Biology subjects

Bruford, M. W.

Publications and source records attributed to Bruford, M. W..

4 recordsLinked to original sources

bioRxiv2026

Forging together: Parallel adaptation to minewater pollution in brown trout (Salmo trutta L.).

Mining pollution is an important stressor of freshwater communities worldwide. Persistence in these environments requires adaptation, yet identifying the mechanisms responsible in wild systems remains challenging due to differing water chemistries and genetic backgrounds. Parallel evolution presents a powerful framework for identifying adaptive mechanisms through repeated directional change. Here, we seek to understand the mechanisms that enable brown trout (Salmo trutta) to survive in metal-polluted rivers. Using low-coverage Whole Genome Resequencing (lc-WGS) we analyse paired metal-polluted and non-polluted brown trout populations across the British Isles. Metal-impacted populations show reduced nucleotide diversity and increased genomic divergence from paired control populations. We observe strong signatures of parallel adaptation in populations with shared geography, emphasising the importance of standing genetic variation in rapid adaptation to pollution. We identify a candidate region of 0.5 Mb on chr25 that shows strong parallel adaptation across multiple pairwise comparisons, including a shared signal among populations experiencing highly divergent water chemistries. The chr25 region contains the genes oestrogen receptor (esr2b) and a potassium-gated ion channel (kcnh5b), both of which are linked to developmental and osmoregulatory functions known to be disrupted by metals. Using population branch statistics (PBS) and scans for selective sweeps, we also identify population-specific candidate loci, yet putatively selected regions repeatedly converge on shared gene families and functional pathways. Our findings reveal both parallel and unique evolutionary responses to anthropogenic pollution in wild fish, highlighting convergent adaptive pathways to diverse pollutants in teleosts.

evolutionary biology↗

bioRxiv2024

Genomic signatures of island colonization in highly diverse primates

Understanding how small populations cope with loss of genetic diversity and deleterious variation is crucial to address the current biodiversity crisis. Insular populations are particularly interesting as they have often persisted at low population sizes and higher inbreeding than their mainland counterparts. While the genome-wide consequences of inbreeding in threatened insular species have received some attention, comparative genomics between insular and mainland populations of wide-spread and genetically diverse species have rarely been performed. Yet, they are particularly well suited to inform about the consequences of drastic population declines from initially large populations - a phenomenon that is becoming increasingly common. The spot-nosed monkey (Cercopithecus petaurista), the Campbells monkey (Cercopithecus campbelli) and the green monkey (Chlorocebus sabaeus) are common and genetically diverse West African primates. Insular populations can be found at the Bijagos Archipelago, Guinea-Bissau. Here, we assessed the genome-wide diversity, inbreeding, genetic load and adaptive variation using whole genome sequencing data from insular and mainland populations. In the three species, island populations showed lower genome-wide diversity and higher inbreeding. Genetic drift has likely promoted the conversion of masked genetic load into realized load without increased purging of deleterious variation. Additionally, we found no evidence for accumulation of deleterious variation, suggesting that these populations are not yet at risk of extinction by genetic factors and may act as reservoirs of mainland genetic diversity. We highlight, however, that other anthropogenic factors are threatening these insular primates and therefore conservation management should target their immediate threats and safeguard against additional loss of diversity.

genomics↗

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2021

Multiple adaptive solutions to face climatic constraints: novel insights in the debate over the role of convergence in local adaptation

The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. To bring new insights to this debate we set up a framework which aimed to compare the adaptive trajectories of two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the more than 430 adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different adaptive mechanisms in these two closely related species. Such diversity of adaptive pathways may result from a high number of biological functions involved in adaptation to multiple eco-climatic gradients, and provides more arguments for the role of contingency and stochasticity in adaptation rather than repeatability.

evolutionary biology↗