Biology subjects

Tobias, J.

Publications and source records attributed to Tobias, J..

17 recordsLinked to original sources

bioRxiv2025

Shifting baselines increase the risk of misinterpreting biodiversity trends

Ecological studies quantifying the impact of land-use change on biodiversity may be sensitive to the choice of reference points - or baselines - particularly when sampling across human land-use gradients and other space-for-time comparisons. Much depends on whether the chosen baseline has already undergone shifts in species composition because of hunting, habitat loss and degradation. However, few studies have assessed the influence of shifting baselines on estimates of anthropogenic impacts. Using new survey data from five West African land-use gradients, we examine how habitat patch size and structure influences the estimated impact of land-use change on bird species richness and functional diversity. We show that smaller forests have already lost many forest-dependent birds, particularly those with large body size or specialised ecological niches, leading to reduced estimates of biodiversity loss after deforestation. The steepest biodiversity loss was found in mid-sized forests whereas relatively shallow declines were estimated for the most extensive forests - despite their richer taxonomic and functional diversity. In these larger forest blocks, accurate estimates of biodiversity loss may require longer transects extending beyond the biodiversity shadow caused by the more extensive spillover of forest species into the surrounding landscape, potentially linked to source-sink dynamics. These findings suggest that biodiversity assessments are highly sensitive to baseline selection and transect design, highlighting the risk of underestimating land-use impacts unless shifting baselines are carefully considered.

ecology↗

bioRxiv2025

EGFR activation in cholangiocytes promotes extrahepatic bile duct regeneration after injury

Background & AimsThe epidermal growth factor (EGF) receptor family of tyrosine kinases regulates development and homeostasis of digestive organs including the liver and bile ducts. It consists of four receptors, EGF receptor (EGFR) and erythroblastoma oncogene B 2-4 (ERBB2-4), and their corresponding ligands. EGF signaling promotes intrahepatic cholangiocyte proliferation, bipotent cell transdifferentiation into cholangiocytes, bile duct branching, and cholangiocarcinoma (CCA) aggressiveness. The EGF family signaling contribution to extrahepatic bile duct (EHBD) regeneration is not well defined. This work is aimed at determining the fundamental role of the EGF signaling network in the biliary proliferative response to EHBD obstruction. ApproachWe used mouse bile duct ligation to model obstructive EHBD injury, and human and mouse EHBD organoids for in vitro studies. We tested activating and inhibitory paradigms with recombinant EGF family ligands and receptor antagonists. Transcriptomic and immunohistochemistry analyses informed EGF signaling changes and cellular localization at homeostasis and after obstruction. ResultsAt homeostasis, the EHBD expressed EGFR ligands Tgfa, Btc, Hb-egf and Nrg4 in cholangiocytes, and Egf in stromal cells. Erbb2 and Erbb3 were predominant receptors expressed in cholangiocytes and Egfr in stromal cells at baseline. After EHBD obstruction, injury-induced biliary hyperproliferation was associated with increased abundance of Areg, Hb-egf, Tgf and Btc ligands and Egfr receptor in cholangiocytes with resulting epithelial EGFR activation. In biliary organoids, EGFR ligands induced organoid growth, and inhibition of EGFR, but not ERBB2, dampened cholangiocyte proliferation. Accordingly, EGFR inhibition in mice led to a decrease in the biliary proliferative response after EHBD obstruction. ConclusionThe obstruction-induced biliary proliferation is an EGFR-mediated response suggesting context-and receptor-specific EGF signaling network involvement in EHBD regeneration after injury.

physiology↗

bioRxiv2025

Projected impacts of climate change on plant-frugivore interactions across the Americas

