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https://hdl.handle.net/10784/26726

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Dynamics of species composition of small non-volant mammals from the northern Cordillera Central of Colombia
(De Gruyter, 2015-11-01) Díaz-Nieto, J.F.; Sanchez, Camilo; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
On the basis of our recent fieldwork and historical records, we document the diversity of small non-volant mammals in the northern end of Cordillera Central of Colombia, an important region in the context of vertebrate biodiversity.
Phylogenetic relationships of Chacodelphys (Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences
(Oxford University Press, 2016-03-01) Díaz-Nieto, J.F.; Voss, Robert S; Jansa, Sharon A; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys, which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys
DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genus Marmosops (Didelphidae: Thylamyini)
(Oxford University Press, 2016-04-01) Diaz-Nieto, Juan F.; Jansa, Sharon A.; Voss, Robert S.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
A revision of the didelphid marsupial genus Marmosops part 1. Species of the subgenus Sciophanes.
(AMER MUSEUM NATURAL HISTORY, 2016-05-01) Diaz, Juan Fernando; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Mitochondrial genome characterization of Tecia solanivora (Lepidoptera: Gelechiidae) and its phylogenetic relationship with other lepidopteran insects
(Elsevier, 2016-05-01) Ramírez-Ríos, V.; Franco-Sierra, N.D.; Alvarez, J.C.; Saldamando-Benjumea, C.I.; Villanueva, Diego Fernando; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
The complete mitogenome of the potato tuber moth Tecia solanivora (Lepidoptera: Gelechiidae) was sequenced, annotated, characterized and compared with 140 species of the order Lepidoptera. The circular genome is 15,251 bp, containing 37 genes (13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region). The gene arrangement was identical to other lepidopteran mitogenomes but different from the ancestral arrangement found in most insects for the tRNA-Met gene (A + T-region, tRNA-I, tRNA-Q, tRNA-M). The mitogenome of T. solanivora is highly A + T-biased (78.2%) and exhibits negative AT- and GC-skews. All PCGs are initiated by canonical ATN start codons, except for Cytochrome Oxidase subunit 1 (COI), which is initiated by CGA. Most PCGs have a complete typical stop codon (TAA). Only NAD1 has a TAG stop codon and the COII and NAD5 genes have an incomplete stop codon consisting of just a T. The A + T-rich region is 332 bp long and contains common features found in lepidopteran mitogenomes, including the `ATAGA' motif, a 17 bp poly (T) stretch and a (AT)(8) element preceded by the `ATTTA' motif. Other tandem repeats like (TAA)(4) and (TAT), were found, as well as (T)(6) and (A)(10) mononucleotide repeat elements. Finally, this mitogenome has 20 intergenic spacer regions. The phylogenetic relationship of T. solanivora with 28 other lepidopteran families (12 superfamilies) showed that taxonomic classification by morphological features coincides with the inferred phylogeny. Thus, the Gelechiidae family represents a monophyletic group, suggesting that T. solanivora and Pectinophora gossypiella have a recent common ancestor. (C) 2016 Elsevier B.V. All rights reserved.
Revisión de las localidades fosilíferas del departamento de Antioquia, Colombia
(Geological Engineering Curriculum Program, Geosciences and Environment College of Mines Faculty, National University of Colombia - Medellin Headquarters, 2016-08-01) Cardenas, Andres Leonardo; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Planktic foraminiferal diversity: Logistic growth overprinted by a varying environment
(Universidad Nacional de Colombia, 2016-09-01) Cárdenas-Rozo, A.L.; Harries, P.J.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
This study statistically assesses the relationship between the planktic foraminiferal long-term diversity pattern (~170 Ma to Recent) and four major paleobiological diversification models: (i) the ‘Red Queen’ (Van Valen, 1973; Raup et al., 1973), (ii) the turnover-pulse (Vrba, 1985; Brett and Baird, 1995), (iii) the diversity-equilibrium (Sepkoski, 1978; Rosenzweig, 1995), and (iv) the ‘complicated logistic growth’ (Alroy, 2010a). Our results suggest that the long-term standing diversity pattern and the interplay between origination and extinction rates displayed by this group do not correspond to the first three models, but can be more readily explained by the fourth scenario. Consequently, these patterns are likely controlled by a combination of planktic foraminiferal interspecific competition as well as various environmental changes such as marine global temperatures that could impacted the niches within the upper mixed layer within the oceans. Moreover, as other global long-term patterns have been interpreted as reflecting ‘complicated logistic growth’, this study further suggests that the interplay between abiotic and biotic factors are fundamental elements influencing the evolutionary processes over the extensive history of the biota. © 2016 Author(s).
