Mathew Seymour- PhD
- Professor (Assistant) at The University of Hong Kong
Mathew Seymour
- PhD
- Professor (Assistant) at The University of Hong Kong
About
75
Publications
34,456
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
3,940
Citations
Introduction
I'm a Molecular/eDNA ecologist specialized in analyzing large datasets to assess environmental influences on biological communities. I obtained my BA at the University of Wyoming, Msc at Holar University in Iceland, and PhD at ETH in Switzerland. I've worked in research institutions in the USA, UK, and Sweden before joining The University of Hong Kong. I started the eDNA and eEcology lab at The University of Hong Kong to advance our understanding and use of eDNA for assessing ecological systems.
Current institution
Additional affiliations
August 2007 - May 2009
Position
- field and lab technician
Description
- Worked for multiple labs doing field collections, genetic wet-lab work, and statistical analyses. Was initially suppose to start a Msc project, but had to restart the search process due to lack of support right before i was suppose to start. This period was essentially a holdover to getting into an Msc program.
August 2020 - February 2022
Position
- Researcher
Description
- Was initially suppose to be part of a large project, ended up being a bridge job while i worked on previous research and applied for other jobs due to lack of leadership at the location.
March 2016 - February 2020
Education
June 2011 - October 2014
May 2009 - May 2011
September 2004 - December 2007
Publications
Publications (75)
Organismal abundance tends to decline with increasing body size. Metabolic theory links this size structure with energy use and productivity across levels of biological organization, predicting a size abundance slope of -0.75 that is invariant across environments. We tested whether the size-abundance relationship is robust to a gradient of protist...
Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-tempora...
Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-...
The field of environmental DNA (eDNA) has rapidly advanced in recent years, providing a non‐invasive and time‐saving method for assessing biodiversity. The First International Environmental DNA (eDNA) Workshop in Hong Kong was held from 16 to 27 October 2023 and provided early career professionals with hands‐on training and collaboration opportunit...
The Arctic charr (Salvelinus alpinus) is a species of cultural, economic and conservation importance, but hitherto, investigations of critical early life stages have been few. Here, at a lake in the United Kingdom, we used swim-up traps to investigate the phenology of fry emergence and associations between fry density and habitat. The first emergen...
Inventories of biodiversity are crucial for helping support conservation and management efforts, yet the deep-sea, which is the largest biome on earth remains vastly understudied. Recent advances in molecular detection methods offer alternative techniques for studying inaccessible ecosystems, including those at depth. In this study we utilized envi...
1. Our ability to rapidly monitor species is essential for effective resource manage-ment and for establishing conservation practices. Current monitoring practices for many fish species are not effective across multiple habitats due to limited re-sources, permit restrictions, etc. In response, environmental DNA (eDNA)- based surveying and monitorin...
Inventories of biodiversity are crucial for helping support conservation efforts, yet the deep sea, which is the largest biome on earth remains vastly understudied. Recent advances in molecular detection methods offer alternative techniques for studying inaccessible ecosystems, including those at depth. In this study we utilized environmental DNA m...
Global gradients in species biodiversity are expected to reflect tighter packing of species closer to the equator. Yet, empirical validation of these patterns has so far focused on less diverse taxa, with comparable assessments of mega-diverse groups historically constrained by the taxonomic impediment. Here we assess the temporal and spatial turno...
Aim: Global gradients in species biodiversity may or may not be associated with greater species replacement closer to the equator. Yet, empirical validation of these patterns has so far focused on less diverse taxa, with comparable assessments of mega-diverse groups historically constrained by the taxonomic impediment.
Location: Global
Time period:...
Aim: The aim of this chapter is to introduce the concepts and applications of environmental DNA (eDNA) for species detection and biomonitoring of freshwater ecosystems. Environmental assessment of inland waters is currently undergoing a revolution due to the increased utilization of eDNA and major advancements in molecular techniques. Several aspec...
This publication is an output from EU COST Action DNAqua-Net (CA 15219 - Developing new genetic tools for bioassessment of aquatic ecosystems in Europe) and would not have been possible without the opportunities for international collaboration provided by the network, supported by COST (European Cooperation in Science and Technology). Therefore, ou...
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...
Safeguarding marine ecosystems is essential for maintaining ecosystem function and biodiversity, but effective monitoring of marine habitats can be logistically challenging, costly, and difficult to regularly implement. Environmental DNA-based biomonitoring is a rapidly growing tool that is non-destructive, cost-effective, and reliable. However, di...
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...
Rapidly assessing biodiversity is essential for environmental monitoring; however, traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers enhanced scope for assessing biodiversity, while also increasing sampling efficiency and reducing processing time, compared to traditi...
Species diversity is presently declining and homogenizing globally due to human land use changes and climate change effects. However, the causes of these declines are difficult to determine due to complex ecological interactions. Lepidopterans are a diverse and ecologically important group of insects that are declining in Britain and other parts of...
Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used for riverine environmental assessments due to their wide biological, functional and phylogenetic diversity and t...
Rapidly assessing biodiversity is essential for environmental monitoring, however traditional approaches are limited in the scope needed for most ecological systems. Environmental DNA (eDNA) based assessment offers increased scope, while reducing cost and time, compared to traditional methods. Here we investigated the effects of landuse and seasona...
Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used for riverine environmental assessments due to their wide biological, functional and phylogenetic diversity and t...
Overview of work I've been involved with in relation to understanding biodiversity processes over the past years
Current approaches to ecological assessment are limited by traditional morpho-taxonomic methods presently employed and the inability to meet increasing demands for rapid assessments. Advancements in high throughput sequencing now enable rapid high-resolution ecological assessment using environmental DNA (eDNA). Here we test the ability of using eDN...
Summary of findings from my efforts since 2016 working as a postdoc working in the Conwy and wider wales area.
Environmental DNA based research is a new field within molecular ecology that is seeing an amazing increase in research activity. In our Communications Biology article, we studied the degradation of eDNA in variable systems. Presented here is a short overview of eDNA science and current research activities underway in North Wales. Mathew Seymour di...
Environmental DNA analysis has emerged as a key component of biodiversity and environmental monitoring. However, the state and fate of eDNA in natural environments is still poorly understood for many ecological systems. Here we assess the state and fate of eDNA derived from the water flea, Daphnia magna, using a full factorial mesocosm experiment....
Abstract Divergence in phenotypic traits is facilitated by a combination of natural selection, phenotypic plasticity, gene flow, and genetic drift, whereby the role of drift is expected to be particularly important in small and isolated populations. Separating the components of phenotypic divergence is notoriously difficult, particularly for multiv...
The analysis of environmental DNA (eDNA) using metabarcoding has increased in use as a method for tracking biodiversity of ecosystems. Little is known about eDNA in marine human-modified environments, such as commercial ports, which are key sites to monitor for anthropogenic impacts on coastal ecosystems. To optimise an eDNA metabarcoding protocol...
Losses and gains in species diversity affect ecological stability1–7 and the sustainability of ecosystem functions and services8–13. Experiments and models have revealed positive, negative and no effects of diversity on individual components of stability, such as temporal variability, resistance and resilience2,3,6,11,12,14. How these stability com...
New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict biomass of different taxa from bulk communities remains unclear, while PCR‐free whole mitochondrial gen...
Bista etal 2018, Supplementary Material
Accurate quantification of biodiversity is fundamental to understanding ecosystem function and for environmental assessment. Molecular methods using environmental DNA (eDNA) offer a non-invasive, rapid, and cost-effective alternative to traditional biodiversity assessments, which require high levels of expertise. While eDNA analyses are increasingl...
The Rogers Research Site (RRS) is an approximate 320-acre (~129-hectare) area in southeast Wyoming that was bequeathed to the University of Wyoming in 2002 by Colonel William C. Rogers. The site in the Laramie Mountains includes important wildlife habitat and was donated to UW, in part, for forestry- and wildlife-related research. Previous habitat...
An overview of my efforts and outlooks for LOFRESH and collaborative efforts.
The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing (‘HTS’) platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed ‘environmental DNA’ or ‘eDNA’). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called ‘...
This study reviewed current evidence to inform selection of environmental predictors for Active Management Systems in classified shellfish harvesting areas.
The aims of this study were to: (1) undertake a literature review of the factors that influence faecal contamination of shellfish; (2) Establish relationships between Escherichia coli (E. coli)...
The development of video-based monitoring methods allows for rapid, dynamic and accurate monitoring of individuals or communities, compared to slower traditional methods, with far reaching ecological and evolutionary applications. Large amounts of data are generated using video-based methods, which can be effectively processed using machine learnin...
Scatterplot of trajectories in principal component space from videos of three experimental units (Tetra = Tetrahymena thermophila, none = control (no ciliates), and Loxo = Loxocephalus sp.).
A 90% confidence interval ellipse is fitted to each of the three experimental units to identify background noise in component space. The observations that fall...
Morphological boundaries for training data.
(PDF)
Output model 1.
(PDF)
Output model 4.
(PDF)
Sensitivity and specificity of alternative classifiers such as support vector machines (SVM) and Naive Bayes (NB), compared to random forest (RF) and manual classifiers.
All provide similar classification success for the ciliate species. SVM and NB are even slightly better than RF in terms of classifying noise.
(TIF)
A single frame of one video, with particles labeled by their trajectory ID.
For each trajectory, we obtained morphology and movement properties that were later used for classification into the respective species.
(JPG)
In each panel, a point is a trajectory, with its position on PC1 corresponding to overall size, and PC2 to variability in size, and turning behaviour.
Trajectories from microcosms containing ciliates are shown in black, yellow dots are trajectories from the controls (no ciliates). Panel codes: Colp = Colpidium striatum, Dexio = Dexiostoma campylum,...
