Biology subjects

Burgarella, C.

Publications and source records attributed to Burgarella, C..

11 recordsLinked to original sources

bioRxiv2026

Lineage-specific positive selection on stress-response genes in wild wheat relatives

Understanding how crop wild relatives (CWR) adapt to diverse environments is important both for evolutionary biology and for the development of climate-resilient agriculture. CWR represent an important reservoir of adaptive variation that can be exploited for future crop improvement. To investigate how natural selection has shaped adaptation in these species, we analysed whole-transcriptome data from four diploid wild wheat relatives with contrasting mating systems: the outcrossing species Aegilops speltoides and Aegilops mutica, and the selfing species Aegilops tauschii and Triticum urartu. We combined the imputed McDonald--Kreitman test (MKT) with lineage-specific estimates of divergence obtained from branch-specific models of molecular evolution. This framework reduces biases caused by slightly deleterious mutations and enables adaptive substitutions to be assigned to individual evolutionary lineages. We detected marked differences among species in the prevalence of positive selection. Evidence of adaptive evolution was concentrated in the outcrossing species, whereas few positively selected genes were identified in the selfing species. Comparisons between standard and branch-specific MKT approaches showed that some signals initially inferred as shared among species were reassigned to individual lineages when divergence was estimated on a branch-specific basis, emphasizing the importance of accurately localizing adaptive substitutions. Functional annotation revealed several candidate genes containing domains associated with abiotic and biotic stress responses. Our study provides a framework for detecting positive selection in wild wheat relatives and identifies candidate genes that may contribute to adaptation and represent valuable targets for future functional analyses and wheat improvement programs.

evolutionary biology↗

bioRxiv2026

Rethinking human AMY1 copy number evolution in light of demographic history

Dietary change is often invoked as a major selective force in recent human evolution, with increased copy number of the salivary amylase gene (AMY1) widely cited as an adaptation to starch-rich agricultural diets. However, most evidence for this model comes from limited geographical sampling and analyses that do not fully account for shared ancestry. Here we combine newly generated droplet digital PCR estimates from 390 individuals representing 30 Sub-Saharan African populations with published copy number data from up to 1,307 individuals worldwide and re-evaluate AMY1 evolution using ancestry-aware and phylogenetically informed models. Across Africa, AMY1 copy number shows no consistent association with agriculture once population structure is accounted for. At a global scale, differences between agriculturalists and non-agriculturalists are substantially smaller than previously reported and are largely explained by shared ancestry rather than diet. Phylogenetic analyses further reveal baseline differences in AMY1 copy number between Sub-Saharan and non-Sub-Saharan populations, pointing to deep demographic processes shaping present-day variation. These results challenge the long-standing "agriculture hypothesis" and identify demographic history, rather than subsistence strategy, as the primary driver of AMY1 CN evolution worldwide.

evolutionary biology↗

bioRxiv2024

Traits related to pollination and mating result in diverse reproductive strategies in angiosperms

O_LIFlowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes are associated with floral and life-history traits that have evolved together, making it difficult to interpret correlations between traits. C_LIO_LIWe analysed variation in 21 traits related to flowers, pollination, mating, sexual systems and life history from 361 species representative of flowering plant diversity. C_LIO_LIOutcrossing was mainly found among long-lived, large-stature plants, but hermaphroditic outcrossers and dioecious species appeared as largely non-overlapping strategies in the trait space. Level of floral investment was the main difference between these strategies, with dioecious species having generally smaller, less rewarding flowers, a pattern that also occurred in biotically pollinated species. C_LIO_LIThis multi-trait study shows that pollination can be achieved in many, often contrasting, ways. Despite extensive variation in reproductive traits, dioecy stands out as being linked to floral traits primarily, while correlations with lifespan and dispersal traits appear spurious. We provide a conceptual framework based on lifespan, floral investment, and sexual separation that can be used to integrate pollination, reproduction and plant growth in future research on plant evolution and ecology. C_LI

evolutionary biology↗

bioRxiv2023

The genetic legacy of the expansion of Bantu-speaking peoples in Africa

With the largest genomic dataset to date of Bantu-speaking populations, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we shed fresh light on the expansion of peoples speaking Bantu languages that started [~]4000 years ago in western Africa. We have genotyped 1,740 participants, including 1,487 Bantu speakers from 143 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals. Our results show that Bantu speakers received significant gene-flow from local groups in regions they expanded into. We show for the first time that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the DRC as possible crossroads of interaction. Using spatially explicit methods and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial founder migration model. Finally, we discuss the utility of our dataset as an exhaustive modern-day African comparative dataset for ancient DNA studies. These new findings and data will be important to a wide range of disciplines from science and humanities as well as to the medical sector studying human genetic variation and health in African and African-descendant populations. One-sentence summaryA comprehensive genetic analysis of the expansion of people speaking Bantu languages reveals a complex history of serial founder events, variable levels of contact with local groups, and spread-over-spread events.

evolutionary biology↗

bioRxiv2023

Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives

How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used the Aegilops/Triticum grass species, a group characterized by contrasted mating systems (from obligate out-crossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and more generally for our understanding of the fundamental drivers of genetic diversity.

evolutionary biology↗

bioRxiv2022

Trait-dependent diversification in angiosperms: patterns, models and data

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species ecology, demography and genetics.

evolutionary biology↗

bioRxiv2020

The road to sorghum domestication: evidence from nucleotide diversity and gene expression patterns

Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and 9 wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a genetic bottleneck in the domestication history of sorghum, although several genes showed also patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyses revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totalizing 2449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that domestication and improvement do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome during the domestication event and the improvement process. Overall, these analyses pave the way towards the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

evolutionary biology↗

bioRxiv2018

Adaptive introgression: an untapped evolutionary mechanism for crop adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as \"adaptive introgression\". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

evolutionary biology↗

bioRxiv2018

Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping

History and environment shape crop biodiversity, particularly in areas with vulnerable human communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries--a time of agricultural intensification well before the Inka and Spanish conquests--and then between the 13th century and today--a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural trajectories.

ecology↗

bioRxiv2018

Pervasive hybridizations in the history of wheat relatives

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

evolutionary biology↗

bioRxiv2017

Demographic inference through approximate-Bayesian-computation skyline plots

The skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of the demographic trajectory. Because of this flexibility in shape, skyline plots can, in principle, provide realistic descriptions of the complex demographic scenarios that occur in natural populations. Currently, demographic estimates needed for skyline plots are estimated using coalescent samplers or a composite likelihood approach. Here, we provide a way to estimate historical effective population sizes using an Approximate Bayesian Computation (ABC) framework. We assess its performance using simulated and actual microsatellite datasets. Our method correctly retrieves the signal of contracting, constant and expanding populations, although the graphical shape of the plot is not always an accurate representation of the true demographic trajectory, particularly for recent changes in size and contracting populations. Because of the flexibility of ABC, similar approaches can be extended to other types of data, to multiple populations, or to other parameters that can change through time, such as the migration rate.

evolutionary biology↗