Biology subjects

Holland, B.

Publications and source records attributed to Holland, B..

11 recordsLinked to original sources

bioRxiv2026

Non-convergent aridity adaptation despite pervasive linked selection in Eucalyptus

Whether independent lineages evolve similar genetic solutions when faced with the same environmental pressure is central to understanding how repeatable and predictable adaptation is. Answering this question is increasingly urgent as climate change intensifies drought and aridity worldwide, a shared pressure to which many species must independently adapt. Here we characterised genomic adaptation in Eucalyptus across three independent species pairs, each comprising two closely related lineages that have diverged from wetter into drier environments. Across all pairs we found concordant genome-wide landscapes of diversity and divergence, and strong evidence for pervasive linked selection. Because linked selection acts most strongly in the same conserved features of the genome, this shared architecture could concentrate differentiation in the same regions across lineages, creating an appearance of convergent adaptation. Despite this, the genomic regions associated with the transition to drier environments were largely non-convergent, with almost no sharing of outlier loci among pairs, demonstrating that each lineage adapted through a largely independent genetic route. Some convergence was instead evident at the level of biological function, indicating that lineages reached similar functional outcomes using different genes. We further identified large genomic islands of differentiation, which were dominated by the signature of linked selection rather than elevated divergence, though several harboured candidate genes within the drought and abscisic acid regulatory networks. Together, our results indicate that adaptation to aridity in Eucalyptus is complex and polygenic, and largely unpredictable at the level of individual loci.

evolutionary biology↗

bioRxiv2025

Assessing the Performance of AF2 and AF3-Implementations on Antibody-Antigen Complexes

Accurate determination of antibody-antigen (Ab-Ag) complex structures is critical for therapeutic development. While AI-based methods, beginning with AlphaFold2 (AF2), have revolutionized multimer predictions, the optimal strategies for Ab-Ag modeling and the reliability of their confidence scores remain active areas of research. This study evaluates the performance of AF2, Boltz-1, Boltz-1x, Boltz-2, Chai-1, Protenix and ESMFold, on a curated dataset of 200 antibody-antigen (Ab-Ag) complexes. Our findings reveal that AF2 remains a strong predictor against newer AlphaFold3 (AF3)-inspired methods in Ab-Ag complex prediction. Chai-1 consistently ranks as the second-best performer across multiple success metrics. We observed diverse effects of recycling iterations, with AF2, Chai-1 and Protenix benefiting from increased cycles, unlike Boltz variants. We analyzed various model confidence scores, noting high precision from pDockQ2 and high recall from pTM. By integrating these two scores, we developed AntiConf, a novel metric that achieves superior performance for all methods in terms of precision and recall. These strengths make AntiConf a valuable post score for both computational predictions and downstream experimental workflows, reflecting its potential to improve Ab-Ag complex predictions by AF2 and AF3 architectures. Altogether, this study addresses current limitations in AI-based Ab-Ag complex prediction, showcasing the potential of AntiConf for future predictions and assessments of these complexes, and providing a guideline for improving the accuracy of Ab-Ag complex prediction.

bioinformatics↗

bioRxiv2025

Conserved strategies underpin the replicated evoluton of aridity tolerance in trees

Predicting forest responses to climate change requires a detailed understanding of trait-environment coordination. Adaptation to environment comprises both conserved and labile components of trait variation. However, few studies explore the decomposition of trait-environment relationships in a rigorous phylogenetic framework. Combining a revised phylogeny with trait, climate and soil data to achieve unprecedented species coverage ([~]85%), we identified patterns of replicated evolution that allowed the evergreen tree genus, Eucalyptus, to rapidly radiate across Australia in response to aridification. Eucalypts from arid regions are short, produce dense wood, and have small, physically robust leaves with high nitrogen content, promoting hydraulic safety and economies in photosynthetic water use. Phylogenetic modelling reveals strong niche conservatism, with adaptation to aridity occurring primarily via clade-level divergences, followed by phylogenetically independent adjustments to local conditions. Ancestral state reconstructions accounting for trends in the paleoclimate record indicate that transitions in aridity tolerance are associated with distinct signals of environmental filtering and directional selection on functional trait variation. However, astonishing repeatability of trait changes in different clades reveals a narrow optimal solution to water availability, opening a path to predict future species distributions from phylogenetically structured trait data and signalling major implications for functional and species diversity under progressive climate change.

