Guillaume Besnard

French National Centre for Scientific Research | CNRS · EDB (Evolution et Diversite Biologique)

• Background. Unraveling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes, and improving breeding programs. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long...

Aim Grasses (Poaceae) are found in all major habitats of Madagascar and have a particular importance in C 4 grasslands, whose origins are controversial. We aimed to estimate the number, age and origins of endemic grass lineages in the Madagascar region, and to compare the diversification of C 3 and C 4 taxa. Location Madagascar and the surrounding...

Species trees have traditionally been inferred from a few selected markers, and genome‐wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historic species diversity. The genomes of an increasing number of species, includi...

C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ∼ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temper...

Self-incompatibility (SI) has evolved independently multiple times and prevents self-fertilization in hermaphrodite angiosperms. Several groups of Oleaceae such as jasmines exhibit distylous flowers, with two compatibility groups each associated with a specific floral morph. Other Oleaceae species in the olive tribe have two compatibility groups wi...

The recently published study by Liu et al. (2024) on a high quality, chromosome‐level genome of Eleocharis vivipara provides new insight into the multiple evolution of C4 photosynthesis in Cyperaceae and in particular in Eleocharis. The species studied has the rare feature of alternately using C3 photosynthesis underwater and C4 photosynthesis on l...

Grasses (Poaceae) comprise c . 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome‐scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new re...

Figure S3: Full results of ancestral range estimation in Oleaceae

Figure S1: Best maximum likelihood tree of Oleaceae, with all accessions represented

Figure S2: Best maximum likelihood tree of Oleaceae, with all accessions and node support information

Background and Aims Progress in the systematic studies of the olive family (Oleaceae) during the last two decades provides the opportunity to update its backbone phylogeny and to investigate its historical biogeography. We additionally aimed to understand the factors underlying the disjunct distribution pattern between East Asia and both West Asia...

Grasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a ne...

The classification of the Olive tree complex (Olea europaea L.) underwent numerous taxonomic changes before a consensus was seemingly reached two decades ago through the combination of morphological, chemical, cytological and molecular evidence that supported the identification of six subspecies in the Old World. While several authors claimed that...

Rapid and minimally destructive methods for estimating the endogenous organic content of subfossil bone save time, lab consumables, and valuable ancient materials. Fourier transform infrared (FTIR) spectroscopy is an established method to estimate bone protein content, and portable spectroscopes enable field applications. We review the ability of b...

Societal Impact Statement Recognizing Loudetia ‐dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascar's biodiversity. A better understanding of the plant species that form grassland ecosystems is necessary for effective land management strategies...

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions,...

The common yellow jasmine (Chrysojasminum fruticans; Oleaceae) is a distylous shrub occurring in the wild in southwestern Europe and the Mediterranean Basin. Little is known about the genetics of its populations and such information would be necessary to investigate its spread and mating strategies. Here, the organization of its genetic diversity w...

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions,...

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs ( Potamochoerus larvatus ) and red river hogs ( P. porcus ) are recognised as separate species due to morphological distinctio...

Clarifying generic circumscriptions within Oleaceae improves its complicated infrafamilial classification. Focusing on the small and disjunctly-distrubted subtribe Schreberinae, we use phylogenomic data from plastid and nuclear DNA from an extensive sampling to assess its phylogenetic patterns and biogeographic history. Results show paraphyly among...

Digitaria is a large pantropical genus, which includes a number of economically problematic agricultural weeds. Difficulties in species identification and the circumscription of the genus have previously hindered progress in understanding its evolution and developing a stable classification. We investigate the evolutionary history of Digitaria by c...

Three decades ago, worldwide biodiversity hotspots were founded on the distributions of continental plants and vertebrates. Here, we question the timeliness of refining the geography of hotspots by basing their definition on more taxa, thanks to the molecular data available for hyper-diverse organisms such as insects, fungi and marine biota. To do...

The new combination Notelaea lanceolata Hong-Wa & Besnard in Dupin et al. (2022: 377) was made when transferring species of Nestegis Rafinesque (1838: 10) to Notelaea Ventenat (1803: 25) as a result of a phylogenetic study that focused on Oleaceae taxa from the Macaronesian, Mediterranean and Pacific regions (Dupin et al. 2022), namely Nestegis,...

1) Research Aims — The extent of Madagascar’s grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C 4 fire-adapted grass, Loudetia simplex , as a proxy for estimating grassland change through time. In the absence of population genomic resources, we used target-enrichment data. We carefully...

The olive tree (Olea europaea L.) is one of the species best adapted to a Mediterranean-type climate. Nonetheless, the Mediterranean Basin is deemed to be a climate change ‘hotspot’ by the Intergovernmental Panel on Climate Change because future model projections suggest considerable warming and drying. Within this context, new environmental challe...

Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human‐driven deforestation is intense throughout Madagascar, exceptions in areas like the Loky‐Manambato region (North) raise questions. Such regions also harbor a rich and endemic flora, whose evolutionary origin remains po...

Tackling the complicated infrafamilial classification of the economically important Oleaceae requires a piecemeal approach that addresses generic circumscriptions. Here, focusing on the distinct clade formed by the generic complex Nestegis, Notelaea, Osmanthus, Phillyrea and Picconia in subtribe Oleinae, we aim to elucidate their boundaries and rel...

Depuis plusieurs années, certains membres de la Société Botanique d’Alsace travaillent sur la taxinomie des fétuques d'Alsace et des territoires avoisinants à l’aide de marqueurs morphologiques, anatomiques et cytogénétiques. Ces travaux bien avancés ont conduit à la description de nouveaux taxons de fétuques à feuilles fines. Les unes méconnues en...

Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenoty...