Construction of probe of the plant growth-promoting bacteria Bacillus subtilis useful for fluorescence in situ hybridization
(Elsevier, 2016-09-01) Posada, L.F.; Alvarez, J.C.; Hu, C.-H.; de-Bashan, L.E.; Bashan, Y.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Strains of Bacillus subtilis are plant growth-promoting bacteria (PGPB) of many crops and are used as inoculants. PGPB colonization is an important trait for success of a PGPB on plants. A specific probe, based on the 16 s rRNA of Bacillus subtilis, was designed and evaluated to distinguishing, by fluorescence in situ hybridization (FISH), between this species and the closely related Bacillus amyloliquefaciens. The selected target for the probe was between nucleotides 465 and 483 of the gene, where three different nucleotides can be identified. The designed probe successfully hybridized with several strains of Bacillus subtilis, but failed to hybridize not only with B. amyloliquefaciens, but also with other strains such as Bacillus altitudinis, Bacillus cereus, Bacillus gibsonii, Bacillus megaterium, Bacillus pumilus; and with the external phylogenetic strains Azospirillum brasilense Cd, Micrococcus sp. and Paenibacillus sp. The results showed the specificity of this molecular probe for B. subtilis. (C) 2016 Elsevier B.V. All rights reserved.
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
(BioMed Central Ltd., 2016-12-16) Narayanasamy, S.; Jarosz, Y.; Muller, E.E.L.; Heintz-Buschart, A.; Herold, M.; Kaysen, A.; Laczny, C.C.; Pinel, N.; May, P.; Wilmes, P.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases. Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license).
Reviewing microbial behaviors in ecosystems leading to a natural quorum quenching occurrence
(INST TECNOLOGIA PARANA, 2017-01-01) Sierra Zapata, Laura; Romero Tabarez, Magally; Correa Alvarez, Javier; Villegas Escobar, Valeska; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Quorum sensing is considered one of the most important discoveries in cell-to-cell communication. Although revealed in Bacteria, it has been identified as well as a mechanism present in the other two domains, Eukaryota and Archaea. This phenomenon consists mainly of an exchange and sensing of "words" produced by each cell: chemical signals known as autoinducers. The process takes places at high cell densities and confined environments, triggering the expression of specific genes that manifest in a determined phenotype. Quorum sensing has a fundamental importance in the organisms' fitness in natural ecosystems since it activates many of the traits needed by cells to survive under specific conditions, and thus a wide variety of chemical signals, which are detailed throughout the review, have evolved in response to the needs of an organism in the ecosystem it inhabits. As a counterpart, derived from the natural occurrence of quorum sensing, comes it's antagonistic process named quorum quenching. Acting in the exact opposite way, quorum quenching interferes or degrades the autoinducers confusing and stopping communication, hence affecting transcriptional regulation and expression of a specific phenotype. The main reasons for stopping this mechanism go from fading their own signals when perceiving scarce nutrients conditions, to degrading competitors' signals to take advantage in the ecosystem. Some of the most studied purposes and means known up to date to be used by cells for making quorum quenching in their ecosystems is what will be discussed along this review, offering information for future works on quorum quencher molecules bioprospection.
Directional Landscapes: Using Parametric Loudspeakers for Sound Reproduction in Art
(Taylor and Francis Ltd., 2017-01-01) Alunno, M.; Yarce Botero, A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
As new technologies appear, the expressive palette of creators broadens. Parametric loudspeakers are one of such new technologies that makes it possible to direct sound as though it were a light beam. Since their debut in the market, they have thus far received little attention from part of the artistic world. Some peculiarities concerning the sound reproduction might explain why musicians in particular are hesitating to use an otherwise highly attractive acoustic innovation. Due to such peculiarities, a proper use of parametric loudspeakers in art must start with investigating a whole array of different topics (i.e. non-linear acoustics and ultrasonic transducers) in order to understand how this technology works and utilize it at its best. The result of our project is ultimately a sound installation that makes use of directional sound to ruminate on issues concerning sound perception and the responsible use of our sound environment. © 2016 Informa UK Limited, trading as Taylor & Francis Group.
