Charles C.Y. Xu

McGill University | McGill · Department of Biology

All species of big cats, including tigers, cheetahs, leopards, lions, snow leopards, and jaguars, are protected under the Convention on the International Trade in Endangered Species (CITES). This is due in large part to population declines resulting from anthropogenic factors, especially poaching and the unregulated and illegal trade in pelts, bone...

Species composition in high-alpine ecosystems is a useful indicator for monitoring climatic and environmental changes at the upper limits of habitable environments. We used environmental DNA (eDNA) analysis to document the breadth of high-alpine biodiversity present on Earth’s highest mountain, Mt. Everest (8,849 m a.s.l.) in Nepal’s Khumbu region....

Understanding the factors that influence avian reproductive output is critical for bird conservation as they reveal key considerations that directly impact a species’ long term survival and should be integrated into management plans. To better this understanding for the little bittern Ixobrychus minutus, we investigated how their breeding success r...

Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km ² Ailaoshan reserve in Yunnan, China. From 30,468 leeche...

We investigated the relationships between the breeding success of the Common Moorhen Gallinula chloropus and its breeding time, nest size, and egg size in a man-made wetland (Ab-bandan) during the 2008 breeding season in Mazandaran Province, northern Iran. For each nest, the date of the first laid egg, the first hatching, and the first fledgling wa...

In 2008, we investigated the relationships between the hatching success of the Little Grebe 13 Tachybaptus ruficollis with egg laying onset, nest diameter, as a proxy of nest size, and egg weight, as a proxy 14 of egg size, in an artificial wetland in Mazandaran Province, northern Iran. The first egg was laid on April 23 15 and the last chick hatch...

Representation is crucial in building more inclusive communities in science, technology, engineering, mathematics, and medicine (STEMM) fields. STEMM Diversity is a student-driven initiative that was founded to promote equity, diversity, and inclusion (EDI) at McGill University. Here, we discuss the lessons learned while developing STEMM Diversity...

We demonstrate that simple, non-invasive environmental DNA (eDNA) methods can detect transgenes of genetically modified (GM) animals from terrestrial and aquatic sources in invertebrate and vertebrate systems. We detected transgenic fragments between 82-234 bp through targeted PCR amplification of environmental DNA extracted from food media of GM f...

Agricultural pollution with fertilizers and pesticides is a common disturbance to freshwater biodiversity. Bacterioplankton communities are at the base of aquatic food webs, but their responses to these potentially interacting stressors are rarely explored. To test the extent of resistance and resilience in bacterioplankton communities faced with a...

Insect pests destroy ~15% of all U.S. crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick, and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella, is a major invasive pest threatening the multibillion-dollar apple in...

Freshwater biodiversity is threatened by fertilizers and pesticides from agricultural sources. Microbial communities can be resistant (i.e., community composition stays largely the same) or resilient (i.e., composition changes but then returns to its initial state) to these contaminants. Even after changes in composition, communities may continue t...

Community rescue occurs when ecological or evolutionary processes restore positive growth in a highly stressful environment that was lethal to the community in its ancestral form, thus averting biomass collapse in a deteriorating environment. Laboratory evidence suggests that community rescue is most likely in high-biomass communities that have pre...

Protected areas are central to meeting biodiversity conservation goals, but measuring their effectiveness is challenging. We address this challenge by using DNA from leech-ingested bloodmeals to estimate vertebrate occupancies across the 677 km ² Ailaoshan reserve in Yunnan, China. 163 park rangers collected 30,468 leeches from 172 patrol areas. We...

The Grey Hypocolius Hypocolius ampelinus is a small passerine and migratory breeding bird in Iran known to be enigmatic and elusive among ornithologists. Here, we offer direct observations of its basic natural history including breeding phenology and diet of a population at Dez National Park in Khuzestan Province, southwestern Iran in 2011. In addi...

Biological invasions are both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating biodiversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands on which brown anole lizards (Anolis sagrei) were the native top predato...

Background The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) am...

In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cy-tochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an i...

Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underl...

In diet metabarcoding analyses, insufficient taxonomic coverage of PCR primer sets generates false negatives that may dramatically distort biodiversity estimates. In this paper, we investigated the taxonomic coverage and complementarity of three cytochrome c oxidase subunit I gene (COI) primer sets based on in silico analyses and we conducted an in...

Evolutionary rescue occurs when adaptation prevents local extinction in deteriorating environments. Laboratory experiments with microorganisms have shown that the likelihood of evolutionary rescue is greatest in large populations that have previously experienced sublethal doses of stress. To assess this result in natural communities, we conducted a...

Background The use of environmental DNA, ‘eDNA,’ for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the two most important risks of eDNA: sample contamination and taxonomic mis-assignment. These risks arise from the need for PCR amplification to detect the trace a...

Adaptive evolution can occur when genetic change affects traits subject to natural selection. Although selection is a deterministic process, adaptation can be difficult to predict in finite populations because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these connections using a combination of fiel...

The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such ‘keystone genes’ (KGs) would underlie traits involved in species interactions or causing critical bio...

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and came...

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because t...

For birds, habitat quality is largely determined by local vegetation, and reproductive performance can therefore be negatively influenced by anthropogenic activities. A tree logging event enabled us to examine the effect of removing trees of different maturities and types on the reproductive performance of Blue Tits (Cyanistes caeruleus). Against e...

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because t...

Noninvasive genetic sampling enables biomonitoring without the need to directly observe or disturb target organisms. This paper describes a novel and promising source of noninvasive spider and insect DNA from spider webs. Using black widow spiders (Latrodectus spp.) fed with house crickets (Acheta domesticus), we successfully extracted, amplified,...

Noninvasive genetic approaches enable biomonitoring without the need to directly observe or disturb target organisms. Environmental DNA (eDNA) methods have recently extended this approach by assaying genetic material within bulk environmental samples without a priori knowledge about the presence of target biological material. This paper describes a...

1. Using environmental DNA (eDNA) to detect aquatic macroorganisms is a new survey method with broad applicability. However, the origin, state, and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified, and assayed - are poorly unde...

1. Detecting aquatic macroorganisms with environmental DNA (eDNA) is a new survey method with broad applicability. However, the origin, state, and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified, and assayed - are poorly under...