Mehrdad Hajibabaei

Mehrdad Hajibabaei
University of Guelph | UOGuelph · Department of Integrative Biology

PhD

About

242
Publications
89,692
Reads
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17,931
Citations
Additional affiliations
January 2012 - present
University of New Brunswick
January 2011 - present
Concordia University Montreal
January 2008 - present
Smithsonian Institution

Publications

Publications (242)
Article
Full-text available
The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate this approach, we studied the ants, springtails and termites of 100 paired soil samples...
Article
Full-text available
There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxono...
Preprint
Full-text available
There is increasing need for biodiversity monitoring, especially in places where potential anthropogenic disturbance may significantly impact ecosystem health. We employed a combination of traditional morphological and bulk macroinvertebrate metabarcoding analyses to benthic samples collected from Toronto Harbour (Ontario, Canada) to compare taxono...
Preprint
Canonical distance and dissimilarity measures can fail to capture important relationships in high-throughput sequencing datasets since these measurements are unable to represent feature interactions. By learning a dissimilarity using decision tree ensembles, we can avoid this important pitfall. We used 16S rRNA data from the lumen and mucosa of the...
Article
Full-text available
Background Identification of biomarkers, which are measurable characteristics of biological datasets, can be challenging. Although amplicon sequence variants (ASVs) can be considered potential biomarkers, identifying important ASVs in high-throughput sequencing datasets is challenging. Noise, algorithmic failures to account for specific distributio...
Preprint
Fungi are primary agents of coarse woody debris (CWD) decay in forests, playing an essential role in nutrient cycling and carbon storage. Characterizing fungal communities within CWD will promote further understanding of the fungal controls on CWD decomposition. We compared fungal community assemblages using alpha and beta diversity metrics, carbon...
Preprint
Full-text available
Freshwater systems are experiencing rapid biodiversity losses resulting from high rates of habitat degradation. Ecological condition is typically determined through identifying either macroinvertebrate or diatom bioindicator assemblages and comparing them to their known tolerance to stressors. These comparisons are typically conducted at family or...
Article
Logging road development is considered as potentially more damaging to a tropical forest than the felling of the actual trees. However, little work has been conducted to determine how logging road development impacts the soil microbial communities and associated C and N cycle activities in tropical forests. This study was conducted within an upland...
Article
Full-text available
Background Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process...
Article
Full-text available
There is an urgent need for rapid, standardised, accurate and accessible monitoring techniques to better detect and quantify change given the increasing threat of degradation and biodiversity loss in freshwater ecosystems. Community-based monitoring projects have been proven successful for the collection of meaningful biological data from a range o...
Preprint
Full-text available
Background: Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to proces...
Chapter
River bioassessment programs require robust methods to accurately observe the status of aquatic biodiversity, as it is well understood that physico-chemical monitoring alone is not sufficient to support current policy and management objectives. Whereas traditional microscopy-based identification of organisms can be expensive and laborious, direct s...
Article
Full-text available
Robust data to refute or support claims of global insect decline are currently lacking, particularly for the soil fauna in the tropics. DNA metabarcoding represents a powerful approach for rigorous spatial and temporal monitoring of the taxonomically challenging soil fauna. Here, we provide a detailed field protocol, which was successfully applied...
Article
Full-text available
Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding,...
Article
Full-text available
Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequenc-ing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxo-nomic gr...
Article
Full-text available
Preservation of DNA in bulk environmental samples is conventionally achieved using ethanol; however, transportation restrictions on ethanol, particularly from remote locations, are problematic, and ethanol requires a lengthy evaporation period to avoid polymerase chain reaction inhibition. We examined the efficacy of an easily accessible, non-toxic...
Article
Full-text available
Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely important for recovery of soil N and C after deforestation, yet little is known of their soil microbiomes nor how land use impacts them. Soils from both trees in a primary and secondary forest were assessed for N-cycle metrics and DNA sequence-based comp...
Article
Full-text available
The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcodi...
Article
Full-text available
Tropical forests are fundamental ecosystems, essential for providing terrestrial primary productivity, global nutrient cycling, and biodiversity. Despite their importance, tropical forests are currently threatened by deforestation and associated activities. Moreover, tropical regions are now mostly represented by secondary forest regrowth, with hal...
Article
Full-text available
DNA barcoding and metabarcoding are techniques that focus on signature genomic regions that in theory provide species level resolution, but in practice this is not always possible. We place animal-focused COI metabarcoding in context with respect to the use of marker gene sequencing in microbial and fungal ecology. We focus on three specific aspect...
Article
Full-text available
Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were col...
Preprint
Full-text available
Background Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as in ecological and environmental studies. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are used to process anima...
Preprint
Full-text available
The Biodiversity-Ecosystem Function hypothesis postulates that higher biodiversity is correlated with ecosystem function by providing a high number of filled niches through species response types and resource use patterns. Through their high spatio-temporal habitat diversity, floodplains are highly productive ecosystems, supporting communities that...
Preprint
Full-text available
The deep ocean is the largest biome on Earth and faces increasing anthropogenic pressures from climate change and commercial fisheries. Our ability to sustainably manage this expansive habitat is impeded by our poor understanding of its inhabitants and by the difficulties in surveying and monitoring these areas. Environmental DNA (eDNA) metabarcodi...
Article
Full-text available
Aims Legacy attributes from land-use history have lingering effects on soil and its below-ground components undergoing succession that has important consequences for regenerating tropical secondary forests. Yet, even landscapes of similar origins with analogous land-use histories have exhibited differing routes of forest recovery with different out...
Article
Full-text available
We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rainforest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World...
Preprint
Full-text available
Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic grou...
Article
Full-text available
The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace–Athabasca Delta (PAD) is a large inland wetland complex in north...
Article
Full-text available
Environmental DNA (eDNA) metabarcoding is an increasingly popular method for rapid biodiversity assessment. As with any ecological survey, false negatives can arise during sampling and, if unaccounted for, lead to biased results and potentially misdiagnosed environmental assessments. We developed a multi-scale, multi-species occupancy model for the...
Preprint
Full-text available
Hurricanes rapidly deposit large amounts of canopy material onto tropical forest floors, stimulating metabolic processes involved in the decomposition of these materials and production of N and C resources into the food web. However, little is known about the effects that hurricanes have on specific soil microbial taxa or functional groups involved...
Preprint
The isolation and analysis of environmental DNA (eDNA) for ecosystem assessment and monitoring has become increasingly popular. A majority of studies have taken a metabarcoding approach--that is, amplifying and sequencing one or more gene targets of interest. Shotgun sequencing of eDNA--also called metagenomics--while popular in microbial community...
Preprint
Full-text available
Maintaining the integrity of DNA in bulk environmental samples from source to laboratory is crucial for capturing the true range of taxa present within an ecosystem. Preservation consideration of DNA is particularly important if samples are being collected in remote areas and by non-specialist citizen scientists in nationwide programs. Traditionall...
Article
Full-text available
Biomonitoring programs have evolved beyond the sole use of morphological identification to determine the composition of invertebrate species assemblages in an array of ecosystems. The application of DNA metabarcoding in freshwater systems for assessing benthic invertebrate communities is now being employed to generate biological information for env...
Article
Full-text available
Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish...
Article
Full-text available
Classical biomonitoring techniques have focused primarily on measures linked to various biodiversity metrics and indicator species. Next-generation biomonitoring (NGB) describes a suite of tools and approaches that allow the examination of a broader spectrum of organizational levels—from genes to entire ecosystems. Here, we frame 10 key questions t...
Article
Full-text available
Threatened freshwater ecosystems urgently require improved tools for effective management. Food web analysis is currently under-utilized, yet can be used to generate metrics to support biomonitoring assessments by measuring the stability and robustness of ecosystems. Using a previously developed analysis pipeline, we combined taxonomic outputs from...
Article
Full-text available
An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a suitable scale to detect and manage critical global change processes. A major hurdle has been the time-consuming and challenging process of sorting and identification of organisms, but the rapid development of DNA metabarcoding as a bio...
Preprint
Full-text available
The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large-scales. The Peace-Athabasca Delta (PAD) is a large inland wetland complex in north...
Article
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has...
Conference Paper
Meiobenthic organisms are key components of estuarine environments, providing invaluable functions and services. In particular, meiofaunal organisms participate actively in nutrient cycles and energy flux, supporting higher trophic levels, as well as the stabilization of sediments. Due to their small size (between 30 µm and 1mm) and high dispersal...
Article
Full-text available
Mixed community or environmental DNA marker gene sequencing has become a commonly used technique for biodiversity analyses in freshwater systems. Many cytochrome c oxidase subunit I (COI) primer sets are now available for such work. The purpose of this study is to test whether COI primer choice affects the recovery of arthropod richness, beta diver...
Article
Full-text available
Since the introduction of white-nose syndrome (WNS) in North America, numerous species of bat have dwindled in numbers. These declines observed are often species-specific and thus provides opportunity for a natural experiment to test for shifts in diet through relaxed resource partitioning in bat communities post-introduction of WNS. Acoustic monit...
Article
Full-text available
DNA-based methodology has proven to be a vital tool for ecosystem assessment and monitoring. Increasingly, high-throughput approaches such as DNA metabarcoding are being used to address more complex questions, including ecological network analyses through machine learning. Despite the technological advances which allow for such questions to be pose...
Preprint
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been suffic...
Preprint
Full-text available
Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish...
Preprint
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been suffic...
Preprint
Full-text available
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids ecosystem assessment. However , it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been suffic...
Conference Paper
https://doi.org/10.1139/gen-2019-0083 Genome, 2019, 62(6): 372 Background: DNA metabarcoding provides a practical approach to investigate communities hard to track through traditional morphological approaches as, for instance, the estuarine meiofauna. In this study, we examined the patterns of small-scale spatial variation of meiofaunal communiti...
Article
This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the Northern Zone of Costa Rica, suggesting the possible use of this practice as a restoration strategy for local land owners. Soil samples from a primary forest (PF), secondary forest...
Article
Full-text available
The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of or...
Preprint
Full-text available
An ongoing challenge for ecological studies has been the collection of data with high precision and accuracy at a sufficient scale to detect effects relevant to management of critical global change processes. A major hurdle for many workflows has been the time-consuming and challenging process of sorting and identification of organisms, but the rap...
Preprint
Full-text available
Biomonitoring programs have evolved beyond the sole use of morphological identification to determine the composition of invertebrate species assemblages in an array of ecosystems. The application of DNA metabarcoding in freshwater systems for assessing benthic invertebrate communities is now being employed to generate biological information for env...
Preprint
Full-text available
DNA-based biodiversity analysis has gained major attention due to the use of high throughput sequencing technology in approaches such as mixed community or environmental DNA metabarcoding. Many cytochrome c oxidase subunit I (COI) primer sets are now available for such work. The purpose of this study is to look at how COI primer choice affects the...
Article
Aquatic macroinvertebrate communities are often used to assess the ecological integrity of streams. However, conventional methods involving morphometric identification of macroinvertebrates are usually costly and time-consuming. Here we compare stream macroinvertebrate community metrics based on conventional morphometrics vs. non-destructive DNA me...
Preprint
Full-text available
The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of or...