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Ranaviruses can cause mass mortality events in amphibians, thereby becoming a threat to populations that are already facing dramatic declines. Ranaviruses affect all life stages and persist in multiple amphibian hosts. The detrimental effects of ranavirus infections to amphibian populations have already been observed in the UK and in North America. In Central and South America, the virus has been reported in several countries, but the presence of the genus Ranavirus (Rv) in Colombia is unknown. To help fill this knowledge gap, we surveyed for Rv in 60 species of frogs (including one invasive species) in Colombia. We also tested for co-infection with Batrachochytrium dendrobatidis (Bd) in a subset of individuals. For Rv, we sampled 274 vouchered liver tissue samples collected between 2014 and 2019 from 41 localities covering lowlands to mountaintop páramo habitat across the country. Using quantitative polymerase chain reaction (qPCR) and end-point PCR, we detected Rv in 14 individuals from 8 localities, representing 6 species, including 5 native frogs of the genera Osornophryne, Pristimantis and Leptodactylus, and the invasive American bullfrog Rana catesbeiana. Bd was detected in 7 of 140 individuals, with 1 co-infection of Rv and Bd in an R. catesbeiana specimen collected in 2018. This constitutes the first report of ranavirus in Colombia and should set off alarms about this new emerging threat to amphibian populations in the country. Our findings provide some preliminary clues about how and when Rv may have spread and contribute to understanding how the pathogen is distributed globally.
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Anfibios , Infecciones por Virus ADN , Ranavirus , Animales , Anfibios/microbiología , Anfibios/virología , Anuros/microbiología , Anuros/virología , Batrachochytrium/fisiología , Coinfección/veterinaria , Colombia/epidemiología , Infecciones por Virus ADN/complicaciones , Infecciones por Virus ADN/epidemiología , Infecciones por Virus ADN/veterinaria , Micosis/complicaciones , Micosis/veterinaria , Rana catesbeiana/microbiología , Rana catesbeiana/virología , Ranavirus/fisiologíaRESUMEN
Colombia is the country with the highest bird diversity in the world. Despite active research in ornithology, compelling morphological information of most bird species is still sparse. However, morphological information is the baseline to understand how species respond to environmental variation and how ecosystems respond to species loss. As part of a national initiative, the Instituto Alexander von Humboldt in collaboration with 12 Colombian institutions and seven biological collections, measured up to 15 morphological traits of 9,892 individuals corresponding to 606 species: 3,492 from individuals captured in field and 6,400 from museum specimens. Species measured are mainly distributed in high Andean forest, páramo, and wetland ecosystems. Seven ornithological collections in Colombia and 18 páramo complexes throughout Colombia were visited from 2013 to 2015. The morphological traits involved measurements from bill (total and exposed culmen, bill width and depth), wing (length, area, wingspan, and the distance between longest primary and longest secondary), tail (length and shape), tarsus (length), hallux (length and claw hallux), and mass. The number of measured specimens per species was variable, ranging from 1 to 321 individuals with a median of four individuals per species. Overall, this database gathered morphological information for >30% of Colombian bird diversity. No copyright, proprietary, or cost restrictions apply; the data should be cited appropriately when used.
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Aves , Ecosistema , Animales , Colombia , Fenotipo , HumedalesRESUMEN
Recent declines of insect populations at high rates have resulted in the need to develop a quick method to determine their diversity and to process massive data for the identification of species of highly diverse groups. A short sequence of DNA from COI is widely used for insect identification by comparing it against sequences of known species. Repositories of sequences are available online with tools that facilitate matching of the sequences of interest to a known individual. However, the performance of these tools can differ. Here we aim to assess the accuracy in identification of insect taxonomic categories from two repositories, BOLD Systems and GenBank. This was done by comparing the sequence matches between the taxonomist identification and the suggested identification from the platforms. We used 1,160 COI sequences representing eight orders of insects from Colombia. After the comparison, we reanalyzed the results from a representative subset of the data from the subfamily Scarabaeinae (Coleoptera). Overall, BOLD systems outperformed GenBank, and the performance of both engines differed by orders and other taxonomic categories (species, genus and family). Higher rates of accurate identification were obtained at family and genus levels. The accuracy was higher in BOLD for the order Coleoptera at family level, for Coleoptera and Lepidoptera at genus and species level. Other orders performed similarly in both repositories. Moreover, the Scarabaeinae subset showed that species were correctly identified only when BOLD match percentage was above 93.4% and a total of 85% of the samples were correctly assigned to a taxonomic category. These results accentuate the great potential of the identification engines to place insects accurately into their respective taxonomic categories based on DNA barcodes and highlight the reliability of BOLD Systems for insect identification in the absence of a large reference database for a highly diverse country.
