Biology subjects

Burke, T.

Publications and source records attributed to Burke, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomic quantification of inbreeding depression in wild vertebrate populations

Inbreeding depression is a critical driver of extinction risk in fragmented populations, yet its magnitude in the wild has historically been estimated using sparse pedigrees or low-resolution molecular markers. The transition to genomic metrics of inbreeding offers unprecedented precision in quantifying realized homozygosity and its fitness costs. We conducted a systematic review and multi-level meta-analysis of 91 effect sizes from 20 wild vertebrate populations to provide a global benchmark for genomic inbreeding depression. Our results confirm a pervasive and significant negative relationship between fitness and genomic inbreeding. Males exhibited significantly stronger inbreeding depression than females. Fitness costs were consistent across life stages (developmental, adult and lifetime) and across types of fitness traits (survival vs. reproduction). We found no significant association between the magnitude of inbreeding depression and IUCN conservation status or historical isolation (discretely measured as "isolated" or "non-isolated"). As we enter a genomics era that will provide realised estimates of inbreeding, future studies can be added to this meta-analysis to provide a more comprehensive view of inbreeding depression and potentially identify patterns pertinent to evolutionary biology and conservation science.

evolutionary biology↗

bioRxiv2026

Inbreeding depression by polygenic load following a severe population bottleneck

It is poorly understood how populations survive extreme bottlenecks despite severe inbreeding. We investigate the genomic architecture of inbreeding in the once critically endangered Seychelles warbler (Acrocephalus sechellensis) using 37 years of individual-based monitoring and 1.8 million SNPs. Linkage disequilibrium patterns reveal a historical effective population size of [~]270 that plummeted to [~]13 coinciding with human colonisation events of the Seychelles archipelago. Contemporary genomes are over one-third inbred from recent inbreeding measured by runs of homozygosity (ROH) formed since human colonisation of the Seychelles, 50 generations ago (mean FROH < 50 generations ago = 0.38), and we identify significant inbreeding depression across cross key fitness traits. On average, a 17.9% reduction in lifespan and a 15.1% reduction in lifetime offspring production were associated with each 10% increase in individual inbreeding. Genome-wide scans reveal this depression is caused by a polygenic load. Our results suggest that a history of small population size could have facilitated the selective purging of severe genetic load, while mildly deleterious alleles escaped selection via drift. A partitioned genetic load architecture potentially enabled species recovery despite the inbreeding depression that followed near-extinction.

evolutionary biology↗

bioRxiv2026

A Seychelles warbler genomic toolkit

Understanding evolutionary processes is greatly facilitated by high-quality data on genetic variation. We report the development of a genomic toolkit for a recently bottlenecked, long-term studied species, the Seychelles warbler (Ptimerl dezil; Acrocephalus sechellensis). This toolkit comprises a reference genome assembled into 31 chromosomes, together with functional annotations and reference-panel-free imputation of whole-genome sequences from 1,935 individuals. The genomic data have been used to assign the sequenced individuals into a genetic pedigree. Individual genomic data are associated with a suite of phenotypic metadata, amassed from three decades of fieldwork in this closed, long-term monitored population. We compared sex and parentage assigned using the genomic data with the previously recorded sex and parentage metadata to identify and correct 41 sample DNA samples labelled with the wrong identity. This population resource enables a wide range of analyses, that include, but are not limited to phylogenetics, metabarcoding, recombination rates, linkage patterns, adaptation, heritability, demographic history, selection, and inbreeding estimates. We wish to encourage interest from researchers seeking to collaborate on future analyses and data collection. Overall, our methods demonstrate the potential of next generation sequencing and statistical tools to provide dense genomic datasets at large sample sizes for wild populations.

genomics↗

bioRxiv2025

Life-history traits as predictors of expected genetic contributions 15 years later in a cooperatively breeding bird

