Biology subjects

Miraldo, A.

Publications and source records attributed to Miraldo, A..

4 recordsLinked to original sources

bioRxiv2024

Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar

We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, weekly Malaise trap samples were collected at 203 locations within 100 sites in Sweden and at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of COI (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.

ecology↗

bioRxiv2024

High-throughput biodiversity surveying sheds new light on the brightest of insect taxa

Sampling of species-rich taxa followed by DNA metabarcoding is quickly becoming a popular high-throughput method for biodiversity inventories. Unfortunately, we know little about its accuracy and efficiency, as the results mostly pertain to poorly-known organism groups in underexplored environments or regions of the world. Here we ask what an extensive sampling effort based on Malaise trapping and metabarcoding can tell us about the lepidopteran fauna of Sweden - one of the best-understood insect taxa in one of the most-surveyed countries of the world. Specifically, we deployed 197 Malaise traps for a single year across Sweden in a systematic sampling design, then metabarcoded the resulting 4,749 bulk samples, and compared the results to existing data sources. We detected more than half (1,535) of the 2,990 lepidopteran species ever recorded as occurring in Sweden, and 323 species not reported during the sampling period by other data providers. Full-length barcoding of individual specimens confirmed three new species for the country and extensive range extensions for two species. It also corroborated eight genetically distinct COI variants that may represent new species to science, one of which has since been described. Most of the new records are for small and inconspicuous species and poorly surveyed regions, suggesting that they represent previously overlooked components of the fauna. Our findings, corroborated by independent metagenomic analyses, show that DNA metabarcoding can be a highly efficient and accurate method of biodiversity sampling, to the extent that it can generate significant new discoveries even for the most well-known of insect faunas.

zoology↗

bioRxiv2024

Biotic and abiotic drivers of ecosystem functioning differ between a temperate and a tropical region

Any single ecosystem will provide many ecosystem functions. Whether these functions tend to increase in concert or trade off against each other is a question of much current interest. Equally topical are the drivers behind ecosystem function rates. Yet, we lack large-scale systematic studies that investigate how abiotic factors can directly or indirectly -- via effects on biodiversity -- drive ecosystem functioning. In this study, we assessed the impact of climate, landscape and biotic community on ecosystem functioning and multifunctioning in the temperate and tropical zone, and investigated potential trade-offs among ecosystem functions in both zones. To achieve this, we measured a diverse set of insect-related ecosystem functions -- including herbivory, seed dispersal, predation, decomposition and pollination -- at 50 sites across Madagascar and 171 sites across Sweden, and characterized the insect community at each site using Malaise traps. We used structural equations models to infer causality of the effects of climate, landscape, and biodiversity on ecosystem functioning. For the temperate zone, we found that abiotic factors were more important than biotic factors in driving ecosystem functioning, while in the tropical zone, effects of biotic drivers were most pronounced. In terms of trade-offs among functions, in the temperate zone, only seed dispersal and predation were positively correlated, while all other functions were uncorrelated. By contrast, in the tropical zone, most ecosystem functions increased in concert, highlighting that tropical ecosystems can simultaneously provide a diverse set of functions. These correlated functions in Madagascar could for the most part be explained by similar responses to local climate, landscape, and biota. Our study suggests that the functioning of temperate and tropical ecosystems differs fundamentally in patterns and drivers. Without a better understanding of these differences, it will be impossible to correctly predict shifts in ecosystem functioning in response to environmental disturbances. To identify global patterns and drivers of ecosystem functioning, we will next need replicate sampling across biomes - as here achieved for two regions, thus paving the road and setting the baseline expectations.

ecology↗

bioRxiv2022

Optimizing insect metabarcoding using replicated mock communities

Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundances, and biomass. Here we use mock community experiments and a simple probabilistic model to evaluate the performance of different metabarcoding protocols. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization?; and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Tiny insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalizes better across species for homogenates. We conclude that a non-destructive, mild lysis approach shows the highest promise for presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.

ecology↗