publications

2025

1. Temporal genomics reveal a century of genomic diversity shifts across a biodiversity hotspot avian assemblage

   Joseph D Manthey, Amie E Settlecowski, Yonas Meheretu, and 5 more authors

   Genome Biology and Evolution, Aug 2025

   Abs DOI

   Biodiversity has experienced tremendous shifts in community, species, and genetic diversity during the Anthropocene. Understanding temporal diversity shifts is especially critical in biodiversity hotspots, i.e., regions that are exceptionally biodiverse and threatened. Here, we use museomics and temporal genomics approaches to quantify temporal shifts in genomic diversity in an assemblage of eight generalist highland bird species from the Ethiopian Highlands (part of the Eastern Afromontane Biodiversity Hotspot). With genomic data from contemporary and historical samples, we demonstrate an assemblage-wide trend of increased genomic diversity through time, potentially due to improved habitat connectivity within highland regions. Genomic diversity shifts in these generalist species contrast with general trends of genomic diversity declines in specialist or imperiled species. In addition to genetic diversity shifts, we found an assemblage-wide trend of decreased realized mutational load, indicative of overall trends for potentially deleterious variation to be masked or selectively purged. Across this avian assemblage, we also show that shifts in population genomic structure are idiosyncratic, with species-specific trends. These results are in contrast with other charismatic and imperiled African taxa that have largely shown strong increases in population genetic structure over the recent past. This study highlights that not all taxa respond the same to environmental change, and generalists, in some cases, may even respond positively. Future comparative conservation genomics assessments on species groups or assemblages with varied natural history characteristics would help us better understand how diverse taxa respond to anthropogenic landscape changes.

2. Urban life shapes genetic diversity in the green anole, Anolis carolinensis

   Yann Bourgeois, Simon Lailvaux, and Stéphane Boissinot

   Molecular Ecology, Aug 2025

   Abs DOI

   ABSTRACT Urbanisation presents unique environmental pressures that drive rapid evolutionary adaptations, particularly in species inhabiting fragmented and anthropogenised landscapes. In this study, we investigate the genomic differentiation between urban and non-urban populations of Anolis carolinensis, focusing on two main aspects: (1) the effect of habitat fragmentation on inbreeding and mutational load and (2) genomic adaptation to the urban habitat. We found that urban populations can exhibit a reduced mutational load, which is a direct consequence of systemic inbreeding. Using genome-wide scans of selection and analyses of genetic diversity, we identify key genomic regions exhibiting significant divergence between urban and non-urban populations. These regions are enriched for genes associated with immunity, behaviour and development, suggesting that urban adaptation is polygenic and involves traits related to stress response, locomotion and thermoregulation. Scans for association with the urban environment reveal a large genomic region in chromosome 2 encompassing the HOXC gene cluster. We also detect a signal of both association and increased differentiation on chromosome 1 in a region previously identified as a candidate for convergent adaptation in another Anolis species, A. cristatellus. Although evidence for convergent evolution at the gene level remains limited, potential signatures of urban adaptation in loci involved in immune response, locomotion and behaviour support the hypothesis that urban environments exert similar selective pressures across species. These results provide evidence for redundancy and polygenic adaptation and highlight the complexity of urban evolution. Future work with denser population sampling and time-series data will be essential to confirm the role of urban selective pressures and track the genetic dynamics of urban populations over time.

2024

1. The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi

   Yann Bourgeois, Ben H Warren, and Steve Augiron

   Molecular Ecology, Aug 2024

   Abs DOI

   Abstract Anthropogenic impact is causing the decline of a large proportion of species worldwide and reduces their genetic diversity. Island species typically have smaller ranges than continental species. As a consequence, island species are particularly liable to undergo population bottlenecks, giving rise to conservation challenges such as inbreeding and unmasking of deleterious genetic load. Such challenges call for more detailed assessments of the genetic make-up of threatened island populations. The Mascarene islands (Indian Ocean) present many prime examples, being unusual in having been pristine until first human arrival  400 years ago, following which anthropogenic pressure was unusually intense. A threatened harrier (Circus maillardi) endemic to the westernmost island of the archipelago is a good example of the challenges faced by species that have declined to small population size following intense anthropogenic pressure. In this study, we use an extensive set of population genomic tools to quantify variation at near-neutral and coding loci, in order to test the historical impact of human activity on this species, and evaluate the species’ (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from  3000 to 300 individuals in the past 1000 years, with a more recent drop  100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants but is unlikely to have allowed the purging of mildly deleterious variants. Our study shows how using relatively affordable methods can reveal the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.

2. Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon

   Nikolaos Minadakis, Lars Kaderli, Robert Horvath, and 5 more authors

   Genetics, Aug 2024

   Abs DOI

   Synchronizing the timing of reproduction with the environment is crucial in the wild. Among the multiple mechanisms, annual plants evolved to sense their environment, the requirement of cold-mediated vernalization is a major process that prevents individuals from flowering during winter. In many annual plants including crops, both a long and short vernalization requirement can be observed within species, resulting in so-called early-(spring) and late-(winter) flowering genotypes. Here, using the grass model Brachypodium distachyon, we explored the link between flowering-time-related traits (vernalization requirement and flowering time), environmental variation, and diversity at flowering-time genes by combining measurements under greenhouse and outdoor conditions. These experiments confirmed that B. distachyon natural accessions display large differences regarding vernalization requirements and ultimately flowering time. We underline significant, albeit quantitative effects of current environmental conditions on flowering-time-related traits. While disentangling the confounding effects of population structure on flowering-time-related traits remains challenging, population genomics analyses indicate that well-characterized flowering-time genes may contribute significantly to flowering-time variation and display signs of polygenic selection. Flowering-time genes, however, do not colocalize with genome-wide association peaks obtained with outdoor measurements, suggesting that additional genetic factors contribute to flowering-time variation in the wild. Altogether, our study fosters our understanding of the polygenic architecture of flowering time in a natural grass system and opens new avenues of research to investigate the gene-by-environment interaction at play for this trait.

3. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role

   Robert Horvath, Nikolaos Minadakis, Yann Bourgeois, and 1 more author

   Elife, Aug 2024

   Abs DOI

   Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass \textitBrachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural \textitB. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild \textitB. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in \textitB. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.

4. Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca

   Andrea Mira-Jover, Eva Graciá, Andrés Giménez, and 3 more authors

   Plos one, Aug 2024

   Abs DOI

   Background Obtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome. Among chelonians, tortoises (Testudinidae) are considered one of the most endangered taxa, which calls for more genomic resources. Here we make the most of high synteny conservation in chelonians to produce the first chromosome-level genome assembly of the genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: Testudo graeca. Results We used high-quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome-level reference of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25,998 protein-coding genes, and identified 41.2% of the assembly as repeats. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) that were consistent with previously suggested phylogeographic patterns for the species. This outlines the value of such reference-guided assemblies for phylogeographic studies. Conclusions Our results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our annotated genome of T. graeca paves the way to delve deeper into the species’ evolutionary history and provides a valuable resource to enhance direct conservation efforts on their threatened populations.

2023

1. What lies behind a fruit crop variety name? A case study of the barnı̄ date palm from al-‘Ulā oasis, Saudi Arabia

   Muriel Gros-Balthazard, Vincent Battesti, Jonathan M Flowers, and 8 more authors

   Plants, People, Planet, Aug 2023

   Abs DOI

   Societal Impact Statement The oasis of al-‘Ulā is subject to a vast development operation by the central government of the Saudi monarchy. Agriculture is not strictly speaking the first objective of this initiative, the emphasis being on tourism and thus on the vast historical heritage and landscape qualities of the region. Nevertheless, agriculture and, in particular, phoeniculture remain the main resource for the inhabitants. Characterizing the local date palm agrobiodiversity is key to the sustainable development of oases. In al-‘Ulā, documenting indigenous knowledge about the locally predominant barnī variety and characterizing its genetic integrity and mode of propagation represents the essential leverage needed by farm development project planners to develop local production. Summary Understanding how farmers name and categorize their crops in relation to the way they are propagated is critical for a proper assessment of agrobiodiversity. Yet, indigenous knowledge is often overlooked in genetic studies, which may result in an underestimation of crop diversity, thereby preventing its conservation and mobilization for developing sustainable agroecosystems. Here, we focus on the barnī date palm variety, a local elite variety of al-‘Ulā oasis, Saudi Arabia. We conducted an ethnobotanical survey on local phoeniculture practices and generated whole-genome data to determine whether or not barnī palms are exclusively clonally (vegetatively) propagated. Further, we contrasted the genomes of barnī and two other palms from al-‘Ulā with 112 Phoenix spp. to provide an initial insight into date palm diversity in this oasis. The survey reveals that the dates of the barnī palm bear distinct names, depending on their quality. Results show that barnī is a true-to-type cultivar, indicating clonal propagation by offshoots with name maintenance, even between distinct cultivating situations in al-‘Ulā and a nearby oasis. Nonetheless, it is distinct from the prominent barnī cultivated in Oman. Its ancestry is comparable to other West Asian date palms, but another palm from this oasis shows influence from North Africa. What lies behind the cultivar name barnī in al-‘Ulā and further afield in the Arabian Peninsula has been deciphered through the key disciplinary combination of social anthropology and genetics. Future studies will provide additional insights into the original genetic make-up of this millennia-old oasis.