An individuals life history plays an important role in how successful individuals are in passing on their genes to future generations. However, exactly which life-history traits best approximate an individuals long-term genetic contributions remains poorly studied, especially in cooperative breeders. Here, we use a genetic pedigree and long-term data of the closed population of the Seychelles warbler (Acrocephalus sechellensis) to calculate the expected individual genetic contributions (IGC) after 15 years (or [~]3 generations) across 11 cohorts. Using a Bayesian analysis we then quantified and compared how well six important life-history traits predict IGC in each sex of this cooperatively breeding species. The life-history traits compared were: acquisition of a dominant breeding position, age at first breeding attempt, tenure as a dominant breeder, lifespan, and LRS (measured as both the number of independent [surviving 3 months+] and recruited [surviving 1 year+] offspring produced over an individuals lifetime). An individuals lifetime reproductive success (LRS) was the strongest predictor of IGC and this predictive power did not differ across the different measurements used. However, this predictive power did differ between sexes, explaining [~]61-62% of IGC variation in males versus [~]47-49% in females owing to the larger variation among males in their annual reproductive success. Across other life-history traits the predictive power of IGC was similar across both sexes but differed between life-history traits considerably (2-37%). Comparing these predictive powers suggested that lifespan and the duration of a dominant breeding position are far more important in shaping long-term genetic contributions than if and when in their life they acquired dominance. Overall, these findings give insight into the individual and population-level processes influencing future gene pools and illustrate how life-history evolution is shaped by sex-specific reproductive patterns and cooperative breeding dynamics.

evolutionary biology↗

bioRxiv2025

Examining the genetic and phenotypic correlation between survival and fecundity in a wild bird

There is intraspecific variation in reproduction and survival, which has been hypothesised to be the result of trade-offs in investment. However, we lack compelling evidence that trade- offs drive variation within species, perhaps because genetic trade-offs are masked by environmental variation. We used a long-term dataset of breeding records for a closed population of house sparrows (Passer domesticus) and its associated pedigree to separate the genetic and environmental covariance between fecundity and survival. We measured age-specific changes in reproductive outputs and estimated the heritability of both offspring production and survival in multivariate animal models. Our results show no evidence for survival costs to reproductive output. Nor did we find evidence that individuals fecundity and survival are correlated either the genetic or permanent environment level. Our findings show no evidence that variation in fecundity is driven by the offspring-production/survival trade-off. Instead, our results show that individuals are only somewhat consistent in their reproductive output, and suggest this is a possible mechanism why selection cannot act on individual quality.

evolutionary biology↗

bioRxiv2025

PBDE flame retardant exposure causes neurobehavioral and transcriptional effects in first-generation but not second-generation offspring fish

Environmental pollutants can have lasting effects that extend beyond the exposure period, potentially impacting multiple generations. Despite the widespread presence of polybrominated diphenyl ether (PBDE) flame retardants in the environment including oceans globally, there is limited understanding of their potential for multigenerational toxicity. We investigated whether exposures to 2,2,4,4,5-pentaBDE (BDE-99), a predominant PBDE congener, can induce neurobehavioral and molecular effects across two generations using the marine vertebrate model fish Fundulus heteroclitus (Atlantic killifish). To assess how exposure route influences outcomes, we conducted two complementary experiments: in the progenitor exposure experiment, adult fish were exposed to BDE-99 through diet, leading to maternal transfer into F1 eggs, while in the direct embryonic exposure experiment, embryos were exposed to BDE-99 via waterborne exposure, achieving comparable embryonic doses. Both exposure routes resulted in altered photomotor responses in F1 larvae, but additional effects differed by exposure route. In the progenitor exposure, maternally exposed F1 juvenile fish exhibited reduced anxiety-like behavior and changes in brain gene expression, while in the direct embryonic exposure, F0 fish showed no detectable effects within their generation but caused behavioral alterations in F1 descendants. The lack of effects in direct F0 individuals suggests that neurobehavioral effects observed in maternally exposed F1 fish were not solely due to BDE-99 transfer but were influenced by additional maternal factors. In the progenitor exposure, neither behavioral nor gene expression effects persisted in the F2 generation. We conclude that maternal influences play a key role in shaping multigenerational effects of BDE-99 exposure, as indicated by the strong effects observed in maternally exposed F1 fish but not in F2 descendants, as well as the differences between maternally exposed fish and those exposed to comparable doses of BDE-99 alone.

