
Alfried VoglerImperial College London | Imperial · Department of Life Sciences
Alfried Vogler
PhD
About
486
Publications
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Introduction
Alfried Vogler currently works at the Department of Life Sciences, Imperial College London. Alfried does research in Genetics, Systematics (Taxonomy) and Evolutionary Biology.
Publications
Publications (486)
Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable versus dynamic habitat specialists, but...
Nuclear genome sequencing is resource-intensive and not practical for building densely sampled phylogenetic trees of the most species rich lineages of animals, while mitochondrial genomes can be sequenced and analysed with relative ease. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs w...
Introduction
Historic museum collections hold a wealth of biodiversity data that are essential to our understanding of the rapidly changing natural world. Novel curatorial practices are needed to extract and digitise these data, especially for the innumerable pinned insects whose collecting information is held on small labels.
Methods
We piloted s...
Introduction
DNA barcoding in insects has progressed rapidly, with the ultimate goal of a complete inventory of the world’s species. However, the barcoding effort to date has been driven by a few national campaigns and leaves much of the world unsampled. This study investigates to what degree the current barcode data cover the species diversity acr...
Aim
Knowledge of taxonomy and species distributions in highly diverse lineages of invertebrates remains too incomplete for the study of biogeographical patterns at the global scale. This limits the understanding of processes leading to the formation and maintenance of boundaries between major biogeographical realms. Site‐based metagenomic approache...
Sampling is one of the most important and fundamental processes in field biology. Among many sampling methods in entomology, window traps have long been considered one of the most effective and standardized methods. Unfortunately, the DNA quality of samples collected by window traps is typically low due to incursion by water, mainly via rainfall. W...
This study addresses the long-standing uncertainty about the internal classification of soldier beetles (Elateroidea: Canthari-dae). Four datasets were compiled and analysed: 66 genes for 14 terminals, 15 mtDNA genes for 79 terminals, one mtDNA and two rRNA genes for 217 terminals, and barcodes for 576 terminals. Based on congruent topologies, Chau...
Bombus flavescens Smith is one of the most widespread bumblebee species in the Oriental region. Due to colour polymorphisms, this species or species-complex has been a challenge for taxonomy. This study aims to assess the taxonomic status of the flavescens-complex using evidence from COI barcodes and morphology. We then reconstruct its biogeographi...
Understanding the relative contributions of ecological and evolutionary processes to the structuring of ecological communities is needed to improve our ability to predict how communities may respond to future changes in an increasingly human-modified world. Metabarcoding methods make it possible to gather population genetic data for all species wit...
Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA a...
Complex bulk samples of insects from biodiversity surveys present a challenge for taxonomic identification, which could be overcome by high‐throughput imaging combined with machine learning for rapid classification of specimens. These procedures require that taxonomic labels from an existing source data set are used for model training and predictio...
Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai-Tibetan P...
Species are fundamental biological units, but their discovery and delimitation requires appropriate data and methods. To better circumscribe species, we must improve our species concepts and bolster the underlying data resources necessary to enact them. Here, we provide six prescriptions for better collecting and synergizing our knowledge on specie...
Species are fundamental biological units, but their discovery and delimitation requires appropriate data and methods. To better circumscribe species, we must improve our species concepts and bolster the underlying data resources necessary to enact them. Here, we provide six prescriptions for better collecting and synergizing our knowledge on specie...
Given the current era of rapid biodiversity loss, there is an urgent need to understand the mechanisms driving the biodiversity dynamics in biodiversity hotspots because these results could guide make conservation actions to protect species under threat from rapid environmental changes and extensive human impacts. To achieve this goal, we have orga...
Mitochondrial genomes have been widely used for phylogenetic reconstruction and evolutionary analysis in various groups of Insecta. Gene rearrangements in the mitogenome can be informative characters for phylogenetic reconstruction and adaptive evolution. Trichoptera is one of the most important groups of aquatic insects. Prior to this study, compl...
Background
MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on...
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...
Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) ap...
Quantifying species trophic interaction strengths is crucial for understanding community dynamics and has significant implications for pest management and species conservation. DNA‐based methods to identify species interactions have revolutionized these efforts, but a significant limitation is the poor ability to quantify the strength of trophic in...
