Biology subjects

Thomas, C. D.

Publications and source records attributed to Thomas, C. D..

9 recordsLinked to original sources

bioRxiv2026

Short and long-term consequences of Habitat Transformation for Biodiversity

Humans have dramatically altered the Earths surface and the distributions of species, but coherent patterns distinguishing cause from effect are hard to discern. Community composition and ecosystem function can change as rapidly as local land-use, and we lack robust principles to understand the outcomes of these changes. This hampers assessments of ecosystem collapse or robustness. Here we create theoretical ecosystems using a community assembly framework in which we manipulate environmental filtering via both the local land-use and species traits. This isolates the impacts of environmental filtering into land-use, land-use change, and species trait diversity, allowing us to extract clear patterns and relationships. First, we identify the paradox of maladaptation. We find that better land-use adaptation reduces species richness in the habitat but increases species abundance and ecosystem complexity. Increasing diversity amongst species traits reduces species richness via a similar mechanism. Additionally, whilst over long time scales there is very little effect of land-use change, on very short time scales there is a predominantly negative effect on richness. Together, this highlights the need for careful facilitation and management of land-use change in the face of an ever-changing world. Author SummaryHumans have dramatically altered the Earths surface, primarily through land-use change and changing where species are and where they can go. This has resulted in extinctions, immigration, and, most of all, variation in where species end up. Here, we use simulations to compare how habitat, habitat change, and species adaptations create variation in outcomes due to land-use change. First, we show that while adaptation is good for individual species, it also reduces the overall diversity (number of species) of the ecosystem; similarly, well-adapted species out-perform and exclude less well-adapted species, also lowering the resulting diversity of the ecosystem. Secondly, we find that habitat change has different short- and long-term consequences. Habitat change can create dramatic declines on short time scales due to the different pressures experienced by species based on which species they eat (trophic level). But, on long time scales it has very little effect on diversity, as communities acquire new species adapted to the new conditions. We conclude that short-term declines in diversity due to recent or ongoing habitat change could be eased by helping well-adapted species to immigrate to form ecological communities in the new environment.

ecology↗

bioRxiv2026

Synthetic reconstitution of planar polarity initiation reveals collective migration as a symmetry-breaking cue

Planar cell polarity (PCP) organizes cellular behaviors along tissue axes, yet how symmetry is broken to initiate polarity across initially symmetric tissues remains unknown. We reconstituted tissue-scale polarity emergence ex vivo using an engineered epithelial system. A collective migration cue induces front-back enrichment of CELSR junctions, establishing aligned multicellular polarity that tracks migration direction and speed. A migration-onset wave consistently precedes the polarity-initiation wave, indicating that individual cells directly interpret the global cue rather than acquire polarity through intercellular relay. Strikingly, CELSR polarity arises without reciprocal VANGL-FZD interactions, identifying CELSR as the driver for planar polarization. These findings reveal how a global migratory cue can break symmetry and coordinate PCP across molecular, cellular, and tissue scales, providing a framework for engineering polarized tissues.

developmental biology↗

bioRxiv2025

Development of the invertebrate faunas of anthropogenic habitats

AimWe aimed to determine the relationships between species association with humans, their levels of habitat specialisation, and the extent to which their geographic ranges have increased or decreased. LocationGreat Britain. Time periodPresent (1981-2020) Major taxa studiedTerrestrial invertebrates (n=1,722 species). MethodsWe determined the habitat associations for each of 1,722 species from 14 taxonomic groups in each of 18 land cover types in Great Britain. We used these values to calculate a human association index (based on whether species occupy human-modified land cover types, such as urban, suburban and coniferous plantation habitats, or occur in relatively unmodified land covers, such as several coastal habitats and marshlands) and habitat specialisation index (whether they are restricted to a few land cover types, or widely distributed across different land cover types) for each species. We then investigated the relationship between human association and habitat specialisation, as well as the relationship between human association and two metrics of range change between 1981-2000 and 2001-2020. ResultsContrary to previous hypotheses, we find no evidence that species associated with human-modified environments are more likely to be habitat generalists. Furthermore, human-associated species were more likely to increase. On average, the geographic distributions of the most human-associated third of species increased by 58% over the study period, whereas the least human associated third of species declined by 7.1%. Main conclusionsHumans have had increasingly large impacts on the worlds ecosystems, generating an intensity gradient of human-modification, including novel (anthropogenic) environments. Our findings show that new environments have provided opportunities for species to colonise, generating faunas which include species that have become human-associated specialists. The ongoing expansions of species in ecosystems with relatively high levels of human modification are key components of the future of biodiversity in the Anthropocene.