AimFrugivorous animals provide crucial seed-dispersal functions in terrestrial ecosystems. However, the potential effects of climate change on the interactions between plants and frugivores are largely unknown. In this study, we map plant-frugivore interactions across the Americas and then project potential changes in this interaction diversity under future scenarios of climate change. LocationNorth, South and Central America. Time PeriodPresent (1980-2010) and future (2070-2100). Major Taxa StudiedFrugivorous birds and fruit-bearing plants. MethodsBased on a trait-matching framework, we estimated interaction probabilities between frugivorous birds (n = 629 species) and fruit-bearing plants (n = 3283 species) to construct ecoregion-level plant-frugivore networks. To estimate future climate impacts, we compared the climatic niches of birds with ecoregion climates and weighted interaction probabilities based on the overlap between avian climatic niches and current and future ecoregion climates. Lastly, we used simulations to examine how avian dispersal and dietary flexibility may buffer the future diversity of plant-frugivore interactions. ResultsUnder future climate scenarios, our models projected a decline in interaction diversity across most ecoregions, especially in tropical and subtropical ecoregions and biomes. In addition, simulations indicated that interaction rewiring through dispersal and dietary flexibility had the potential to mitigate future losses of interaction diversity, particularly in tropical forests. Main conclusionsOur results suggest that plant-frugivore interactions are at risk of losing diversity under continued rapid climate change, which may undermine their stability and resilience. However, projected losses of interactions depend on the capacity of frugivorous bird species to modify their ranges or dietary preferences in future. As it is unknown to what extent these factors can buffer the stability of future interaction networks, the maintenance of high plant-frugivore interaction diversity in current networks is crucial to buffer ecosystems against future climatic changes, especially in the tropics.

ecology↗

bioRxiv2025

Drivers of avian genomic change revealed by evolutionary rate decomposition

Modern bird diversity spans a striking array of forms, behaviours, and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change, but disentangling the drivers of rate variation has been difficult across large numbers of whole-genomes. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds, we show that clutch size, generation length, and beak shape are dominant predictors of genome-wide mutation rates. To identify the major axes of evolutionary rate variation, we employ covariance matrix eigendecomposition from rates estimated for branches of the avian phylogeny and across genomic loci. We find that the majority of rate variation occurs along the terminal branches of the phylogeny associated with extant families of birds. Additionally, we use principal components analyses to show that several axes of variation are linked with rapid evolution in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in evolutionary rates in the machineries for meiosis, heart performance, and RNA splicing, surveillance, and translation. They also correlate with the diversification of ecological niches reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolutionary rates through time, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage, and niche expansion near the beginning of the Palaeogene period.

evolutionary biology↗

bioRxiv2025

Land-use change undermines the stability of avian functional diversity

Land-use change causes widespread shifts in the composition and functional diversity (FD) of species assemblages, yet the impacts on ecosystem resilience remain uncertain. Stability of ecosystem functioning may increase after land-use change because the most sensitive species are removed, leaving more resilient survivors (Balmford, 1996; Clavel et al., 2010; McKinney & Lockwood, 1999). Alternatively, ecosystems may be destabilized if land-use change reduces functional redundancy, accentuating the ecological impacts of further species loss (Fonseca & Ganade, 2001; McCann, 2000). Current evidence is inconclusive, partly because trait data have not been available to quantify functional stability at sufficient scale. Here, we use morphological measurements of 3696 bird species to estimate shifts in functional redundancy following recent anthropogenic land-use change at 1281 sites worldwide, and then assess the sensitivity of these altered assemblages to future species loss. We find that the proportion of disturbance-tolerant species increases after land-use change, but that this does not increase stability. Instead, we show that functional redundancy is reduced and that further species loss will destabilize ecosystem function because relatively few additional extinctions lead to accelerated losses of FD, particularly in trophic groups delivering important ecological services such as seed dispersal and insect predation. Our analyses reveal that land-use change may have major undetected impacts on the stability of key ecological functions, hindering the capacity of natural ecosystems to absorb further declines in functionality caused by ongoing perturbations.

ecology↗

bioRxiv2023

Biophysical constraints on avian adaptation and diversification

The capacity of organisms to adapt to vacant niches or changing environments is limited by physical constraints on morphological evolution. Substantial progress has been made in identifying how these constraints shape the form and function of producers (plants), but our understanding of evolutionary limits in consumers (animals) remains highly limited, in part because the requisite data have not been available at sufficient scale. Using morphometric measurements for all birds, we demonstrate that observed variation is highly restricted--both for beak shape and overall body shape--to triangular regions of morphospace with clearly defined boundaries and vertices. By combining morphometric data with new information on physical functions of measured traits, we provide evidence that the extent of avian morphospace is constrained by biophysical trade-offs between three functional objectives (strength, reach and engulfment capacity) that characterize resource acquisition and processing by the beak, and three locomotory modalities (aerial, aquatic and terrestrial) that characterize avian lifestyles. Our results suggest that over avian evolutionary history, trajectories of morphological change trend towards the vertices, with birds evolving from a core of biophysical generalists to biophysical specialists, associated with faster macroevolutionary turnover of lineages at the periphery or morphospace. Our analyses reveal that the structure of avian morphological diversity follows relatively simple rules defined by biophysical constraints and trade-offs, shedding light on the process shaping modern animal diversity and responses to environmental change.