Metazoan metabarcoding is emerging as an essential strategy for inventorying biodiversity, with diverse projects currently generating massive quantities of community-level data. The potential for integrating across such data sets offers new opportunities to better understand biodiversity and how it might respond to global change. However, large-sca...
Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the Tephritidae family, due to their wide host range and high invasiveness potential. Here, we used restriction...
Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean fruit fly Ceratitis capitata is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae due to their wide host range and high invasiveness. Here, we used restriction site-asso...
Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco‐evolutionary processes driv...
New methods are required for biomonitoring of poorly known tropical ecosystems, but biological assessments of environmental status are limited by insufficient information on taxonomy, composition and ecology of local communities. The current work applies DNA‐based assessment to establish the impact of various types of anthropogenic disturbances on...
Most insect communities are composed of evolutionarily diverse lineages, but detailed phylogenetic analyses of whole communities are lacking, in particular in species-rich tropical faunas. Likewise, our knowledge of the Tree-of-Life to document evolutionary diversity of organisms remains highly incomplete and especially requires the inclusion of un...
Our current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species. This is due to inherent problems with obtaining high-quality arthropod data. Novel high throughput sequencing app...
Spatial turnover of biological communities is determined by both dispersal and environmental constraints. However, we lack quantitative predictions about how these factors interact and influence turnover across genealogical scales. In this study, we have implemented a predictive framework based on approximate Bayesian computation (ABC) to quantify...
Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a...
Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera commun...
Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here we take advantage of a relatively young and dynamic oceanic island to advance our understanding of eco-evolutionary processes driv...
Complex bulk samples of invertebrates from biodiversity surveys present a great challenge for taxonomic identification, especially if obtained from unexplored ecosystems. High-throughput imaging combined with machine learning for rapid classification could overcome this bottleneck. Developing such procedures requires that taxonomic labels from an e...
Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical dat...
Dermestidae (Bostrichoidea) exploit diverse food sources including fungal mycelia, but notably they as saprophagous, feeding on decomposing and dried flesh and keratin of animals and plants. Some of them live in spider webs, vertebrate and social insect nests, while others cause damage in human dwellings. Here, we use mitogenomics to reconstruct th...
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerab...
Disentangling the relative role of environmental filtering and dispersal limitation in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical...
Disentangling the relative role of environmental filtering and dispersal limitation in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical...
The gut microbiome plays an important role in a host’s development and adaption to its dietary niche. In this study, a group of bamboo-feeding insects are used to explore the potential role of the gut microbiota in the convergent adaptation to extreme diet specialization. Specifically, using a 16S rRNA marker and an Illumina sequencing platform, we...
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerab...
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerab...
Complex communities of fungi are regularly characterised by deep sequencing with standard barcode markers, especially the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus. Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations or for early detection of pathogen...
Plant invasions often act as ecosystem ‘simplifiers’ to simplify diversity and community structure of soil biota. However, inconsistent relationships between plant invasion and soil fauna have been found and few studies have addressed how soil fauna communities change upon plant invasions across taxa and feeding guilds. Here, we investigated the ef...
1. Metabarcoding has revolutionized the study of ecological communities, but PCR bias hampers quantitative analyses, as required in studies of trophic interactions. Direct DNA shotgun sequencing can avoid the amplification step when unassembled reads are mapped to a reference database, enabling identification and quantification of prey items.
2. Tw...
Biodiversity hotspots of the world are increasingly exposed to anthropogenic pressures and resulting ecosystem breakdowns. However, biotic surveys for ecological status assessment are rarely conducted in poorly characterised, yet highly diverse ecosystems in the tropics and subtropics. Here, we addressed the challenge of developing a monitoring sys...
Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co‐amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence...
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...
For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partition...
Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high‐throughput‐sequencing approach to generate comparative data for thou...
Cerambycidae (longhorn beetles) and related families in the superfamily Chrysomeloidea are important components of forest ecosystems and play a key role in nutrient cycling and pollination. Using full mitochondrial genomes and dense taxon sampling, the phylogeny of Chrysomeloidea with a focus on Cerambycidae and allied families was explored. We use...
Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput-sequencing approach to generate comparative...
Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence...