ecology↗

bioRxiv2024

Assisted colonisation prospects for the black-veined white butterfly in England

The black-veined white butterfly, Aporia crataegi, reached the north-western edge of its European geographic distribution in the British Isles in the 19th century, but became extinct in the early 20th century, following several cold decades. Substantial areas of potential breeding habitat in southern Britain are currently available to this species, which requires scattered hawthorn (Crataegus monogyna) and suckering blackthorn scrub (Prunus spinosa), including infrequently cut hedgerows. These habitats are needed at a relatively large scale as the butterfly occurs as networks of colonies (metapopulations), ranging over large tracts of connected landscape. A number of events have increased habitat availability over the past 70 years (myxomatosis reduced rabbit populations, which permitted host plant scrub regeneration; hedgerow management policies reduced cutting frequencies; rewilding and landscape connectivity initiatives are resulting in additional scrub). However, while A. crataegi males occasionally disperse several kilometres, it is unlikely that A. crataegi females will cross the English Channel in sufficient numbers to establish populations in southern England, without assistance. Here, we (i) provide a review of the literature on species interactions, the habitat requirements, distribution and dispersal of A. crataegi and (ii) provide evidence that southern, eastern and central England are likely to be climatically suitable for reintroductions of A. crataegi. Substantial areas of England are already expected to be amongst the climatically most suitable parts of Europe for this insect. We identify a landscape of at least 100 km2 containing multiple patches of suitable habitats, and highlight co-benefits for other species that inhabit scrubland and successional mosaics. We use a climate-matching approach to assess climatically-similar locations to obtain source material most likely to establish in Britain. Areas of northern France and mid elevations in the Iberian Peninsula, including in the Pyrenees, provide potential suitable source locations due to close climatic matching and a large number of species records. We recommend reestablishment from more than one source, providing genetic diversity in the reintroduced population, enabling subsequent local adaptation to British conditions. We highlight the opportunity for monitored releases to be undertaken within the landscape highlighted here, so as to evaluate population growth, host plant use, and rates of colonisation away from release sites that differ in their management, habitat, host plant characteristics, and proximity to other sites. This approach would aim to develop knowledge as a living lab to inform future best practice releases. In conclusion, the black-veined white, A. crataegi, has potential to become a model species for assisted colonisation projects where natural and human-created barriers have prevented range expansion into regions where the 21st century climate is suitable for a species.

ecology↗

bioRxiv2023

Globally abundant birds disproportionately inhabit anthropogenic environments

Research into biodiversity change predominantly focuses on rarity and declines, but many ecological processes are governed by abundant species. Analysing 3,146 terrestrial bird species across 5,454 field-sampled sites, we find that three times more species in the top quartile for global abundance are more likely to occur in ecosystems characterised by major human land-cover modification (croplands, plantation forest, urban areas and pasture), compared with species in the bottom quartile. The likelihood of inhabiting human-modified environments consistently increases with global abundance across species with different dietary requirements, whereas low abundance species tend to have increased probabilities of occurrence (within their ranges) in relatively unmodified environments. Our findings suggest that human modification of the Earths land surface has favoured anthrophilic species able to thrive in widespread anthromes. One-Sentence SummaryThe worlds most abundant birds disproportionately inhabit croplands, plantation forests, urban areas and pastures.

ecology↗

bioRxiv2023

Increased dispersal explains increasing local diversity with global biodiversity declines