2. Beyond morphs: Inter-individual colour variation despite strong genetic determinism of colour morphs in a wild bird

   Maya C Mould, Michèle Huet, Lou Senegas, and 4 more authors

   Journal of Evolutionary Biology, Aug 2023

   Abs DOI

   Abstract Categorizing individuals into discrete forms in colour polymorphic species can overlook more subtle patterns in coloration that can be of functional significance. Thus, quantifying inter-individual variation in these species at both within- and between-morph levels is critical to understand the evolution of colour polymorphisms. Here we present analyses of inter-individual colour variation in the Reunion grey white-eye (Zosterops borbonicus), a colour polymorphic wild bird endemic to the island of Reunion in which all highland populations contain two sympatric colour morphs, with birds showing predominantly grey or brown plumage, respectively. We first quantified colour variation across multiple body areas by using a continuous plumage colour score to assess variation in brown-grey coloration as well as smaller scale variation in light patches. To examine the possible causes of among-individual variation, we tested if colour variation in plumage component elements could be explained by genotypes at two markers near a major-effect locus previously related to back coloration in this species, and by other factors such as age, sex and body condition. Overall, grey-brown coloration was largely determined by genetic factors and was best described by three distinct clusters that were associated to genotypic classes (homozygotes and heterozygote), with no effect of age or sex, whereas variation in smaller light patches was primarily related to age and sex. Our results highlight the importance of characterizing subtle plumage variation beyond morph categories that are readily observable since multiple patterns of colour variation may be driven by different mechanisms, have different functions and will likely respond in different ways to selection.

3. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

   S Cotton, MP McHugh, R Dewar, and 8 more authors

   Journal of Hospital Infection, Aug 2023
4. The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches

   Nikolaos Minadakis, Hefin Williams, Robert Horvath, and 5 more authors

   Peer Community Journal, Aug 2023
5. Mechanisms of intrinsic postzygotic isolation: from traditional genic and chromosomal views to genomic and epigenetic perspectives

   Radka Reifová, S Lorena Ament-Velásquez, Yann Bourgeois, and 7 more authors

   Cold Spring Harbor Perspectives in Biology, Aug 2023

2022

1. Varied diversification patterns and distinct demographic trajectories in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley

   Joseph D Manthey, Yann Bourgeois, Yonas Meheretu, and 1 more author

   Molecular ecology, Aug 2022

   Abs DOI

   Abstract Taxon-specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species-specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole-genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species’ dispersal ability was negatively correlated with levels of population differentiation. Isolation with migration models indicated varied patterns of population differentiation and connectivity among populations of the focal species. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.

2. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B. 1.617. 2) compared with alpha (B. 1.1. 7) variants of concern: a cohort study

   Katherine A Twohig, Tommy Nyberg, Asad Zaidi, and 8 more authors

   The Lancet Infectious Diseases, Aug 2022
3. Experimentally heat-induced transposition increases drought tolerance in Arabidopsis thaliana

   Michael Thieme, Arthur Brêchet, Yann Bourgeois, and 3 more authors

   New Phytologist, Aug 2022

   Abs DOI

   Summary Eukaryotic genomes contain a vast diversity of transposable elements (TEs). Formerly often described as selfish and parasitic DNA sequences, TEs are now recognised as a source of genetic diversity and powerful drivers of evolution. However, because their mobility is tightly controlled by the host, studies experimentally assessing how fast TEs may mediate the emergence of adaptive traits are scarce. We exposed Arabidopsis thaliana high-copy TE lines (hcLines) with up to c. eight-fold increased copy numbers of the heat-responsive ONSEN TE to drought as a straightforward and ecologically highly relevant selection pressure. We provide evidence for increased drought tolerance in five out of the 23 tested hcLines and further pinpoint one of the causative mutations to an exonic insertion of ONSEN in the ribose-5-phosphate-isomerase 2 gene. The resulting loss-of-function mutation caused a decreased rate of photosynthesis, plant size and water consumption. Overall, we show that the heat-induced transposition of a low-copy TE increases phenotypic diversity and leads to the emergence of drought-tolerant individuals in A. thaliana. This is one of the rare empirical examples substantiating the adaptive potential of mobilised stress-responsive TEs in eukaryotes. Our work demonstrates the potential of TE-mediated loss-of-function mutations in stress adaptation.