Revisiting the phylogeny of phylum Ctenophora: a molecular perspective
(F1000 Research Ltd., 2017-02-01) Arteaga, Luis; Sanchez, Valentina; Franco Sierra, Nicolás David; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
The phylogenetic relationships of deep metazoans, specifically in the phylum Ctenophora, are not totally understood. Previous studies have been developed on this subject, mostly based on morphology and single gene analyses
Rol de la función mitocondrial en el corazón y sus implicaciones en disfunciones cardíacas
(Fondo Editorial Universidad EAFIT, 2017-11-01) Franco, Nicolas David; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Enhanced molecular visualization of root colonization and growth promotion by Bacillus subtilis EA-CB0575 in different growth systems
(Elsevier GmbH, 2018-01-01) Posada, L.F.; Álvarez, J.C.; Romero-Tabarez, M.; de-Bashan, L.; Villegas-Escobar, V.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Bacillus subtilis EA-CB0575 is a plant growth-promoting bacterium (PGPB) associated with banana and tomato crops. Root colonization is an important trait for PGPB microorganisms and potentiates the bacterial effect related to the mechanisms of plant growth promotion. Therefore, detection of bacterial colonization of roots in different culture systems is important in the study of plant–microorganism interactions. In this study, fluorescent in situ hybridization (FISH) and catalyzed reporter deposition–FISH (CARD–FISH) were evaluated to determine the colonization ability of B. subtilis EA-CB0575 on banana and tomato roots planted on solid and liquid Murashige and Skoog medium (MS(S) and MS(L), respectively) and in soil for tomato plants. Results showed B. subtilis colonization 0–30 days post inoculation for banana and tomato plants in different culture systems with differential distribution of bacterial cells along tomato and banana roots. FISH and CARD–FISH methodologies were both successful in detecting B. subtilis colonies, but CARD–FISH proved to be superior due to its enhanced fluorescence signal. The presence of bacteria correlated with the promotion of plant growth in both plant species, providing clues to relate rhizospheric colonization with improvement in plant growth. FISH and CARD–FISH analysis results suggested the presence of native microbiota on the roots of in vitro banana plants, but not on those of tomato plants. © 2018 Elsevier GmbH
Unsupervised fuzzy binning of metagenomic sequence fragments on three-dimensional Barnes-Hut t-Stochastic Neighbor Embeddings
(Institute of Electrical and Electronics Engineers Inc., 2018-01-01) Ariza-Jimenez L.; Quintero O.L.; Pinel N.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Shotgun metagenomic studies attempt to reconstruct population genome sequences from complex microbial communities. In some traditional genome demarcation approaches, high-dimensional sequence data are embedded into two-dimensional spaces and subsequently binned into candidate genomic populations. One such approach uses a combination of the Barnes-Hut approximation and the t -Stochastic Neighbor Embedding (BH-SNE) algorithm for dimensionality reduction of DNA sequence data pentamer profiles; and demarcation of groups based on Gaussian mixture models within humanimposed boundaries. We found that genome demarcation from three-dimensional BH-SNE embeddings consistently results in more accurate binnings than 2-D embeddings. We further addressed the lack of a priori population number information by developing an unsupervised binning approach based on the Subtractive and Fuzzy c-means (FCM) clustering algorithms combined with internal clustering validity indices. Lastly, we addressed the subject of shared membership of individual data objects in a mixed community by assigning a degree of membership to individual objects using the FCM algorithm, and discriminated between confidently binned and uncertain sequence data objects from the community for subsequent biological interpretation. The binning of metagenome sequence fragments according to thresholds in the degree of membership opens the door for the identification of horizontally transferred elements and other genomic regions of uncertain assignment in which biologically meaningful information resides. The reported approach improves the unsupervised genome demarcation of populations within complex communities, increases the confidence in the coherence of the binned elements, and enables the identification of evolutionary processes ignored in hard-binning approaches in shotgun metagenomic studies. © 2018 IEEE.
