Douglas W Yu

• Ph.D.
• Professor at University of East Anglia

There is profound interest in knowing the degree to which China's institutions are capable of protecting its natural forests and biodiversity in the face of economic and political change. China's 2 most important forest-protection policies are its National Forest Protection Program (NFPP) and its national-level nature reserves (NNRs). The NFPP was...

Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challeng...

To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high-quality standard...

There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a...

Ecology Letters (2011) 14: 1300–1312 We review recent work at the interface of economic game theory and evolutionary biology that provides new insights into the evolution of partner choice, host sanctions, partner fidelity feedback and public goods. (1) The theory of games with asymmetrical information shows that the right incentives allow hosts to...

The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics a...

Technological advances are enabling ecologists to conduct large‐scale and structured community surveys. However, it is unclear how best to extract information from these novel community data. We metabarcoded 48 vertebrate species from their eDNA in 320 ponds across England and applied the ‘internal structure' approach, which uses joint species dist...

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into ‘many-row (observation), many-column (species)‘ datasets, with homo...

Metacommunity theory unites community and spatial ecology. Recent innovations in sequencing technology may now allow us, for the first time, to confront this theory with entire trophic community data at large scales. We metabarcoded vertebrate eDNA from 320 ponds in England. Using this "novel community data", we calculated the "internal structure"...

Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homo...

DNA-based biodiversity surveys involve collecting physical samples from survey sites and assaying the contents in the laboratory to detect species via their diagnostic DNA sequences. DNA-based surveys are increasingly being adopted for biodiversity monitoring. The most commonly employed method is metabarcoding, which combines PCR with high-throughp...

To help address the underrepresentation of arthropods and Asian biodiversity from climate-change assessments, we carried out year-long, weekly sampling campaigns with Malaise traps at different elevations and latitudes in Gaoligongshan National Park in southwestern China. From these 623 samples, we barcoded 10,524 beetles and compared scenarios of...

The accurate extraction of species‐abundance information from DNA‐based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food‐web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inferen...

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...

Species richness, abundance and biomass of insects have recently undergone marked declines in Europe. We metabarcoded 211 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging had an impact on ca. 3000 species of flying insects in silver fir Pyrenean forests. While forest dieback had no measurable...

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet reconstruction and quantitative food webs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the in...

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this PCR amplification is carried out with primers designed to target a taxonom...

Background The cuticular microbiomes of Acromyrmex leaf-cutting ants pose a conundrum in microbiome biology because they are freely colonisable, and yet the prevalence of the vertically transmitted bacteria Pseudonocardia , which contributes to the control of Escovopsis fungus garden disease, is never compromised by the secondary acquisition of oth...

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to detect plant and animal taxa in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to...

Marked decline in insect species richness, abundance and biomass have recently been quantified in Europe. We metabarcoded 224 Malaise-trap samples to investigate whether drought-induced forest dieback and subsequent salvage logging have an impact on flying insects ( ca . 3000 insect species) in silver fir Pyrenean forests. We found no evidence that...

China has recently announced a reform of forestry policy, with a major goal being to transform from plantation to heterogeneous forests, which have higher resistance to pests and disease and house more biodiversity. One driver of reform is increased intensity and frequency of pest-induced tree-dieback events. To inform management, we ask what effec...

Species interactions are known to structure ecological communities. Still, the influence of climate change on biodiversity has primarily been evaluated by correlating individual species distributions with local climatic descriptors, then extrapolating into future climate scenarios. We ask whether predictions on arctic arthropod response to climate...

De novo OTU picking from large metabarcoding read datasets is at the same time a current and a complex task, and several methods coexist to perform it. We present here the outcome of a collective project developed within Working Group on « Data Analysis and Storage » in DNAqua.net. Our aim has been to organize a thorough comparison of OTU compositi...

Despite widespread recognition of its great promise to aid decision‐making in environmental management, the applied use of metabarcoding requires improvements to reduce the multiple errors that arise during PCR amplification, sequencing and library generation. We present a co‐designed wet‐lab and bioinformatic workflow for metabarcoding bulk sample...

High‐throughput sequencing (HTS) is increasingly being used for the characterisation and monitoring of biodiversity. If applied in a structured way, across broad geographic scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated indepe...

Human activities change natural landscapes, and in doing so endanger biodiversity and associated ecosystem services. To reduce the net impacts of these activities, such as mining, disturbed areas are rehabilitated and restored. During this process, monitoring is important to ensure that desired trajectories are maintained. In the Carajás region of...

Cuticular microbiomes of Acromyrmex leaf-cutting ants are exceptional because they are freely colonizable, and yet the prevalence of Pseudonocardia , a native vertically transmitted symbiont that controls Escovopsis fungus-garden disease, is never compromised. Game theory suggests that competition-based screening can allow the selective recruitment...

1. Despite widespread recognition of its great promise to aid decision-making in environmental management, the applied use of metabarcoding requires improvements to reduce the multiple errors that arise during PCR amplification, sequencing, and library generation. We present a co-designed wet-lab and bioinformatic workflow for metabarcoding bulk sa...

Public goods are produced at all levels of the biological hierarchy, from the secretion of diffusible molecules by cells to social interactions in humans. However, the cooperation needed to produce public goods is vulnerable to exploitation by free-riders — the Tragedy of the Commons. The dominant solutions to this problem of collective action are...

Human adaptation depends on the integration of slow life history, complex production skills, and extensive sociality. Refining and testing models of the evolution of human life history and cultural learning benefit from increasingly accurate measurement of knowledge, skills, and rates of production with age. We pursue this goal by inferring hunters...

Public goods are produced at all levels of the biological hierarchy, from the secretion of diffusible molecules by cells to social interactions in humans. However, the cooperation needed to produce public goods is vulnerable to exploitation by free-riders — the Tragedy of the Commons. The dominant solution to this problem of collective action is th...