evolutionary biology↗

bioRxiv2025

The genetic architecture of polygenic adaptation under a network-derived trait

The genetic architecture of adaptation varies across species, populations, and traits. While existing models capture aspects like the number of loci, effect sizes, and allele frequencies, they often overlook the molecular processes underlying trait expression. We investigated how gene regulatory networks influence quantitative variation during adaptation by examining the negative autoregulation (NAR) motif in two configurations: K+, with four evolving network components, and K-, with two components. Using forward-time simulations, we tracked populations adapting to a shifted phenotypic optimum under varying genetic architectures. We found that K+ populations maintained rapid adaptation despite low recombination, preserving high genetic variance through positive epistasis and stronger linkage disequilibrium. Under low recombination, K+ populations reached the optimum through diverse molecular configurations, while responses were more uniform under high recombination. In contrast, K- and additive models showed impaired adaptation under low recombination. Our findings demonstrate that network structure fundamentally influences the distribution of variation within the molecular architecture of traits, with certain networks providing unexpected robustness against low recombination rates. This suggests that molecular complexity may confer evolutionary advantages in natural populations.

evolutionary biology↗

bioRxiv2024

Reproductive and ecological adaptations to climate underpin the evolution of sociality in lizards

Identifying the environmental factors associated with group living is important for understanding how social systems originate, persist and diversify. In endothermic birds and mammals, living in social groups is associated with habitat constraints and harsh climatic conditions. We use phylogenetic comparative analyses to test whether climate and habitat have played similar roles in the evolution of social grouping in a globally distributed clade of ectothermic vertebrates, lizards (Nspecies = 1696). Social grouping was strongly associated with cool, dry climates across the lizard phylogeny. However, this climatic signature arose indirectly, by association with live birth (common in cool climates) and a reliance on rock crevices (common in dry climates), traits which increase parent-offspring associations and reduce offspring dispersal. In contrast, direct effects of cool temperature on the evolution of social grouping were marginal and restricted to live bearing species. Our results demonstrate that relationships between climate and sociality may result from climatic adaptations that go on to promote the emergence of grouping behaviour.

evolutionary biology↗

bioRxiv2023

The distribution of fitness effects during adaptive walks using a simple genetic network

The tempo and mode of adaptation depends on the availability of beneficial alleles. Genetic interactions arising from gene networks can restrict this availability. However, the extent to which networks affect adaptation remains largely unknown. Current models of evolution consider additive genotype-phenotype relationships while often ignoring the contribution of gene interactions to phenotypic variance. In this study, we model a quantitative trait as the product of a simple gene regulatory network, the negative autoregulation motif. Using forward-time genetic simulations, we measure adaptive walks towards a phenotypic optimum in both additive and network models. A key expectation from adaptive walk theory is that the distribution of fitness effects of new beneficial mutations is exponential. We found that both models instead harbored distributions with fewer large-effect beneficial alleles than expected. The network model also had a complex and bimodal distribution of fitness effects among all mutations, with a considerable density at deleterious selection coefficients. This behavior is reminiscent of the cost of complexity, where correlations among traits constrain adaptation. Our results suggest that the interactions emerging from genetic networks can generate complex and multimodal distributions of fitness effects.

evolutionary biology↗

bioRxiv2023

Phylogenetically conservative trait correlation: quantification and interpretation