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Escarabajos , Bases de Datos de Ácidos Nucleicos , Animales , Código de Barras del ADN Taxonómico/métodos , Reproducibilidad de los Resultados , Colombia , Insectos , ADN/genética , Escarabajos/genética , FilogeniaRESUMEN
Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars' spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomic diversity and distribution of Lonomia species using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Considering new evidence for seven undescribed species as well as three newly proposed nomenclatural changes, our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species' venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.
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Venenos de Artrópodos , Mariposas Nocturnas , Animales , Humanos , Larva , Venenos de Artrópodos/toxicidad , Hemorragia , América del SurRESUMEN
In this response, we address comments and clarify the rationale behind the choice of hypotheses aimed to describe the Quercus humboldtii phylogeography in the Colombian Andes. Finally, we explain our disagreement with the conclusions of a previous critique, since these are not necessarily adequate under the implemented population genetics approach.
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We introduce the FunAndes database, a compilation of functional trait data for the Andean flora spanning six countries. FunAndes contains data on 24 traits across 2,694 taxa, for a total of 105,466 entries. The database features plant-morphological attributes including growth form, and leaf, stem, and wood traits measured at the species or individual level, together with geographic metadata (i.e., coordinates and elevation). FunAndes follows the field names, trait descriptions and units of measurement of the TRY database. It is currently available in open access in the FIGSHARE data repository, and will be part of TRY's next release. Open access trait data from Andean plants will contribute to ecological research in the region, the most species rich terrestrial biodiversity hotspot.
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Biodiversidad , Plantas , Fenotipo , Hojas de la Planta , MaderaRESUMEN
The climatic and geological changes that occurred during the Quaternary, particularly the fluctuations during the glacial and interglacial periods of the Pleistocene, shaped the population demography and geographic distribution of many species. These processes have been studied in several groups of organisms in the Northern Hemisphere, but their influence on the evolution of Neotropical montane species and ecosystems remains unclear. This study contributes to the understanding of the effect of climatic fluctuations during the late Pleistocene on the evolution of Andean mountain forests. First, we describe the nuclear and plastidic DNA patterns of genetic diversity, structure, historical demography, and landscape connectivity of Quercus humboldtii, which is a typical species in northern Andean montane forests. Then, these patterns were compared with the palynological and evolutionary hypotheses postulated for montane forests of the Colombian Andes under climatic fluctuation scenarios during the Quaternary. Our results indicated that populations of Q. humboldtii have high genetic diversity and a lack of genetic structure and that they have experienced a historical increase in connectivity from the last glacial maximum (LGM) to the present. Furthermore, our results showed a dramatic reduction in the effective population size followed by an expansion before the LGM, which is consistent with the results found by palynological studies, suggesting a change in dominance in Andean forests that may be related to ecological factors rather than climate change.
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Albizia saman is a multipurpose tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically cultivated in silvopastoral and other agroforestry systems around the world, a trend that is bound to increase in light of multimillion hectare commitments for forest and landscape restoration. The effective conservation and sustainable use of A. saman requires detailed knowledge of its genetic diversity across its native distribution range of which surprisingly little is known to date. We assessed the genetic diversity and structure of A.saman across twelve representative locations of SDTF in Colombia, and how they may have been shaped by past climatic changes and human influence. We found four different genetic groups which may be the result of differentiation due to isolation of populations in preglacial times. The current distribution and mixture of genetic groups across STDF fragments we observed might be the result of range expansion of SDTFs during the last glacial period followed by range contraction during the Holocene and human-influenced movement of germplasm associated with cattle ranching. Despite the fragmented state of the presumed natural A. saman stands we sampled, we did not find any signs of inbreeding, suggesting that gene flow is not jeopardized in humanized landscapes. However, further research is needed to assess potential deleterious effects of fragmentation on progeny. Climate change is not expected to seriously threaten the in situ persistence of A. saman populations and might present opportunities for future range expansion. However, the sourcing of germplasm for tree planting activities needs to be aligned with the genetic affinity of reference populations across the distribution of Colombian SDTFs. We identify priority source populations for in situ conservation based on their high genetic diversity, lack or limited signs of admixture, and/or genetic uniqueness.