An exhaustive inventory of Madagascar’s native flora is necessary to optimize its conservation, particularly for highly diversified endemic groups of plants whose many habitats are threatened with short-term loss. The Malagasy olive (Noronhia spp., Oleaceae), with at least 80 species, is recognized as one of the highly diversified tree genera of th...

Studying reproductive strategies of plants is an important topic of research in evolutionary ecology, bringing essential knowledge on their adaptation and diversification, as well as on the ecosystem functioning, with potential applications in biodiversity conservation and crop breeding. Pollination, which allows the transfer of pollen from the ant...

Themeda and Heteropogon are closely related grass genera frequently dominant in tropical C4 grasslands. Relationships between them are poorly resolved, impeding ecological study, especially of T. triandra with a broad distribution from Africa to East Asia, and H. contortus with a pantropical distribution. Our analyses of plastome and nuclear genome...

The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are...

Root-knot nematodes ( Meloidogyne spp.) cause serious damages on most crops. Here, we report a high-quality genome sequence of Meloidogyne exigua (population Mex1, Costa Rica), a major pathogen of coffee. Its mitogenome (20,974 bp) was first assembled and annotated. The nuclear genome was then constructed consisting of 206 contigs, with an N50 leng...

The Laperrine’s olive is endemic to the Saharan Mountains. Adapted to arid environments, it may constitute a valuable genetic resource to improve water-stress tolerance in the cultivated olive. However, limited natural regeneration coupled with human pressures make it locally endangered in Central Sahara. Understanding past population dynamics is t...

In the absence of strong reproductive barriers, genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes, and influence rates of hybridisation. How these dynamics...

Ecologically dominant species are primary determinants of ecosystem function, especially in grassy ecosystems, but the history and biology of grassy ecosystems in Madagascar are poorly understood compared to those of Africa. Loudetia simplex is a C4 perennial grass that is adapted to fire and common to dominant across Africa. It is also widespread...

Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The...

The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The n...

Ecologically dominant species are primary determinants of ecosystem function, especially in grassy ecosystems, but the history and biology of grassy ecosystems in Madagascar are poorly understood compared to those of Africa. Loudetia simplex is a C4 perennial grass that is adapted to fire and common to dominant across Africa. It is also widespread...

The island of Madagascar, situated off the southeast coast of Africa, shows the first evidence of human presence ~ 10,000 years ago; however, other archaeological data indicates a settlement of the modern peoples of the island distinctly more recent, perhaps > 1500 years ago. Bushpigs of the genus Potamochoerus (family Suidae), are today widely dis...

Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exception in areas like the Loky-Manambato region (North) raises questions. This region also harbors a rich and endemic flora, whose evolutionary origin remains po...

C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photo- synthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the...

Long-read sequencing technologies are having a major impact on our approaches to studying non-model organisms and microbial communities. By significantly reducing the cost and facilitating the genome assembly pipelines, any laboratory can now develop its own genomics program regardless of the complexity of the genome studied. The most crucial curre...

Cultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) fr...

Discovered in the 1960s, Meloidogyne graminicola is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, usi...

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act...

Wild subspecies of Olea europaea constitute a source of genetic variability with huge potential for olive breeding to face global changes in Mediterranean-climate regions. We intend to identify wild olive genotypes with optimal adaptability to different environmental conditions to serve as a source of rootstocks and resistance genes for olive breed...

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this single species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we i...

Self-incompatibility (SI) is the main mechanism that favors outcrossing in plants. By limiting compatible matings, SI interferes in fruit production and breeding of new cultivars. In the Oleeae tribe (Oleaceae), an unusual diallelic SI system (DSI) has been proposed for three distantly related species including the olive (Olea europaea), but empiri...

Crop wild relatives are important but often poorly known. This is the case for subtribe Saccharinae (Poaceae: Andropogoneae) which includes sugarcane (Saccharum) and sorghum (Sorghum). We present a phylogenetic and taxonomic account of the Malagasy endemic genus Lasiorhachis, previously included in Saccharum. New plastome and nuclear sequences were...

Debates regarding the origin of tropical savannas attempt to disentangle the role of people, biotic, and abiotic factors. Understanding savanna origins remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of na...

Molecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear mic...

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act...

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the main molecule determining the rate of photosynthesis. The small subunit of the protein, encoded by the rbcS gene, was shown to influence the catalytic efficiency, CO2 specificity, assembly, activity, and stability of RuBisCO. However, the evolution of the rbcS gene is...

Supplementary Information - Salmona et al. 2019. Late Miocene origin and recent population collapse of the savanna Malagasy olive (Noronhia lowryi). Biological Journal of the Linnean Society, doi: 10.1093/biolinnean/blz164.

The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio‐economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA‐seq data for 68 wild and cultivated oli...

C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared with C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to...

A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism’s adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its...

C4 photosynthesis is a complex trait that boosts productivity in tropical conditions. Compared to C3 species, the C4 state seems to require numerous novelties, but species comparisons can be confounded by long divergence times. Here, we exploit the photosynthetic diversity that exists within a single species, the grass Alloteropsis semialata, to de...

Meloidogyne graminicola is a facultative meiotic parthenogenetic root-knot nematode (RKN) that seriously threatens agriculture worldwide. We have little understanding of its origin, genomic structure, and intraspecific diversity. Such information would offer better knowledge of how this nematode successfully damages rice in many different environme...

C4 photosynthesis is a complex trait that boosts productivity in warm environments. Paradoxically, it evolved independently in numerous plant lineages, despite requiring specialised leaf anatomy. The anatomical modifications underlying C4 evolution have previously been evaluated through interspecific comparisons, which capture numerous changes besi...