4. Genomic analyses reveal association of ASIP with a recurrently evolving adaptive color pattern in frogs

   Sandra Goutte, Imtiyaz Hariyani, Kole Deroy Utzinger, and 2 more authors

   Molecular Biology and Evolution, Aug 2022

   Abs DOI

   Traits shared among distantly related lineages are indicators of common evolutionary constraints, at the ecological, physiological, or molecular level. Here, we show that the vertebral stripe, a cryptic color pattern, has evolved hundreds of times in the evolutionary history of anurans (frogs and toads) and is favored in terrestrial habitats. Using a genome-wide association study, we demonstrate that variation near the Agouti signaling protein gene (ASIP) is responsible for the different vertebral stripe phenotypes in the African grass frog Ptychadena robeensis. RNAseq and real-time quantitative PCR revealed that differential expression of the gene and an adjacent long non-coding RNA is linked to patterning in this species. Surprisingly, and although the stripe phenotypes are shared with closely related species, we found that the P. robeensis alleles are private to the species and unlikely to evolve under long-term balancing selection, thus indicating that the vertebral stripe phenotypes result from parallel evolution within the group. Our findings demonstrate that this cryptic color pattern evolved rapidly and recurrently in terrestrial anurans, and therefore constitutes an ideal system to study repeated evolution.

2021

1. A two-locus system with strong epistasis underlies rapid parasite-mediated evolution of host resistance

   Camille Ameline, Yann Bourgeois, Felix Vögtli, and 4 more authors

   Molecular biology and evolution, Aug 2021

   Abs DOI

   Parasites are a major evolutionary force, driving adaptive responses in host populations. Although the link between phenotypic response to parasite-mediated natural selection and the underlying genetic architecture often remains obscure, this link is crucial for understanding the evolution of resistance and predicting associated allele frequency changes in the population. To close this gap, we monitored the response to selection during epidemics of a virulent bacterial pathogen, Pasteuria ramosa, in a natural host population of Daphnia magna. Across two epidemics, we observed a strong increase in the proportion of resistant phenotypes as the epidemics progressed. Field and laboratory experiments confirmed that this increase in resistance was caused by selection from the local parasite. Using a genome-wide association study, we built a genetic model in which two genomic regions with dominance and epistasis control resistance polymorphism in the host. We verified this model by selfing host genotypes with different resistance phenotypes and scoring their F1 for segregation of resistance and associated genetic markers. Such epistatic effects with strong fitness consequences in host–parasite coevolution are believed to be crucial in the Red Queen model for the evolution of genetic recombination.

2. Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity

   Erik Volz, Verity Hill, John T McCrone, and 8 more authors

   Cell, Aug 2021
3. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B. 1.1. 7: an ecological study

   Mark S Graham, Carole H Sudre, Anna May, and 8 more authors

   The Lancet Public Health, Aug 2021
4. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes

   Yann XC Bourgeois, and Ben H Warren

   Molecular Ecology, Aug 2021

   Abs DOI

   Abstract Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.

5. The structural, functional and evolutionary impact of transposable elements in eukaryotes

   Dareen Almojil, Yann Bourgeois, Marcin Falis, and 3 more authors

   Genes, Aug 2021
6. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B. 1.1. 7

   Bo Meng, Steven A Kemp, Guido Papa, and 8 more authors

   Cell reports, Aug 2021
7. Balancing selection for pathogen resistance reveals an intercontinental signature of Red Queen coevolution