The narrative of biodiversity decline in response to human impacts is overly simplistic because different biodiversity metrics show different trajectories at different spatial scales. It is also debated whether human-caused biodiversity changes lead to subsequent, accelerating change (cascades) in ecological communities, or alternatively build increasingly robust community networks with decreasing extinction rates and reduced invasibility. Mechanistic approaches are needed that simultaneously reconcile different metrics of biodiversity change, and explore the robustness of communities to further change. We develop a trophically-structured, mainland-archipelago metacommunity model of community assembly. Varying the parameters across model simulations shows that local alpha diversity (the number of species per island) and regional gamma diversity (the total number of species in the archipelago) depend on both the rate of extirpation per island and on the rate of dispersal between islands within the archipelago. In particular, local diversity increases with increased dispersal and heterogeneity between islands, but regional diversity declines because the islands become biotically similar and local one-island and few-island species are excluded (homogenisation, or reduced beta diversity). This mirrors changes observed empirically: real islands have gained species (increased local and island-scale community diversity) with increased human-assisted transfers of species, but global diversity has declined with the loss of endemic species. However, biological invasions may be self-limiting. High-dispersal, high local-diversity model communities become resistant to subsequent invasions, generating robust species-community networks unless dispersal is extremely high. A mixed-up world is likely to lose many species, but the resulting ecological communities may nonetheless be relatively robust. Significance StatementBiodiversity is commonly regarded as threatened due to human impacts, but biodiversity metrics at different scales produce contradictory results. A framework is needed that can reproduce and connect these results across scales and address whether biodiversity change will inexorably accelerate following perturbation or become self-limiting as new ecological communities form. We address this challenge by constructing size-structured model communities using a mainland/island paradigm and tracking diversity at different scales. Our simulations reproduce the literatures discrepancy across scales and provide new insight. Ecological communities (islands) gain species with increasing (human-assisted) dispersal, but global diversity declines with the consequent loss of endemic species. Communities also become less invasible as dispersal increases, suggesting that human-mediated dispersal favours robust communities that resist subsequent change.

ecology↗

bioRxiv2021

A millennium of increasing ecosystem diversity until the mid-20th century

Land-use change is widely regarded as a simplifying and homogenising force in nature. In contrast, analysing global land-use reconstructions from the 10th to 20th centuries, we found progressive increases in the number, evenness, and diversity of ecosystems (including human-modified land-use types) across the globe. Ecosystem diversity increased more rapidly after [~]1700CE, then slowed or partially reversed (depending on the metric) following the mid-20th century acceleration of human impacts. Differentiation also generally increased across space, with homogenization only evident in the presence-absence analysis of ecosystem types at the global scale. Our results suggest that human land-use changes have primarily driven increases in ecosystem diversity over the last millennium.

ecology↗

bioRxiv2020

Structure-guided point mutations on FusionRed produce a brighter red fluorescent protein

The development of fluorescent proteins (FPs) has revolutionized biological imaging. FusionRed, a monomeric red FP (RFP), is known for its low cytotoxicity and appropriate localization of target fusion proteins in mammalian cells but is limited in application by low fluorescence brightness. We report a brighter variant of FusionRed, FusionRed-MQV, which exhibits an extended fluorescence lifetime (2.8 ns), enhanced quantum yield (0.53), higher extinction coefficient (~140,000 M-1cm-1), increased radiative rate constant and reduced non-radiative rate constant with respect to its precursor. The properties of FusionRed-MQV derive from three mutations - M42Q, C159V and the previously identified L175M. A structure-guided approach was used to identify and mutate candidate residues around the phenol and the acylimine ends of the chromophore. The C159V mutation was identified via lifetime-based flow cytometry screening of a library in which multiple residues adjacent to the phenol end of the chromophore were mutated. The M42Q mutation is located near the acylimine end of the chromophore and was discovered using site-directed mutagenesis guided by x-ray crystal structures. FusionRed-MQV exhibits 3.4-fold higher molecular brightness and a 5-fold increase in the cellular brightness in HeLa cells (based on FACS) compared to FusionRed. It also retains the low cytotoxicity and high-fidelity localization of FusionRed, as demonstrated through assays in mammalian cells.

biophysics↗

bioRxiv2019

Unlocking the potential of historical abundance datasets to study biomass change in flying insects

O_LITrends in insect abundance are well-established in some datasets, but far less is known about how abundance measures translate into biomass trends. Moths (Lepidoptera) provide particularly good opportunities to study trends and drivers of biomass change at large spatial and temporal scales, given the existence of long-term abundance datasets. However, data on the body masses of moths are required for these analyses, but such data do not currently exist. C_LIO_LITo address this data gap, we collected empirical data in 2018 on the forewing length and dry mass of field-sampled moths, and used these to train and test a statistical model that predicts the body mass of moth species from their forewing lengths (with refined parameters for Crambidae, Erebidae, Geometridae and Noctuidae). C_LIO_LIModelled biomass was positively correlated, with high explanatory power, with measured biomass of moth species (R2 = 0.886 {+/-} 0.0006, across 10,000 bootstrapped replicates) and of mixed-species samples of moths (R2 = 0.873 {+/-} 0.0003), showing that it is possible to predict biomass to an informative level of accuracy, and prediction error was smaller with larger sample sizes. C_LIO_LIOur model allows biomass to be estimated for historical moth abundance datasets, and so our approach will create opportunities to investigate trends and drivers of insect biomass change over long timescales and broad geographic regions. C_LI

ecology↗