Complete mitogenome of the biocontroller fungus Purpureocillium sp. (Ascomycota, Ophiocordycipitaceae, Hypocreales)
(Taylor and Francis Ltd., 2018-01-01) Cardona N.L.; Franco-Sierra N.D.; Correa Alvarez J.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
The strain Purpureocillium sp. UdeA0106 is an antagonist of nematodes, fungi, and garden symphylans from crops with high economic importance in Colombia (Salazar 2013; Salazar et al. 2014; Cardona et al. 2014; Gallego et al. 2014) and is being studied to be proposed as new species. It was included on the 1000 fungal genomes project to elucidate its phylogenetic relationships with other fungi. Purpureocillium’s mitogenome has 23,495 bp of circular size. It contains 15 protein-coding genes without duplications (PCGs), corresponding to the 60% of its total length, 23 transfer genes (7.6% tRNA), two of them duplicated (trnR and trnM), and two ribosomal genes (17.6% rRNA) and a GC content of 28.44%. A phylogenetic tree was proposed using their 14 PCGs mitochondrial genes and was compared with other fungi of the Subphylum Pezizomycotina. Phylogenetics relationships showed UdeA0106 to be close to P. chlamydosporia and M. anisopliae forming a cluster with other fungal biocontrol agents and separated the strain of plant pathogenic fungi. © 2018, © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC)
(BioMed Central Ltd., 2018-01-17) Molano, E.P.L.; Cabrera, O.G.; Jose, J.; do Nascimento, L.C.; Carazzolle, M.F.; Teixeira, P.J.P.L.; Alvarez, J.C.; Tiburcio, R.A.; Tokimatu Filho, P.M.; de Lima, G.M.A.; Guido, R.V.C.; Corrêa, T.L.R.; Leme, A.F.P.; Mieczkowski, P.; Pereira, G.A.G.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Background: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. Results: We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. Conclusion: Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity. © 2018 The Author(s).
A Revision of Philander (Marsupialia: Didelphidae), Part 1: P. quica, P. canus, and a New Species from Amazonia
(American Museum of Natural History, 2018-01-31) Voss, R.S.; Díaz-Nieto, J.F.; Jansa, S.A.; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
This is the first installment of a revision of the didelphid marsupial genus Philander, commonly known as gray four-eyed opossums. Although abundant and widespread in lowland tropical forests from southern Mexico to northern Argentina, species of Philander are not well understood taxonomically, and the current literature includes many examples of conflicting species definitions and nomenclatural usage. Our revision is based on coalescent analyses of mitochondrial gene sequences, phylogenetic analyses of mitochondrial and nuclear genes, morphometric analyses, and firsthand examination of relevant type material. Based on these results, we provisionally recognize eight species, of which three are formally treated in this report: P. quica (Temminck, 1824), an Atlantic Forest endemic formerly known as P. frenatus (Olfers, 1818); P. canus (Osgood, 1913), a widespread species formerly treated as a synonym or subspecies of P. opossum (Linnaeus, 1758); and P. pebas, a new species endemic to Amazonia. The remaining, possibly valid, species of Philander can be allocated to two clades. The first is a cis-Andean complex that includes P. andersoni (Osgood, 1913); P. mcilhennyi Gardner and Patton, 1972; and P. opossum. The second is a trans-Andean complex that includes P. melanurus (Thomas, 1899) and P. pallidus (Allen, 1901). Among other nomenclatural acts, we designate a neotype for the long-problematic nominal taxon Didelphis superciliaris Olfers, 1818, and (in an appendix coauthored by Renate Angermann), we establish that Olfers' coeval binomen D. frenata is based on an eastern Amazonian type and is a junior synonym of P. opossum. © American Museum of Natural History 2018.
Identification of Fusarium cf. Verticillioides as The Causal Agent of Pokka Boheng Disease in Sugarcane in the Department of Antioquia, Colombia
(Fondo Editorial Universidad EAFIT, 2018-07-01) Correa, Javier; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación
Implementation of a Non-InvasiveBioprospecting Protocol for Isolation ofLactobacillusfrom Feces of Hens UnderForaging Conditions
(Fondo Editorial Universidad EAFIT, 2018-07-01) Correa, Javier; Universidad EAFIT. Departamento de Ciencias; Biodiversidad, Evolución y Conservación

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