pharmacology and toxicology↗

bioRxiv2025

Early-life PBDE flame retardant exposures cause neurobehavioral alterations in fish that persist into adulthood and vary by sex and route of exposure

Developing organisms exhibit varying susceptibility to environmental pollutants depending on the timing of exposure during development. Early-life development is particularly vulnerable, and many marine species spend early life in nearshore environments, elevating their risk of pollutant exposure. Polybrominated diphenyl ether (PBDE) flame retardants are persistent and ubiquitous pollutants, particularly in nearshore marine environments. They disrupt early-life development and pose ongoing risks for ocean health. However, whether early-life exposure influences neurotoxic effects, and whether those effects are durable throughout life, remains poorly understood. Using Fundulus heteroclitus, we tested whether early-life exposure to 2,2,4,4,5-pentaBDE (BDE-99) leads to persistent behavioral and molecular alterations in adulthood and whether outcomes differ by exposure route. We conducted two complementary experiments comparing progenitor (maternal) exposure and direct waterborne exposure during embryonic development. Similar doses to developing fish were achieved in both experiments. After hatch, all fish were reared in clean water until adulthood over two years later, at which time we assessed impacts on behavior and brain gene expression. Both exposure routes led to long-term hyperactivity and reduced anxiety-like behavior, but specific effects varied by dose and sex. Progenitor exposure altered behavior and the brain transcriptome in F1 males (females not tested), whereas direct embryonic exposure affected behavior in females and not males. These findings highlight the importance of maternal influences, such as chemical metabolites, altered lipid provisioning, small molecules, and epigenetic imprinting, alongside chemical transfer, in shaping the long-term persistence of behavioral and molecular effects from early-life exposure. The distinct effects between exposure routes suggest that dosing with chemical alone is not the only determinant of toxicity. We conclude that maternal factors that are modified by exposure significantly contribute to health outcomes in developing offspring, emphasizing the need to consider exposure route when assessing risks from persistent pollutants. Given that maternal and environmental exposures co-occur in nature, future studies should assess their combined impacts to better predict real-world risks.

pharmacology and toxicology↗

bioRxiv2024

YOLO-Behaviour: A simple, flexible framework to automatically quantify animal behaviours from videos

Manually coding behaviours from videos is essential to study animal behaviour but it is labour-intensive and susceptible to inter-rater bias and reliability issues. Recent developments of computer vision tools enable the automatic quantification of behaviours, supplementing or even replacing manual annotations. However, widespread adoption of these methods is still limited, due to the lack of annotated training datasets and domain-specific knowledge required to optimize these models for animal research. Here, we present YOLO-Behaviour, a flexible framework for identifying visually distinct behaviours from video recordings. The framework is robust, easy to implement, and requires minimal manual annotations as training data. We demonstrate the flexibility of the framework with case studies for event-wise detection in house sparrow nestling provisioning, Siberian jay feeding, human eating behaviours, and frame-wise detections of various behaviours in pigeons, zebras, and giraffes. Our results show that the framework reliably detects behaviours accurately, and retrieve comparable accuracy metrics to manual annotation. However, metrics extracted for event-wise detection were less correlated with manual annotation, and potential reasons for the discrepancy between manual annotation and automatic detection are discussed. To mitigate this problem, the framework can be used as a hybrid approach of first detecting events using the pipeline and then manually confirming the detections, saving annotation time. We provide detailed documentation and guidelines on how to implement the YOLO-Behaviour framework, for researchers to readily train and deploy new models on their own study systems. We anticipate the framework can be another step towards lowering the barrier of entry for applying computer vision methods in animal behaviour.

animal behavior and cognition↗

bioRxiv2024

A path analysis disentangling determinants of natal dispersal in a cooperatively breeding bird