The Belt and Road Initiative (BRI) represents the largest infrastructure and development project in human history, and presents risks and opportunities for ecosystems, economies, and communities. Some risks (habitat fragmentation, roadkill) are obvious, however, many of the BRI’s largest challenges for development and conservation are not obvious a...

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...

Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental‐DNA‐based indices of abundance for long‐term popul...

Metabarcoding increases the taxonomic resolution and geographic scale at which researchers can assess the impacts of climate change on insect communities in forests

Aim China's Grain for Green Program (GFGP) is the largest reforestation programme in the world and has been operating since 1999. The GFGP has promoted the establishment of tree plantations over the restoration of diverse native forests. In a previous study, we showed that native forests support a higher species richness and abundance of birds and...

The ability to identify and quantify the constituent plant species that make up a mixed‐species sample of pollen has important applications in ecology, conservation, and agriculture. Recently, metabarcoding protocols have been developed for pollen that can identify constituent plant species, but there are strong reasons to doubt that metabarcoding...

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (1) a percent‐coverage threshold to filter out fal...

Gauging trends in forest biodiversity and relating these to forest management practice and environmental change requires effective monitoring and assessment of spatio-temporal trends in forest biodiversity. Taxa- and habitat-based surrogate measures of biodiversity, or ‘biodiversity indicators’, are commonly used to convey information about the sta...

Understanding the mechanisms that promote the assembly and maintenance of host-beneficial microbiomes is an open problem. Empirical evidence supports the idea that animal and plant hosts can combine ‘private resources’ with the ecological phenomenon known as ‘community bistability’ to favour some microbial strains over others. We briefly review evi...

Invertebrate‐derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost‐efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statist...

Although the environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends rather than simply assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-te...

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...

Human adaptation depends upon the integration of slow life history, complex production skills, and extensive sociality. Refining and testing models of the evolution of human life history and cultural learning will benefit from increasingly accurate measurement of knowledge, skills, and rates of production with age. We pursue this goal by inferring...

1. The ability to identify and quantify the constituent plant species that make up a mixed-species sample of pollen has important applications in ecology, conservation, and agriculture. Recently, metabarcoding protocols have been developed for pollen that can identify constituent plant species, but there are strong reasons to doubt that metabarcodi...

The accurate quantification of eukaryotic species abundances from bulk samples remains a key challenge for community ecology and environmental biomonitoring. We resolve this challenge by combining shotgun sequencing, mapping to reference DNA barcodes or to mitogenomes, and three correction factors: (1) a percent-coverage threshold to filter out fal...

Streptomyces bacteria are ubiquitous in soils and are well-known for producing secondary metabolites, including antimicrobials. Increasingly, they are being isolated from plant roots and several studies have shown they are specifically recruited to the rhizosphere and the endosphere of the model plant Arabidopsis thaliana . Here we test the hypothe...

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, so...

Understanding the mechanisms promoting the assembly and maintenance of host-beneficial microbiomes is an open problem. An increasing amount of evidence supports the idea that animal and plant hosts can use 'private resources' and the ecological phenomenon known as 'community bistability' to favour some microbial strains over others. We briefly revi...

Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statist...

The emergence of eusociality represents a major evolutionary transition from solitary to group reproduction. The most commonly studied eusocial species, honey bees and ants, represent the behavioral extremes of social evolution but lack close relatives that are non-social. Unlike these species, the halictid bee Lasioglossum albipes produces both so...

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...

Aim: China's Grain-for-Green Program (GFGP) is the largest reforestation program in the world and has been operating since 1999. The GFGP has promoted the establishment of tree plantations over the preservation of diverse native forest. In a previous study (Hua et al. 2016, Nat Comms 7:12717), we showed that native forest supports higher species ri...

Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater, and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and alth...

Pacific salmon are a keystone resource in Alaska, with an economic impact of well over ~US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar...

Many animals and plants recruit beneficial microbes from the environment, enhancing their defence against pathogens. However, we have only a limited understanding of the assembly mechanisms involved. A game-theoretical concept from economics, screening , potentially explains how a host can selectively recruit antibiotic-producing microbes from the...

The use of environmental DNA (eDNA) has become an applicable non‐invasive tool with which to obtain information about biodiversity. A sub‐discipline of eDNA is iDNA (invertebrate‐derived DNA), where genetic material ingested by invertebrates is used to characterise the biodiversity of the species that served as hosts. While promising, these techniq...

Acromyrmex leafcutter ants form a mutually beneficial symbiosis with the fungus Leucoagaricus gongylophorus and with Pseudonocardia bacteria. Both are vertically transmitted and actively maintained by the ants. The fungus garden is manured with freshly cut leaves and provides the sole food for the ant larvae, while Pseudonocardia cultures are reare...

China is credited with undertaking some of the world's most ambitious policies to protect and restore forests, which could serve as a role model for other countries. However, the actual environmental consequences of these policies are poorly known. Here, we combine remote-sensing analysis with household interviews to assess the nature and drivers o...

Southern Asia is a biodiversity hotspot both for terrestrial mammals and for leeches. Many small-mammal groups are under-studied in this region, while other mammals are of known conservation concern. In addition to standard methods for surveying mammals, it has recently been demonstrated that residual bloodmeals within leeches can be sequenced to f...

Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species-level resolution is difficult to obtain. Next-generation sequencing of entire assemblages (metabarcoding) provides a new appr...

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...

Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of natu...

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report...

Field experiment. (CSV)

R script of crayfish eDNA Yunnan. (R)

Standard. (CSV)

Tank experiment analyses. (CSV)

Tank experiment. (CSV)

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...

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii . Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report...

The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used t...