Biology subjects

Braukmann, T. W. A.

Publications and source records attributed to Braukmann, T. W. A..

5 recordsLinked to original sources

bioRxiv2024

Welcome to Hotel Hymenoptera: monitoring cavity-nesting bee and wasp distribution and their trophic interactions using community science and metabarcoding

Essential ecosystem services are provided by many interactions, including plant-pollinator, predator-prey, and host-parasitoid. These services support food and natural systems through pollination and pest control, however they are challenging to qualify, and previous observational studies may underestimate their complexity. The cavity nesting Hymenoptera are a good example showing all these three interactions and they can be monitored using trap nests. For this study, trap nests were installed at schools across Canada by community scientists to investigate cavity-nesting bee and wasp distributions and interactions. DNA metabarcoding was used to identify the occupants and their food sources. New bee and wasp distributions were found that might be the result of previous under-sampling or recent range expansions. Detailed bipartite and tripartite networks describing species interactions suggest some novel bee, wasp, and parasite associations. These results encourage further investigation into these interactions using molecular methods as detailed range maps and networks provide information to natural historians and conservationists alike.

ecology↗

bioRxiv2023

Expansion of GTP cyclohydrolase I copy number in malaria parasites resistant to a pyrimidine biosynthesis inhibitor

Increases in the copy number of large genomic regions, termed genome amplification, are an important adaptive strategy for malaria parasites. Numerous amplifications across the Plasmodium falciparum genome contribute directly to drug resistance or impact the fitness of this protozoan parasite. During the characterization of parasite lines with amplifications of the dihydroorotate dehydrogenase (DHODH) gene, we detected increased copies of an additional genomic region that encompassed 3 genes (~5 kb) including GTP cyclohydrolase I (GCH1 amplicon). While this gene is reported to increase the fitness of antifolate resistant parasites, GCH1 amplicons had not previously been implicated in any other antimalarial resistance context. Here, we further explored the association between GCH1 and DHODH copy number. Using long read sequencing and single read visualization, we directly observed a higher number of tandem GCH1 amplicons in parasites with increased DHODH copies (up to 9 amplicons) compared to parental parasites (3 amplicons). While all GCH1 amplicons shared a consistent structure, expansions arose in 2-unit steps (from 3 to 5 to 7, etc copies). Adaptive evolution of DHODH and GCH1 loci was further bolstered when we evaluated prior selection experiments; DHODH amplification was only successful in parasite lines with pre-existing GCH1 amplicons. These observations, combined with the direct connection between metabolic pathways that contain these enzymes, lead us to propose that the GCH1 locus is beneficial for the fitness of parasites exposed to DHODH inhibitors. This finding highlights the importance of studying variation within individual parasite genomes as well as biochemical connections of drug targets as novel antimalarials move towards clinical approval. Author SummaryMalaria is caused by a protozoan parasite that readily evolves resistance to drugs that are used to treat this deadly disease. Changes that arise in the parasite genome, including extra copies of important genes, directly contribute to this resistance or improve how well the resistant parasite competes. In this study, we identified that extra copies of one gene (GTP cyclohydrolase or GCH1) were more likely to be found in parasites with extra copies of another gene on a different chromosome (dihydroorotate dehydrogenase or DHODH). A method that allows us to view long pieces of DNA from individual genomes was especially important for this study; we were able to assess gene number, arrangement, and boundary sequences, which provided clues into how extra copies evolved. Additionally, by analyzing previous experiments, we identified that extra GCH1 copies improved resistance to drugs that target DHODH. The relationship between these two loci is supported by a direct connection between the folate and pyrimidine biosynthesis pathways that the parasite uses to make DNA. Since GCH1 amplicons are common in clinical parasites worldwide, this finding highlights the need to study metabolic connections to avoid resistance evolution.

genomics↗

bioRxiv2021

Message in a Bottle, Metabarcoding Enables Biodiversity Comparisons Across Ecoregions

BackgroundTraditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study employed DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning three Canadian ecoregions. ResultsThis study revealed the presence of 26,263 arthropod species in the three ecoregions and indicated that at least another 3,000-5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall -diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site with turnover greater than nestedness, suggesting the presence of many transient species. ConclusionsDifferences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric employed in prior efforts to track change in arthropod communities.

ecology↗

bioRxiv2021

Diet composition of reintroduced Red-and-Green Macaws (Ara chloropterus) reflects gradual adaption to life in the wild