Delayed offspring dispersal is an important aspect of the evolution of cooperative breeding. By applying a path-analysis approach to the long-term Seychelles warbler (Acrocephalus sechellensis) dataset, we studied whether and how delayed dispersal is affected by territory quality, the presence of helpers and non-helping subordinates, maternal breeding status, age and fecundity, and offspring sex ratio. We found that offspring are more likely to disperse when their genetic mothers are co-breeders, helpers are absent and territory quality is high. In contrast to earlier findings, our analysis does not support the idea that offspring sex ratio is affected by territory quality and helper presence. Our findings suggest that a complex interplay of ecological and social factors shapes dispersal decisions. Our study underscores the importance of considering proximate factors in understanding cooperative breeding dynamics, and it shows that path analyses offer valuable insights into dissecting the intricate relationships influencing dispersal in wild populations.

ecology↗

bioRxiv2024

Separating the genetic and environmental drivers of body temperature during the development of endothermy in an altricial bird

When altricial birds hatch, they are unable to regulate their own temperature, but by the time they fledge they are thermally independent. Early-life conditions have been shown to be an important factor contributing to an individuals performance in adult life. However, it is currently unknown to what extent body temperature during endothermy development is driven by genetic variation or by the early environment. We use thermal images of cross-fostered house sparrows (Passer domesticus) throughout the nestling period to separate genetic and environmental drivers of body temperature. Our results show small heritability of body temperature. We further found that there are effects from the natal environment which carry over into the late nestling stage. A correlation between early to the mid-nestling period was explained by the natal environment and during this period body temperature and growth follow independent developmental trajectories. Furthermore, higher body temperature is under viability selection independent of body mass. We, therefore, demonstrate the natal environment influences future offspring phenotype in a novel measure; body temperature. Our study provides the first study into the environmental and genetic drivers of body temperature variation in a wild bird, furthering our understanding of how an individuals traits evolve.

evolutionary biology↗

bioRxiv2023

Environmental DNA is more effective than soil-pit hand sorting in evaluating earthworm biodiversity responses to more regenerative agricultural management

Regenerating soil biodiversity is vital to help reverse declines in the health of agricultural soils caused by intensification, and to support sustainable food production and agro-ecosystem services. Earthworms are key functional components of soil biodiversity, with different ecotypes and species delivering specific beneficial soil functions. However, conventional monitoring by hand-sorting from soil pits is highly labour intensive, can reliably identify only adults to species, and may under-record anecics (deep-burrowing ecotypes). Here, we compare soil environmental DNA (eDNA) metabarcoding using two different primer sets and next-generation sequencing, with hand-sorting from standard soil-pits. The experiment comprised four conventionally managed arable fields into which strips of grass-clover ley had been introduced three years earlier. Earthworm population responses had been recorded by hand-sorting for the first two years and our goal was to assess these in the third year and to compare them both by hand and with the use of eDNA. The eDNA method found the same 8 species as hand-sorting, but had greater power for detecting anecic earthworms and quantifying local species richness. Earthworm abundance increased by over 55% into the third year of the leys, surpassing abundances in adjacent permanent grasslands, helping to explain the observed soil health regeneration. Both overall relative abundances and site occupancy proportions of earthworm eDNA were found to have potential as proxies for abundance, and the performance of each of these measures and the implications for further work are discussed. We demonstrate that eDNA can overcome some of the significant barriers and limitations to monitoring earthworm diversity and recommend its wider use both to better understand the earthworm population benefits of different soil management practices, and to guide agricultural policy and practice decisions affecting soil health.

ecology↗

bioRxiv2023

Human Immune Cell Epigenomic Signatures in Response to Infectious Diseases and Chemical Exposures