ecology↗

bioRxiv2023

Land use configuration shapes climate change risk to gallery forests in a savannah ecosystem

Interactions between anthropogenic pressures make it difficult to predict biodiversity change and plan conservation interventions. Climate change is expected to drive widespread ecological change in the tropics over the coming decades, but it is unclear where and when these changes are going to intensify, or reduce, the impacts of additional pressures from human land use. To address this uncertainty, we apply a novel risk assessment framework to show how land use configuration modifies risks arising from climate change to gallery forests, an important vegetation type in tropical savannahs. Our analysis shows that the spatial distribution of climate change (specifically, change in annual rainfall) interacts with the spatial distribution of land use (specifically, cropland), as well as the biophysical context of the study site (the W-Arly-Pendjari transboundary protected area in West Africa), to shape the risk that changes in rainfall pose to gallery forests in the region. Due to the pathways by which rainfall change and land use interact, risks are especially elevated in core protected areas, warranting particular attention from conservation managers. Overall, our work illustrates how unexpected patterns in risks can arise through interactions between pressures on biodiversity, highlighting the importance of considering mechanistic pathways for predicting biodiversity outcomes under multifacetted global environmental change.

ecology↗

bioRxiv2023

Constraints on avian seed dispersal reduce potential for resilience in degraded tropical forests

1. Seed dispersal - one of the many services supplied by biodiversity - is a critical process underpinning the resilience of tropical forests. Forest loss or degradation typically leads to defaunation, altering seed transfer dynamics and impairing the ability of forested habitats to regenerate or recover from perturbation. However, the extent of defaunation, and its likely impacts on the seed dispersers needed to restore highly degraded or clear-felled areas, remains poorly understood, particularly in human-modified tropical forest landscapes. 2. To quantify defaunation of seed-dispersing birds, we used field survey data from more than 400 transects in three regions of Brazil, first comparing the recorded assemblages with those predicted by geographic range maps, and then assessing frugivore habitat associations across gradients of land cover modification at local scales. 3. We found that current bird assemblages have lower functional trait diversity than predicted by species range maps in Amazonia (4-6%), with a greater reduction (28%) for the Atlantic Forest region, which has been more heavily deforested for a longer period. These reductions are probably caused by local extinctions of forest-dependent bird species following land-use change. 4. Direct measures of seed dispersal are difficult to obtain, so we instead focused on the potential for seed transfer inferred from shared species occurrence between land cover types. Of 83 predominantly frugivorous bird species recorded in relatively intact forests, we show that 10% were absent from degraded forest, and 57% absent from the surrounding matrix of agricultural land covers, including many of the large-beaked species. Of 112 frugivorous species using degraded forest, 47% were absent from matrix habitats. 5. Our findings suggest that degraded forest can supply seed dispersal services to adjacent cleared lands, and that direct transfer of seeds from intact forest to cleared areas may be limited, particularly for large-seeded trees. We conclude that resilience of tropical forest landscapes is best achieved by protecting a mosaic of forest types, including sufficient core areas of intact forest surrounded by buffer zones of degraded forest.

ecology↗

bioRxiv2023

A fast-slow trait continuum at the level of entire communities

Across the tree of life, organismal functional strategies form a continuum from slow-to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, the synchronization of these strategies at the entire community level is untested. We combine trait data for >2800 above-and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. Most guilds consistently respond to these drivers through both direct and trophically-mediated effects, resulting in a slow-fast axis at the level of the entire community. Fast trait communities were also associated with faster rates of whole ecosystem functioning. These findings demonstrate that slow and fast strategies can be manifested at the level of whole ecosystems, opening new avenues of ecosystem-level functional classification.

ecology↗

bioRxiv2022

Species-specific traits mediate avian demographic responses under past climate change