Over the last two centuries, the Red-and-green Macaw (Ara chloropterus) has become locally extinct in Argentina. In an attempt to restore its key ecosystem functions as both disperser and regulator of large-seeded plants, a reintroduction project was initiated at the Ibera National Park in northeastern Argentina. The ability of released individuals to find food is crucial, in particular when working with captive-bred animals, as long-term establishment of a self-sustaining population depends on their short-term ability to exploit wild food sources. Monitoring of feeding habits is usually conducted through behavioral observation, but in recent years DNA metabarcoding has emerged as an alternative for obtaining highly resolved data on diet composition. In this study we use a combination of both techniques to characterize the breadth and composition of the reintroduced macaws diet. In addition, we evaluate the efficiency of both direct field observations and metabarcoding of feces as techniques to assess diet composition. Individuals fed on a variety of plant species (n = 49) belonging to a broad phylogenetic spectrum (28 families). Dietary richness estimated by direct observation and metabarcoding was similar, though smaller than the combination of the two datasets as both techniques detected at least 15 species not recorded by the other method. While the total number of detected species was higher for observational data, the rate of species-detection per sampling day was higher for metabarcoding. These results suggest that a combination of both methods is required in order to obtain the most accurate account of the total diversity of the diet of a species. The ability of the reintroduced macaws to successfully exploit local food resources throughout the year indicates a good level of adjustment to the release site, an important step towards the creation of a stable, self-sustaining population of Red-and-green Macaws in Northern Argentina. RESUMENEn el transcurso de los ultimos dos siglos, el Guacamayo Rojo (Ara chloropterus) se ha extinguido en la Argentina. Buscando recuperar su rol ecologico tanto de dispersor como de depredador de semillas de gran tamano, se comenzo un proyecto de reintroduccion de la especie en el Parque Nacional Ibera, en la region noreste del pais. La capacidad para encontrar alimento por parte de los individuos liberados es crucial, particularmente cuando se trabaja con animales provenientes de condiciones de cautiverio, ya que el establecimiento de una poblacion autosuficiente a largo plazo dependera de la habilidad de estos para explotar fuentes de alimento silvestre a corto plazo. El monitoreo de habitos alimenticios se realiza usualmente a traves de observaciones comportamentales. Sin embargo, en los ultimos anos la tecnica del meta-codigo de barras de ADN ha surgido como una alternativa para la obtencion de datos de composicion dietaria con alto nivel de resolucion. En este estudio, utilizamos una combinacion de ambas tecnicas para caracterizar la amplitud y composicion de la dieta de los guacamayos reintroducidos. A su vez, evaluamos la eficiencia de la observacion directa y el codigo de barras genetico de heces como tecnicas para evaluar la composicion de la dieta. Los individuos se alimentaron de una amplia variedad de especies (n = 49), abarcando un amplio espectro filogenetico (28 familias). La riqueza dietaria estimada por observacion directa y por meta-codigo de barras genetico fue similar, aunque menor a la resultante de la combinacion de todos los datos ya que ambas tecnicas detectaron al menos 15 especies no registradas por el otro metodo. Mientras que el numero total de especies detectadas fue mayor para los metodos observacionales, la tasa de deteccion de especies por dia de muestreo fue mayor para el analisis genetico. Estos resultados sugieren que una combinacion de ambos metodos es necesaria para obtener la descripcion mas precisa posible de la diversidad dietaria total de una especie. La capacidad de los guacamayos reintroducidos para explotar recursos alimenticios locales a lo largo del ano estaria indicando un buen nivel de adaptacion al sitio de liberacion, un paso muy importante hacia el establecimiento de una poblacion de Guacamayo Rojo estable y autosuficiente en el norte de Argentina. Palabras claveAra chloropterus, Conservacion, Dieta, Frugivoria, Meta-codigo de barras, Guacamayo Rojo, Reintroduccion, Ecologia trofica LAY SUMMARYO_LIThe Red-and-green Macaw reintroduction project aims to restore this species to Argentina, where it is locally extinct. To assess if reintroduced macaws are successfully adapting to life in the wild, we studied their foraging habits at the Ibera National Park. Their food consumption was observed visually, and their feces were analyzed with molecular methods for traces of the consumed plants. C_LIO_LIMacaws fed from a large diversity of food items, exhibiting a flexible diet which varied with fruit availability in different months. A combination of both methods was required to obtain the most accurate account of the total diversity of the diet of a species. C_LIO_LIThe reintroduced macaws were able to successfully locate and exploit food resources throughout the year, indicating a good level of adjustment to the release site. C_LI

ecology↗

bioRxiv2020

Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples

The Malaise trap has gained popularity for assessing diverse terrestrial arthropod communities because it collects large samples with modest effort. A number of factors that influence collection efficiency, placement being one of them. For instance, when designing larger biotic surveys using arrays of Malaise traps we need to know the optimal distance between individual traps that maximises observable species richness and community composition. We examined the influence of spacing between Malaise traps by metabarcoding samples from two field experiments at a site in Waterloo, Ontario, Canada. For one experiment, we used two trap pairs deployed at weekly increasing distance (3m increments from 3 to 27 m). The second experiment involved a total of 10 traps set up in a row at 3m distance intervals for three consecutive weeks. Results show that community similarity of samples decreases over distance between traps. The amount of species shared between trap pairs shows drops considerably at about 15m trap-to-trap distance. This change can be observed across all major taxonomic groups and for two different habitat types (grassland and forest). Large numbers of OTUs found only once within samples cause rather large dissimilarity between distance pairs even at close proximity. This could be caused by a large number of transient species from adjacent habitat which arrive at the trap through passive transport, as well as capture of rare taxa, which end up in different traps by chance.

ecology↗