The epigenomic landscape of human immune cells is dynamically shaped by both genetic factors and environmental exposures. However, the relative contributions of these elements are still not fully understood. In this study, we employed single-nucleus methylation sequencing and ATAC-seq to systematically explore how pathogen and chemical exposures, along with genetic variation, influence the immune cell epigenome. We identified distinct exposure-associated differentially methylated regions (eDMRs) corresponding to each exposure, revealing how environmental factors remodel the methylome, alter immune cell states, and affect transcription factor binding. Furthermore, we observed a significant correlation between changes in DNA methylation and chromatin accessibility, underscoring the coordinated response of the epigenome. We also uncovered genotype-associated DMRs (gDMRs), demonstrating that while eDMRs are enriched in regulatory regions, gDMRs are preferentially located in gene body marks, suggesting that exposures and genetic factors exert differential regulatory control. Notably, disease-associated SNPs were frequently colocalized with meQTLs, providing new cell-type-specific insights into the genetic basis of disease. Our findings underscore the intricate interplay between genetic and environmental factors in sculpting the immune cell epigenome, offering a deeper understanding of how immune cell function is regulated in health and disease.

genomics↗

bioRxiv2022

Indirect genetic effects improve female extra-pair heritability estimates.

The question of why females engage in extra-pair behaviours is long-standing in evolutionary biology. One suggestion is that these behaviors are maintained through pleiotropic effects on male extra-pair behaviors and lifetime reproductive success (genes controlling extra-pair behaviours are shared between sexes, but only beneficial to one, in this case, males). However, for this to occur extra-pair behaviour must be heritable and positively genetically correlated between sexes. Although previous studies have suggested low heritability with no evidence for between-sex genetic correlations in extra-pair behaviours, indirect genetic effects (those derived from the behaviour of others, IGEs) from the social partner, the influence of the social partners genotype on the phenotype of an individual, have not been considered, despite the potential to uncover hidden heritability. Using data from a closed house sparrow population with a genetic pedigree spanning two decades, we tested the influence of IGEs on heritability and genetic correlation estimates of extra-pair behaviour. We found that the inclusion of IGEs improved model fit for both male and female extra-pair heritability. While IGEs did not change between-sex genetic correlations, we found a reduction in uncertainty in our estimates. Future studies should consider the effect of IGEs on the mechanisms of sex specific extra-pair behaviour.

evolutionary biology↗

bioRxiv2022

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis

Deep learning-based approaches are revolutionizing imaging-driven scientific research. However, the accessibility and reproducibility of deep learning-based workflows for imaging scientists remain far from sufficient. Several tools have recently risen to the challenge of democratizing deep learning by providing user-friendly interfaces to analyze new data with pre-trained or fine-tuned models. Still, few of the existing pre-trained models are interoperable between these tools, critically restricting a models overall utility and the possibility of validating and reproducing scientific analyses. Here, we present the BioImage Model Zoo (https://bioimage.io): a community-driven, fully open resource where standardized pre-trained models can be shared, explored, tested, and downloaded for further adaptation or direct deployment in multiple end user-facing tools (e.g., ilastik, deepImageJ, QuPath, StarDist, ImJoy, ZeroCostDL4Mic, CSBDeep). To enable everyone to contribute and consume the Zoo resources, we provide a model standard to enable cross-compatibility, a rich list of example models and practical use-cases, developer tools, documentation, and the accompanying infrastructure for model upload, download and testing. Our contribution aims to lay the groundwork to make deep learning methods for microscopy imaging findable, accessible, interoperable, and reusable (FAIR) across software tools and platforms.

bioinformatics↗

bioRxiv2022

The optimal clutch size revisited: separating individual quality from the costs of reproduction

Life-history theory, central to our understanding of diversity in morphology, behaviour and senescence, describes how traits evolve through the optimisation of trade-offs in investment. Despite considerable study, there is only minimal support for trade-offs within species between the two traits most closely linked to fitness - reproductive effort and survival - questioning the theorys general validity. We used a meta-analysis to separate the effects of individual quality (positive survival/reproduction correlation) from the costs of reproduction (negative survival/reproduction correlation) using studies of reproductive effort and parental survival in birds. Experimental enlargement of brood size caused reduced parental survival. However, the effect size of brood size manipulation was small and opposite to the effect of phenotypic quality, as we found that individuals that naturally produced larger clutches also survived better. The opposite effects on parental survival in experimental and observational studies of reproductive effort provides the first meta-analytic evidence for theory suggesting that quality differences mask trade-offs. Fitness projections using the overall effect size revealed that reproduction presented negligible costs, except when reproductive effort was forced beyond the maximum level observed within species, to that seen between species. We conclude that there is little support for the most fundamental life-history trade-off, between reproductive effort and survival, operating within a population. We suggest that within species, the fitness landscape of the reproduction-survival trade-off is flat until it reaches the boundaries of the between-species fast-slow life-history continuum. Our results provide a quantitative explanation as to why the costs of reproduction are not apparent and why variation in reproductive effort persists within species.