   Yann Bourgeois, Peter D Fields, Gilberto Bento, and 1 more author

   Molecular Biology and Evolution, Aug 2021

   Abs DOI

   The link between long-term host–parasite coevolution and genetic diversity is key to understanding genetic epidemiology and the evolution of resistance. The model of Red Queen host–parasite coevolution posits that high genetic diversity is maintained when rare host resistance variants have a selective advantage, which is believed to be the mechanistic basis for the extraordinarily high levels of diversity at disease-related genes such as the major histocompatibility complex in jawed vertebrates and R-genes in plants. The parasites that drive long-term coevolution are, however, often elusive. Here we present evidence for long-term balancing selection at the phenotypic (variation in resistance) and genomic (resistance locus) level in a particular host–parasite system: the planktonic crustacean Daphnia magna and the bacterium Pasteuria ramosa. The host shows widespread polymorphisms for pathogen resistance regardless of geographic distance, even though there is a clear genome-wide pattern of isolation by distance at other sites. In the genomic region of a previously identified resistance supergene, we observed consistent molecular signals of balancing selection, including higher genetic diversity, older coalescence times, and lower differentiation between populations, which set this region apart from the rest of the genome. We propose that specific long-term coevolution by negative-frequency-dependent selection drives this elevated diversity at the host’s resistance loci on an intercontinental scale and provide an example of a direct link between the host’s resistance to a virulent pathogen and the large-scale diversity of its underlying genes.

8. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

   Paul Elliott, David Haw, Haowei Wang, and 8 more authors

   Science, Aug 2021

   Abs DOI

   The United Kingdom has high rates of vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exceeding 80% of adults. As immunity wanes and social distancing is relaxed, how are rates of illness and severe disease affected by more infectious variants? Elliott et al. used reverse transcription PCR data from the REACT-1 study, which showed exponential transmission as the Alpha variant (B.1.1.7) was replaced by the Delta variant (B.1.617.2). After adjusting for age and other variables, vaccine effectiveness for the new variant averaged 55% in June and July of 2020. Despite the slower growth of the pandemic in the summer, it looks as if increased indoor mixing in the autumn will sustain transmission of the Delta variant despite high levels of adult vaccination. —CA The SARS-CoV-2 Delta variant increased exponentially in the United Kingdom driven by infection in the young, not yet vaccinated, population. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between  50% and  60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.

9. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

   Thushan I Silva, Guihai Liu, Benjamin B Lindsey, and 8 more authors

   Iscience, Aug 2021

   Abs DOI

   Summary We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.

2020

1. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage

   Yann XC Bourgeois, Joris AM Bertrand, Boris Delahaie, and 3 more authors

   Molecular Ecology, Aug 2020
2. Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

   Yann Bourgeois, Robert P Ruggiero, Imtiyaz Hariyani, and 1 more author

   PLoS genetics, Aug 2020

   Abs DOI

   The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We observed a positive correlation between recombination rate and frequency of TEs and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation. We demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle these mechanisms.

3. An integrated national scale SARS-CoV-2 genomic surveillance network

   The COVID

   The Lancet. Microbe, Aug 2020
4. CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing

   Samuel Robson, Garry Scarlett, Yann Xavier Claude Bourgeois, and 3 more authors

   Aug 2020
5. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

   Samuel Robson, Garry Scarlett, Yann Xavier Claude Bourgeois, and 3 more authors

   Aug 2020
6. COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study

   Samuel Robson, Garry Scarlett, Yann Xavier Claude Bourgeois, and 3 more authors

   Aug 2020

2019

1. Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

   Yann Bourgeois, and Stéphane Boissinot

   Molecular ecology, Aug 2019
2. The mobilome of reptiles: Evolution, structure, and function

   Stéphane Boissinot, Yann Bourgeois, Joseph D Manthey, and 1 more author

   Cytogenetic and genome research, Aug 2019
3. Recent secondary contacts, linked selection, and variable recombination rates shape genomic diversity in the model species Anolis carolinensis

   Yann Bourgeois, Robert P Ruggiero, Joseph D Manthey, and 1 more author

   Genome Biology and Evolution, Aug 2019
4. On the population dynamics of junk: a review on the population genomics of transposable elements

   Yann Bourgeois, and Stéphane Boissinot

   Genes, Aug 2019

2018

1. Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

   Yann Bourgeois, Christoph Stritt, Jean-Claude Walser, and 3 more authors

   The Plant Journal, Aug 2018
2. Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data

   Jacobo Reyes-Velasco, Joseph D Manthey, Yann Bourgeois, and 2 more authors

   PLoS One, Aug 2018
3. The end of a 60-year riddle: identification and genomic characterization of an iridovirus, the causative agent of white fat cell disease in zooplankton

   Elena R Toenshoff, Peter D Fields, Yann X Bourgeois, and 1 more author

   G3: Genes, Genomes, Genetics, Aug 2018
4. Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation

   Ivana Roman, Yann Bourgeois, Jacobo Reyes-Velasco, and 3 more authors

   Biological Journal of the Linnean Society, Aug 2018

2017

1. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird

   Yann XC Bourgeois, Boris Delahaie, Mathieu Gautier, and 8 more authors

   Royal Society open science, Aug 2017
2. The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model

   Gilberto Bento, Jarkko Routtu, Peter D Fields, and 3 more authors

   PLoS Genetics, Aug 2017
3. Parasitism drives host genome evolution: insights from the Pasteuria ramosa–Daphnia magna system

   Yann Bourgeois, Anne C Roulin, Kristina Müller, and 1 more author

   Evolution, Aug 2017
4. LINE insertion polymorphisms are abundant but at low frequencies across populations of Anolis carolinensis

   Robert P Ruggiero, Yann Bourgeois, and Stéphane Boissinot

   Frontiers in genetics, Aug 2017
5. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex

   Boris Delahaie, Josselin Cornuault, Charline Masson, and 4 more authors

   Journal of Evolutionary Biology, Aug 2017

2016

1. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura)

   Guillaume Besnard, Joris AM Bertrand, Boris Delahaie, and 3 more authors

   Biological Journal of the Linnean Society, Aug 2016
2. Population density of the Réunion Grey White-eye Zosterops borbonicus within the summit ecosystems of Réunion, Mascarene Islands

   Joris AM Bertrand, Yann XC Bourgeois, and Christophe Thébaud

   Ostrich, Aug 2016
3. The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird

   Joris AM Bertrand, Boris Delahaie, Yann XC Bourgeois, and 6 more authors

   Journal of Evolutionary Biology, Aug 2016
4. Candidate gene analysis suggests untapped genetic complexity in melanin-based pigmentation in birds

   Yann XC Bourgeois, Joris AM Bertrand, Boris Delahaie, and 4 more authors

   Journal of Heredity, Aug 2016
5. A photoreceptor contributes to the natural variation of diapause induction in Daphnia magna

   Anne C Roulin, Yann Bourgeois, Urs Stiefel, and 2 more authors

   Molecular biology and evolution, Aug 2016

2015

1. Community assembly on remote islands: a comparison of Hawaiian and Mascarene spiders

   Juliane Casquet, Yann XC Bourgeois, Corinne Cruaud, and 3 more authors

   Journal of Biogeography, Aug 2015
2. Morphological and plumage colour variation in the Réunion grey white-eye (Aves: Zosterops borbonicus): assessing the role of selection

   Josselin Cornuault, Boris Delahaie, Joris AM Bertrand, and 4 more authors

   Biological Journal of the Linnean Society, Aug 2015
3. Using molecular tools to guide management of invasive alien species: assessing the genetic impact of a recently introduced island bird population

   Janske Crommenacker, YXC Bourgeois, Ben H Warren, and 4 more authors

   Diversity and Distributions, Aug 2015

2014

1. Extremely reduced dispersal and gene flow in an island bird

   JAM Bertrand, YXC Bourgeois, B Delahaie, and 7 more authors

   Heredity, Aug 2014

2013

1. The role of ecology in the geographical separation of blood parasites infecting an insular bird

   Josselin Cornuault, Aurélie Khimoun, Ryan J Harrigan, and 4 more authors

   Journal of Biogeography, Aug 2013
2. Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome

   Yann XC Bourgeois, Emeline Lhuillier, Timothée Cézard, and 7 more authors

   Molecular Ecology Resources, Aug 2013
3. Génétique évolutive d’un cas extrême de polymorphisme de la coloration du plumage chez un oiseau insulaire, Zosterops borbonicus (Zosteropidae).

   Yann Bourgeois

   Université Paul Sabatier, Aug 2013

2012

1. Hybridization and barriers to gene flow in an island bird radiation

   Ben H Warren, Eldredge Bermingham, Yann Bourgeois, and 4 more authors

   Evolution, Aug 2012
2. Isolation and characterization of twelve polymorphic microsatellite loci for investigating an extreme case of microgeographical variation in an island bird (Zosterops borbonicus)

   Joris AM Bertrand, Ricardo Garcı́a-Jiménez, Yann Bourgeois, and 4 more authors

   Conservation Genetics Resources, Aug 2012
3. Investigating the role of the melanocortin-1 receptor gene in an extreme case of microgeographical variation in the pattern of melanin-based plumage pigmentation

   Yann XC Bourgeois, Joris AM Bertrand, Christophe Thebaud, and 1 more author

   PLoS One, Aug 2012