could have cascading effects on biodiversity by causing additional species coextinctions. However, the scope of this problem – the magnitude of biodiversity that may lose mutualist partners and the consequences of these losses – remains unknown. Methodology/Principal Findings We conducted a systematic review and synthesis of data from a broad range of sources to estimate the threat posed by vertebrate extinctions to the global biodiversity of vertebrate-dispersed and -pollinated plants. Though enormous research gaps persist, our analysis identified Africa, Asia, the Caribbean, and global oceanic islands as geographic regions at particular risk of disruption of these mutualisms; within these regions, percentages of plant species likely affected range from 2.1–4.5%. Widowed plants are likely to experience reproductive declines of 40–58%, potentially threatening their persistence in the context of other global change stresses. Conclusions Our systematic approach demonstrates that thousands of species may be impacted by disruption in one class of mutualisms, but extinctions will likely disrupt other mutualisms, as well. Although uncertainty is high, there is evidence that mutualism disruption directly threatens significant biodiversity in some geographic regions. Conservation measures with explicit focus on mutualistic functions could be necessary to bolster populations of widowed species and maintain ecosystem functions.
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