evolutionary biology↗

bioRxiv2022

Increased opposite sex association is linked with fitness benefits, otherwise sociality is subject to stabilising selection in a wild passerine

Animal sociality, an individuals propensity to associate with others, has fitness consequences through mate choice, for example, directly, by increasing the pool of prospective partners, and indirectly through increased survival, and individuals benefit from both. Annually, fitness consequences are realised through increased mating success and subsequent fecundity. However, it remains unknown whether these consequences translate to life-time fitness. Here, we quantified social associations and their link to fitness annually and over lifetime, using a multi-generational, genetic pedigree. We used social network analysis to calculate variables representing different aspects of an individuals sociality. Sociality showed high within-individual repeatability. We found that birds with more opposite-sex associates had higher annual fitness than those with fewer, but this did not translate to lifetime fitness. Instead, for lifetime fitness, we found evidence for stabilizing selection on opposite-sex sociality, and sociality in general, suggesting that reported benefits are only short-lived in a wild population, and that selection favours an average sociality.

evolutionary biology↗

bioRxiv2021

What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value

Fitness is at the core of evolutionary theory, but it is difficult to measure accurately. One way to measure long-term fitness is by calculating the individuals reproductive value, which represents the expected number of allele copies an individual passes on to distant future generations. However, this metric of fitness is scarcely used because the estimation of individuals reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. Wild study systems therefore use short-term fitness metrics as proxies, such as the number of offspring produced. This study obtained three frequently used short-term proxies for fitness obtained at different offspring life stages (eggs, hatchlings, fledglings and recruits), and compared their ability to predict reproductive values derived from the genetic pedigree of a wild passerine bird population. We used twenty years of precise field observations and a near-complete genetic pedigree to calculate reproductive success, individual growth rate and de-lifed fitness as lifetime fitness measures, and as annual de-lifed fitness. We compared the power of these metrics to predict reproductive values and lineage survival to the end of the study period. The three short-term fitness proxies predict the reproductive values and lineage survival only when measured at the recruit stage. There were no significant differences between the different fitness proxies at the same offspring stages in predicting the reproductive values and lineage survival. Annual fitness at one year old predicted reproductive values equally well as lifetime de-lifed fitness. However, none of the short-term fitness proxies was strongly associated with the reproductive values. In summary, the commonly short-term fitness proxies capture long-term fitness with intermediate accuracy at best, if measured at recruitment stage. As lifetime fitness measured at recruit stage and annual fitness in the first year of life were the best proxies of long-term fitness, we encourage their future use.

evolutionary biology↗

bioRxiv2019

Ageing in house sparrows is insensitive to environmental effects

Variation in individual life histories, and physiology, determines the rates at which new life is generated (reproduction) and lost (death) in a population. Studying the demography of deaths thus reveals fundamental aspects of the biology of individuals within a population. We studied mortality senescence - the increase in mortality rate with age - in wild and captive house sparrows (Passer domesticus), and demonstrate highly similar mortality senescence in both, but markedly lower vulnerability to death (frailty) in captivity. This suggests that house sparrows have a species-specific rate of ageing that is insensitive to environmental effects. Unexpectedly, juvenile and adult mortality co-varied positively across years in the wild, indicating that mortality is not strongly density-dependent. Mortality also varied widely among years, suggesting a strong environmental effect, and we explain the observed patterns using temperature data and predation by birds of prey. We discuss how stochastic environmental effects can affect the evolution of ageing.

evolutionary biology↗