Anticipating species responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking and the traits which mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life-history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction, and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to on-going climate warming. One-Sentence SummaryInteracting traits influence sensitivity of bird population sizes to climate warming and cooling over the past million years.

evolutionary biology↗

bioRxiv2020

Diversity reduces extinction risk at global scales

Increases in biodiversity often lead to greater, and less variable, levels of ecosystem functioning. However, whether species are therefore less likely to go extinct in more diverse systems is unclear. We use comprehensive estimates of avian taxonomic, phylogenetic and functional diversity to characterize the global relationship between multiple dimensions of diversity and extinction risk in birds. We find that more diverse assemblages have lower mean IUCN threat status despite being composed of species with attributes that make them more vulnerable to extinction, such as large body size or small range size. Our analyses also reveal that this reduction of current threat status associated with greater diversity far outweighs the increased risk associated with the accumulation of extinction-prone species in more diverse assemblages. These results suggest that species conservation targets can best be achieved by maintaining high levels of overall biodiversity in natural ecosystems.

ecology↗

bioRxiv2020

The latitudinal gradient in the rate of evolution of a biotic interaction trait

Where is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the "empty niches" hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. Here we tested these contrasting predictions by analyzing rates of bird beak evolution for a global dataset of 1141 sister pairs of birds. Beak size evolves at similar rates across latitudes, while beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. We show in a meta-analysis that trait evolution and recent speciation rates are faster in the temperate zone, while rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are more potent at higher latitudes, thus calling into question multiple hypotheses invoking faster tropical evolution to explain the latitudinal diversity gradient.

evolutionary biology↗

bioRxiv2020

No latitudinal gradients in tempo or mode of morphological evolution in birds

The latitudinal diversity gradient is one of the most striking patterns in nature yet its implications for morphological evolution are poorly understood. In particular, it has been proposed that an increased intensity of species interactions in tropical biota may either promote or constrain trait evolution, but which of these outcomes predominates remains uncertain. Here, we develop tools for fitting phylogenetic models of phenotypic evolution in which the impact of species interactions--namely, competition--can vary across lineages. Deploying these models on a global avian trait dataset to explore differences in trait divergence between tropical and temperate lineages, we find that the effect of latitude on the mode and tempo of morphological evolution is weak and clade- or trait-dependent. Our results indicate that competition does not disproportionately impact morphological evolution in tropical bird families and question the validity of previously reported patterns of slower trait evolution in the tropics.

evolutionary biology↗

bioRxiv2019

Range-wide spatial mapping reveals convergent character displacement of bird song

A long-held view in evolutionary biology is that character displacement generates divergent phenotypes in closely related coexisting species to avoid the costs of hybridisation or ecological competition, whereas an alternative possibility is that signals of dominance or aggression may instead converge to facilitate coexistence among ecological competitors. Although this counter-intuitive process--termed convergent agonistic character displacement--is supported by recent theoretical and empirical studies, the extent to which it drives spatial patterns of trait evolution at continental scales remains unclear. By modeling variation in song structure of two ecologically similar species of Hypocnemis antbird across western Amazonia, we show that their territorial signals converge such that trait similarity peaks in the sympatric zone, where intense interspecific territoriality between these taxa has previously been demonstrated. We also use remote sensing data to show that signal convergence is not explained by environmental gradients and is thus unlikely to evolve by sensory drive (i.e. acoustic adaptation to the sound transmission properties of habitats). Our results suggest that agonistic character displacement driven by interspecific competition can generate spatial patterns opposite to those predicted by classic character displacement theory, and highlight the potential role of social selection in shaping geographical variation in signal phenotypes of ecological competitors.

evolutionary biology↗

bioRxiv2019

Behavior influences range limits and patterns of coexistence across an elevational gradient in tropical bird diversity

Does competition influence patterns of coexistence between closely related taxa? Here we address this basic question in ecology by analyzing patterns of range overlap between related bird species ("sister pairs") distributed along a Neotropical elevational gradient. We explicitly contrast the behavioral dimension of interspecific competition (interference competition) with similarity in resource acquisition traits (exploitative competition). We find that behavioral interactions are generally important in setting elevational range limits and preventing coexistence of closely related species. Specifically, close relatives that defend year-round territories tend to live in non-overlapping elevational distributions, while close relatives that do not defend territories tend to broadly overlap in distribution. In contrast, neither similarity in beak morphology nor evolutionary relatedness was associated with patterns of range limitation. Our main result is that interference competition can be an important driver of species ranges at the scale of entire diverse assemblages. Consequently, we suggest that behavioral dimensions of the niche should be more broadly incorporated in macroecological studies.