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Species traits provide a strong link between an organism's fitness and processes at community and ecosystem levels. However, such data remain scarce for amphibians in the Neotropics. Colombia is the country with the highest number of threatened amphibians and the second greatest number of amphibian species worldwide. We present a data set containing eight morphological traits for 4,623 museum specimens of the seven largest collections in the country corresponding to 293 species of 14 families. The number of measured specimens per species ranged from 1 to 118 individuals with a median of 8 individuals per species. Overall, this database gathered morphological information for 37.6% of Colombian anuran diversity. Species measured were mainly distributed in the high Andean forest, the páramo, and wetland ecosystems, and was part of a national initiative led by the Instituto Alexander von Humboldt. The morphological traits were selected on the basis of their role in species' responses to environmental variability and their contributions to ecosystem processes. These traits were related to habitat use, (forearm length, tibia length, femur length, foot length, and foot webbing), predation and food chains (head width and mouth width), and nutrient recycling (snout-vent length). We expect this data set will be used in studies on functional diversity in amphibians and the development of conservation planning for these taxa. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.
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Abstract Introduction: Neotropical seasonally dry forest (NSDF) climatic constraints increased endemism, and phylogenetic niche conservatism in species that are restricted to this biome. NSDF have a large number of endemic Capparaceae taxa, but it is unknown if phylogenetic niche conservatism has played a role in this pattern. Objective: We carried out an evolutionary analysis of the climatic niche of neotropical species of Capparaceae to identify whether the climatic constraints of NSDF have played a major role throughout the family's evolutionary history. Methods: Using three chloroplastic (ndhF, matK, rbcL) and one ribosomal (rsp3) DNA sequences, we proposed a date phylogeny to reconstruct the evolutionary climatic niche dynamics of 24 Neotropical species of Capparaceae. We tested the relationship between niche dissimilarity and phylogenetic distance between species using the Mantel test. Likewise, we used a set of phylogenetic comparative methods (PGLS) on the phylogeny of Capparaceae to reconstruct the main evolutionary historic events in their niche. Results: Capparaceae originated in humid regions and subsequently, convergent evolution occurred towards humid and dry forest during the aridification phases of the Middle Miocene (16-11 Mya). However, adaptation towards drought stress was reflected only during the precipitation of the coldest quarter, where we found phylogenetic signal (Pagel λ) for gradual evolution and, therefore, evidence of phylogenetic niche conservatism. We found convergent species-specific adaptations to both drought stress and rainfall during the Miocene, suggesting a non-phylogenetic structure in most climatic variables. Conclusions: Our study shows how the Miocene climate may have influenced the Capparaceae speciation toward driest environments. Further, highlights the complexity of climatic niche dynamics in this family, and therefore more detailed analyses are necessary in order to better understand the NSDF climatic constrictions affected the evolution of Capparaceae.
Resumen Introducción: Las limitaciones climáticas del bosque neotropical estacionalmente seco (NSDF) produjeron endemismo y conservadurismo filogenético del nicho en especies restringidas a este bosque. En las Caparáceas neotropicales se ha encontrado endemismo en los NSDF, pero se desconoce si el conservadurismo de nicho filogenético ha influido en su evolución. Objetivos: Se llevó a cabo un análisis evolutivo del nicho climático de las especies neotropicales de Capparaceae para evaluar si las limitaciones climáticas del bosque neotropical estacionalmente seco (NSDF) han jugado un papel importante a lo largo de la historia evolutiva de la familia. Métodos: Usando tres secuencias de ADN cloroplastico (ndhF, matK, rbcL) y una ribosomal (rsp3) se propuso una filogenia datada para reconstruir la dinámica evolutiva del nicho climático de 24 especies Neotropicales de Capparaceae. Utilizando la prueba de Mantel, se realizaron análisis para establecer si hay diferencia de nicho y la distancia filogenética entre especies. Asimismo, se emplearon un conjunto de métodos comparativos filogenéticos sobre la filogenia de la familia para reconstruir los principales eventos históricos evolutivos en su nicho. Resultados: Capparaceae se originó en regiones húmedas y posteriormente se dio una evolución convergente hacia bosque húmedo y seco durante las fases de aridificación del Mioceno Medio (16-11 Ma). Sin embargo, la adaptación al estrés por sequía se reflejó solo en la precipitación del cuarto más frío del año, donde se evidencio señal filogenética, evolución gradual y, por lo tanto, evidencia de conservadurismo de nicho filogenético. También se hallaron especies con adaptaciones convergentes específicas tanto al estrés por sequía como a las lluvias durante el Mioceno, sugiriendo la carencia de estructura filogenética en la mayoría de las variables climáticas. Conclusiones: Este estudio muestra cómo el clima del Mioceno pudo haber influenciado la especiación de Capparaceae hacia ambientes mas secos. Además, la compleja dinámica del nicho climático en esta familia y, por lo tanto, la necesidad de realizar análisis más detallados para comprender mejor como las constricciones climáticas del NSDF afectaron la evolución de Capparaceae.