Initial densities (individuals mL−1) for different richness treatments.
(PDF)
Scatterplot of trajectories in principal component space from videos of three experimental units.
Trajectories reclassified as noise by the Gaussian Mixture Model (GMM) are outlined in black. In this example, only some of the trajectories from the Tetrahymena thermophila culture were classified as noise (i.e. are outlined in black and have their co...
Output model 2.
(PDF)
Output model 3.
(PDF)
1. Technological advances have greatly simplified to take and analyze digital images and videos, and ecologists increasingly use these techniques for trait, behavioral and taxonomic analyses. The development of techniques to automate biological measurements from the environment opens up new possibilities to infer species numbers, observe presence/a...
The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of d...
Supplementary Figures, Supplementary Tables, Supplementary Methods and Supplementary References
* Species and genetic diversity patterns are predicted to co-vary due to similar mechanistic processes. Previous studies assessing species and genetic diversity correlations (SGDCs) have focused primarily on local diversity patterns or island-like systems and ignore the underlying dispersal network. Here we assessed local and regional SGDCs using f...
Data S1. Microsatellite genotypes and collection data for Helicoverpa zea adults collected from Landisville and Rock Springs, PA. Size of each microsatellite allele (in Bp) in an individual is given in two consecutive sets of 3‐digits in the 6‐digit genotype.
Table S1. Pairwise F
ST estimates (upper triangle) for putative population pairs.
Table S2. Summary of population level genetic parameters for the non‐prior DAPC analysis; the non‐prior populations cluster (Pop), number of individuals genotyped (N), mean number of alleles/locus (A), observed heterozygosity (Hobs), expected heterozygosity (Hexp), F...
Figure S1. Simulation saturation for the allelic richness.
Figure S2. DAPC results using no prior assignment of putative population showing the first two axes of the analysis (depicted in the insert plot).
Figure S3. Outcome from STRUCTURE analysis assuming K = 7. Each vertical bar represents a unique individual (x‐axis) with their corresponding...
Seasonal climatic shifts create peripheral habitats that alternate between habitable and uninhabitable for migratory species. Such dynamic peripheral habitats are potential sites where migratory species could evolve high genetic diversity resulting from convergence of immigrants from multiple regionally distant areas. Migrant populations of Helicov...
Large-scale species and genetic metacommunity patterns are influenced by variation in environmental factors and distance between communities, according to previous studies.
However, these studies often used different measures to assess patterns of metacommunity diversity, distances between communities and grain sizes at which environmental variable...
Unveiling the mechanisms that promote coexistence in biological communities is a fundamental problem in ecology. Stable coexistence of many species is commonly observed in natural communities. Most of these natural communities, however, are composed of species from multiple trophic and functional groups, while theory and experiments on coexistence...
Natural communities commonly contain many different species and functional groups, and multiple types of species interactions act simultaneously, such as competition, predation, commensalism or mutualism. However, experimental and theoretical investigations have generally been limited by focusing on one type of interaction at a time or by a lack of...
Landscape connectivity structure, specifically the dendritic network structure of rivers, is expected to influence community diversity dynamics by altering dispersal patterns, and subsequently the unfolding of species interactions. However, previous comparative and experimental work on dendritic metacommunities has studied diversity mostly from an...
Understanding the processes that shape biodiversity is a fundamental topic of ecology and
important in the context of ecosystem services or disease prevention. Metacommunity
ecology assesses the influence of local and spatial processes on the biodiversity of
communities of interacting species connected by dispersal. However, metacommunity studies
h...
Habitat network connectivity influences colonization dynamics, species invasions, and biodiversity patterns. Recent theoretical work suggests dendritic networks, such as those found in rivers, alter expectations regarding colonization and dispersal dynamics compared with other network types. As many native and non-native species are spreading along...
Table S1. Generalized additive models (GAM), explaining individual species abundances (density) relative to experimental setup (single- vs. multiple-species communities), time, and network type (linear vs. dendritic networks).
Table S2. Spread rates for single- and multiple-species experimental setups.
Figure S1. Rate of spread in the linear and de...
Aim
Spatial dynamics and habitat connectivity affect community composition and diversity in many ecosystems. For many decades, diversity patterns in riverine ecosystems were thought to be related to local environmental conditions. Recent theoretical work, however, suggests that diversity in rivers is strongly affected by dispersal along the dendrit...
Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environment...
Pleistocene climatic oscillations have resulted in high rates of speciation. Lesser known are speciation events related to recent glacial retreats. During the early Holocene many Alaskan coastal glaciers receded, exposing much of the Kodiak Island Archipelago (KOD), the Kenai Peninsula, and Prince William Sound (PWS). Using fecal DNA analyses on sa...
Background/Question/Methods
Understanding how habitat structure affects population dynamics and diversity is of high current interest in ecology. Until recently, studies on biodiversity and dispersal have minimally considered the specific structure of landscapes, or were done using landscapes with simplified spatial structure. However, the spatia...