O_LICorrelation across species between two quantitative traits, or between a trait and a habitat property, can suggest that a trait value is effective in sustaining populations in some contexts but not others. It is widely held that such correlations should be controlled for phylogeny, via phylogenetically independent contrasts PICs or phylogenetic generalised least squares PGLS. C_LIO_LITwo weaknesses of this idea are discussed. First, the phylogenetically conservative share of the correlation ought not to be excluded from consideration as potentially ecologically functional. Second, PGLS does not yield a complete or accurate breakdown of A-B covariation, because it corresponds to a generating model where B predicts variation in A but not the reverse. C_LIO_LIMulti-response mixed models using phylogenetic covariance matrices can quantify conservative trait correlation CTC, a share of covariation between traits A and B that is phylogenetically conservative. Because the evidence is from correlative data, it is not possible to split CTC into causation by phylogenetic history versus causation by continuing reciprocal selection between A and B. Moreover, it is quite likely biologically that the two influences have acted in concert, through phylogenetic niche conservatism. C_LIO_LISynthesis: The CTC concept treats phylogenetic conservatism as a conjoint interpretation alongside ongoing influence of other traits. CTC can be quantified via multi-response phylogenetic mixed models. C_LI

ecology↗

bioRxiv2020

Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time

Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adelie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over two time scales: one based on the Adelie penguin samples dating to approximately 46.5 kya, the other dating to the diversification of chordates more than 500 Mya. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long time scales, particularly in exons and regulatory sequence. These often retain length variability, suggesting that they may play a role in the maintenance of evolutionary plasticity.

evolutionary biology↗

bioRxiv2019

Mitogenomic Diversity in Sacred Ibis Mummies sheds light on early Egyptian practices

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from [~]600BC. Although it is known that a very large number of these votive mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred [~]2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild Sacred Ibis for the ritual yearly demand.

evolutionary biology↗

bioRxiv2018

Fishing for Mitochondrial DNA in The Egyptian Sacred Ibis Mummies

The long-term preservation of DNA requires a number of optimal conditions, including consistent exposure to cool, dry, and dark environments. As a result, the successful recovery of ancient DNA from material from warmer climates such as those in Egypt has often been met with scepticism. Egypt has an abundance of ancient mummified animals and humans, whose genetic analyses would offer important insights into ancient cultural practices. To date, the retrieval of complete genomes from ancient Egyptian remains of humans or other animals has been largely unsuccessful. To test for the presence of even short DNA sequences in Egyptian material, we performed second-generation shotgun sequencing of DNA libraries constructed from ancient Sacred Ibis mummies. Since most of the resulting Illumina libraries were shown to contain extremely low levels (less than 0.06%) of endogenous mitochondrial DNA, we aimed to enrich these samples using targeted in-solution hybridisation methods. Using biotinylated RNA baits designed to Sacred Ibis complete mitochondrial sequences, we trialled a number of conditions and parameters and achieved up to 4705-fold enrichment. We also found that a combination of hybridisation temperature and the use of the polymerase KAPA HiFi significantly increased both the efficiency of targeted hybridisation and post-hybridisation amplification respectively. Furthermore, improved enrichment was accompanied with only minor increases in clonality. Our method enabled us to reconstruct the first complete mitochondrial genomes from ancient Egyptian sub-fossil material.

genomics↗

bioRxiv2018

Dimension Reduction and Visualization for Single-copy Alignments via Generalized PCA

Single-copy sequence alignments have been a valuable source of information for genetic studies; their lack of recombination makes phylogenetic analyses tractable [1]. Specifically, mitochondrial DNA will continue to play an important role in genetic studies due to its high mutation rate and high copy per cell count of the molecule [2]. In this paper we develop a new method for the analysis of single-copy sequence data that simultaneously considers the relationships between sequenced individuals and positions of interest in the genome. We then show that tests for relationships between genetic information and qualitative and quantitative characteristics can be calculated. We motivate the use of our method with examples from empirical data.

bioinformatics↗