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Cambio Climático , Bosques , CapparaceaeRESUMEN
Colombia is the country with the largest number of bird species worldwide, yet its avifauna is seriously threatened by habitat degradation and poaching. We built a DNA barcode library of nearly half of the bird species listed in the CITES appendices for Colombia, thereby constructing a species identification reference that will help in global efforts for controlling illegal species trade. We obtained the COI barcode sequence of 151 species based on 281 samples, representing 46% of CITES bird species registered for Colombia. The species analysed belong to nine families, where Trochilidae and Psittacidae are the most abundant ones. We sequenced for the first time the DNA barcode of 47 species, mainly hummingbirds endemic of the Northern Andes region. We found a correct match between morphological and genetic identification for 86-92% of the species analysed, depending on the cluster analysis performed (BIN, ABGD and TaxonDNA). Additionally, we identified eleven cases of high intraspecific divergence based on K2P genetic distances (up to 14.61%) that could reflect cryptic diversity. In these cases, the specimens were collected in geographically distant sites such as different mountain systems, opposite flanks of the mountain or different elevations. Likewise, we found two cases of possible hybridization and incomplete lineage sorting. This survey constitutes the first attempt to build the DNA barcode library of endangered bird species in Colombia establishing as a reference for management programs of illegal species trade, and providing major insights of phylogeographic structure that can guide future taxonomic research.
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Aves/clasificación , Aves/genética , Código de Barras del ADN Taxonómico , Variación Genética , Animales , Análisis por Conglomerados , Colombia , Complejo IV de Transporte de Electrones/genética , Genotipo , Análisis de Secuencia de ADNRESUMEN
BACKGROUND: Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. METHODOLOGY/PRINCIPAL FINDINGS: Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon. CONCLUSION/SIGNIFICANCE: We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.
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ADN de Plantas/genética , Árboles/clasificación , Árboles/genética , Biodiversidad , Análisis por Conglomerados , Procesamiento Automatizado de Datos , Guyana Francesa , Marcadores Genéticos , Modelos Estadísticos , Filogenia , Estaciones del Año , Análisis de Secuencia de ADNRESUMEN
El término -Código de Barras de ADN- se basa en el uso de una región de ADN estandarizada, la cual sirve como una etiqueta para la identificación rápida y de especies. El propósito de un sistema de identificación más eficaz es facilitar la conservación, conocimiento y uso sustentable de la biodiversidad. Después de ocho años de discusión y producción en la literatura científica, el tema sigue generando controversia, debido en parte a la falta de homogeneidad en la definición y el alcance del método entre los autores. En este artículo enfatizamos la definición y metodología de los códigos de barra de ADN, así como su uso para contestar preguntas nuevas en los campos de la ecología, la evolución y la conservación.
DNA barcode of life is a global initiative to populate a database of short, standardized DNA fragments from most eukaryotic species to facilitate the identification of whole or fragmented biological samples. Increasing the ability of non-experts to indentify unknown samples should improve our collective understanding and management of the world s biodiversity. In the eight years following its proposal, DNA barcoding remains controversial in the scientific literature due, in part, to a lack of consensus on how DNA barcoding is defined and what activities are included under this rubric. In the present paper we review the definition, methods and goals of DNA barcoding, highlighting how the massive data sets generated by various DNA barcode of life campaigns may be applied to fundamental and novel questions in ecology, evolution and conservation.