ecology↗

bioRxiv2018

The effect of plasma lipids and lipid lowering interventions on bone mineral density: a Mendelian randomization study

Statin treatment increases bone mineral density (BMD) and reduces fracture risk, but the underlying mechanism is unclear. We used Mendelian randomization (MR) to assess whether this relation is explained by a specific effect in response to statin use, or by a general effect of lipid-lowering. We utilized 400 single nucleotide polymorphisms (SNPs) robustly associated with plasma lipid levels and results from a heel BMD GWAS (derived from quantitative ultrasound) in 426,824 individuals from the UK Biobank. We performed univariate and multivariable MR analyses of low-density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C) and triglyceride levels on BMD. To test whether the effect of statins on BMD was mediated by lowering lipid levels, MR was repeated with and without SNPs in the HMGCR region, the gene targeted by statins. Univariate MR analyses provided evidence for a causal effect of LDL-C on BMD ({beta} = -0.060; -0.084 to -0.036; P = 4x10-6; standard deviation change in BMD per standard deviation change in LDL-C, with 95% CI), but not HDL or triglycerides. Multivariable MR analysis suggested that the effect of LDL-C on BMD was independent of HDL-C and triglycerides, and sensitivity analyses involving MR Egger and weighted median MR approaches suggested that the LDL-C results were robust to pleiotropy. MR analyses of LDL-C restricted to SNPs in the HMGCR region showed similar effects on BMD({beta} = -0.083; -0.132 to -0.034; P = 0.001) to those excluding these SNPs ({beta} = -0.063; -0.090 to -0.036; P = 8x10-6). Bidirectional MR analyses provided some evidence for a causal effect of BMD on plasma LDL-C levels. Our results suggest that effects of statins on BMD are at least partly due to their LDL-C lowering effect. Further studies are required to examine the potential role of modifying plasma lipid levels in treating osteoporosis.

epidemiology↗

bioRxiv2018

Genome-wide mapping identifies beta-1,4-N-acetyl-galactosaminyl-transferase as a novel determinant of sclerostin levels and bone mineral density

In bone, sclerostin is mainly osteocyte-derived and plays an important local role in adaptive responses to mechanical loading. Whether circulating levels of sclerostin also play a functional role is currently unclear, which we aimed to examine by two sample Mendelian Randomisation (MR). A genetic instrument for circulating sclerostin, derived from a genome wide association study (GWAS) meta-analysis of serum sclerostin in 10,584 European-descent individuals, was examined in relation to femoral neck bone mineral density (BMD; n= 32,744) in GEFOS, and estimated BMD by heel ultrasound (eBMD; n=426,824), and fracture risk (n=426,795), in UK Biobank. Our GWAS identified two novel serum sclerostin loci, B4GALNT3 (standard deviation (SD)) change in sclerostin per A allele ({beta}=0.20, P=4.6x10-49), and GALNT1 ({beta}=0.11 per G allele, P=4.4x10-11). B4GALNT3 is an N-acetyl-galactosaminyltransferase, adding a terminal LacdiNAc disaccharide to target glycocoproteins, found to be predominantly expressed in kidney, whereas GALNT1 is an enzyme causing mucin-type O-linked glycosylation. Using these two SNPs as genetic instruments, MR revealed an inverse causal relationship between serum sclerostin and femoral neck BMD ({beta}= -0.12, 95%CI= -0.20 to -0.05) and eBMD ({beta}= -0.12, 95%CI= -0.14 to -0.10), and a positive relationship with fracture risk ({beta}= 0.11, 95%CI= 0.01 to 0.21). Colocalization analysis demonstrated common genetic signals within the B4GALNT3 locus for higher sclerostin, lower eBMD, and greater B4GALNT3 expression in arterial tissue (Probability>99%). Our findings suggest that higher sclerostin levels are causally related to lower BMD and greater fracture risk. Hence, strategies for reducing circulating sclerostin, for example by targeting glycosylation enzymes as suggested by our GWAS results, may prove valuable in treating osteoporosis.

genetics↗