Polymorphic Batesian mimics exhibit multiple protective morphs that each mimic a different noxious model. Here, we study the genomic transitions leading to the evolution of different mimetic wing patterns in the polymorphic Mocker Swallowtail Papilio dardanus. We generated a draft genome (231 Mb over 30 chromosomes) and re-sequenced individuals of...
Bark and ambrosia beetles (Curculionidae: Scolytinae) are known for their symbioses with fungi and play a key role in the dispersal of phytopathogens. The scolytine community of eight pine stands along a latitudinal gradient in the UK was surveyed and beetle-associated fungal communities (mycobiota) were assessed using ITS2 metabarcoding (304 speci...
Climate change is predicted to progressively shift habitat characteristics that will alter the distribution and eco‐physiological responses of organisms. High‐elevation stream insects without extensive dispersal are expected to be highly vulnerable if they are unable to track predicted shifts. Understanding dispersal is therefore crucial to impleme...
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites...
Rodents are the major remaining mammals in many terrestrial ecosystems after the historical loss of megafauna and large-bodied taxa. Niviventer confucianus is a dominant habitat generalist in natural forests in most of China. It is also recorded as an important vector of diverse zoonotic diseases. Here, three mitochondrial and one nuclear DNA fragm...
The high‐level classification of Chrysomelidae (leaf beetles) currently recognizes 12 or 13 well‐established subfamilies, but the phylogenetic relationships among them remain ambiguous. Full mitochondrial genomes were newly generated for 27 taxa and combined with existing GenBank data to provide a dataset of 108 mitochondrial genomes covering all s...
Accessing extreme environments historically unexplored by entomologists poses logistical financial and scientific challenges. Today, much of the world’s natural habitats are under threat, particularly in the Neotropics. Threats from human development, exploration and indeed climate change pose the necessity for rapid arthropod biodiversity discover...
The Asian flea beetles Altica cirsicola, Altica fragariae and Altica viridicyanea are broadly sympatric and morphologically highly similar but feed on distantly related host plants. They have been suggested as a model for ecological speciation studies. However, their phylogeny and species limits remain uncertain. In this study, we added mitochondri...
High-throughput DNA methods hold great promise for the study of the hyperdiverse arthropod fauna of the soil. We used the mitochondrial metagenomic approach to generate 39 mitochondrial genomes from adult and larval specimens of Coleoptera collected from soil samples. The mitogenomes correspond to species from the families Carabidae (6), Chrysomeli...
Biodiversity genomics is a new and fast-growing discipline that uses large-scale DNA data to study species diversity and the processes that generate and maintain this diversity. Genomic technologies have enormous potential for establishing efficient biodiversity monitoring of island communities, in an effort to mitigate the impacts of global change...
Improved taxonomic methods are needed to quantify declining populations of insect pollinators. This study devises a high‐throughput DNA barcoding protocol for a regional fauna (United Kingdom) of bees (Apiformes), consisting of reference library construction, a proof‐of‐concept monitoring scheme, and the deep barcoding of individuals to assess pote...
Improved taxonomic methods are needed to quantify declining populations of insect pollinators. This study devises a high-throughput DNA barcoding protocol for a regional fauna (United Kingdom) of bees (Apiformes), consisting of reference library construction, a proof-of-concept monitoring scheme, and the deep barcoding of individuals to assess pote...
• Metabarcoding of arthropod communities can be used for assessing species diversity in tropical forests but the methodology requires validation for accurate and repeatable species occurrences in complex mixtures. This study investigates how the composition of ecological samples affects the accuracy of species recovery.
• Starting with field‐colle...
One day symposium on Biological Refugia held at Natural History Museum London.
Plastoceridae Crowson, 1972, Drilidae Blanchard, 1845 and Omalisidae Lacordaire, 1857 (Elateroidea) are families of the Coleoptera with obscure phylogenetic relationships and modified morphology showing neotenic traits such as soft bodies, reduced wing cases and larviform females. We shotgun sequenced genomes of Plastocerus, Drilus and Omalisus and...
The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook...
Plastoceridae Crowson, 1972, Drilidae Blanchard, 1845 and Omalisidae Lacordaire, 1857 (Elateroidea) are families of the Coleoptera with obscure phylogenetic relationships and modified morphology showing neotenic traits such as soft bodies, reduced wing cases and larviform females. We shotgun sequenced genomes of Plastocerus, Drilus and Omalisus and...
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...