78 Works

Data from: Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae)

Philip D. Batista, Jasmine K. Janes, Celia K. Boone, Brent W. Murray & Felix A. H. Sperling
Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

Data from: Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging

Olivier J. Hardy, Boris Delaide, Hélène Hainaut, Jean-François Gillet, Pauline Gillet, Esra Kaymak, Nina Vankerckhove, Jérôme Duminil & Jean-Louis Doucet
The natural regeneration of tree species depends on seed and pollen dispersal. To assess if limited dispersal could be critical for the sustainability of selective logging practices, we performed parentage analyses in two Central African legume canopy species displaying contrasted floral and fruit traits: Distemonanthus benthamianus and Erythrophleum suaveolens. We also developed new tools linking forward dispersal kernels with backward migration rates to better characterize long-distance dispersal. Much longer pollen dispersal in D. benthamianus (mean...

Data from: History of the fragmentation of the African rain forest in the Dahomey Gap: insight from the demographic history of Terminalia superba

Boris Demenou, Jean-Louis Doucet & Olivier J. Hardy
Paleo-environmental reconstructions show that the distribution of tropical African rain forests was affected by Quaternary climate changes. They suggest that the Dahomey Gap (DG) - the savanna corridor that currently separates Upper Guinean (UG, West Africa) and Lower Guinean (LG, western Central Africa) rain forest blocks – was forested during the African Humid Holocene period (from at least 9 ka till 4.5 ka), and possibly during other interglacial periods, while an open vegetation developed in...

Data from: Testing and interpreting the shared space-environment fraction in variation partitioning analyses of ecological data

David Bauman, Jason Vleminckx, Olivier J. Hardy & Thomas Drouet
Variation partitioning analyses combined with spatial predictors (Moran’s eigenvector maps, MEM) are commonly used in ecology to test the fractions of species abundance variation purely explained by environment and space. However, while these pure fractions can be tested using a classical residuals permutation procedure, no specific method has been developed to test the shared space-environment fraction (SSEF). Yet, the SSEF is expected to encompass a major driver of community assembly, that is, an induced spatial...

Data from: Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation

A. B. Addisalem, Jérôme Duminil, Doret Wouters, Frans Bongers & Marinus J. M. Smulders
The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a...

Data from: Food dissemination in ants: robustness of the trophallactic network against resource quality

Olivier Bles, Jean-Louis Deneubourg & Stamatios C. Nicolis
Insect societies are often composed of many individuals, achieving collective decisions that depend on environmental and colonial characteristics. For example, ants are able to focus their foraging effort on the most rewarding food source. While this phenomenon is well known, the link between the food source quality and the intranidal food dissemination networks and its dynamics has been neglected. Here we analysed the global dynamics of the food dissemination in Camponotus cruentatus workers, after feeding...

Data from: Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive isolation in allopatry

Helene Martin, Pascal Touzet, Mathilde Dufay, Cécile Godé, Eric Schmitt, Emna Lahiani, Lynda F. Delph & Fabienne Van Rossum
Reproductive isolation can rise either as a consequence of genomic divergence in allopatry or as a byproduct of divergent selection in parapatry. To determine whether reproductive isolation in gynodioecious Silene nutans results from allopatric divergence or from ecological adaptation following secondary contact, we investigated the pattern of postzygotic reproductive isolation and hybridization in natural populations using two phylogeographic lineages, western (W1) and eastern (E1). Experimental crosses between the lineages identified strong, asymmetric postzygotic isolation between...

Data from: Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community

Kevin D'hoe, Stefan Vet, Karoline Faust, Frédéric Moens, Gwen Falony, Didier Gonze, Verónica Lloréns-Rico, Lendert Gelens, Jan Danckaert, Luc De Vuyst & Jeroen Raes
Whereas the composition of the human gut microbiome is well resolved, predictive understanding is still lacking. Here, we followed a bottom-up strategy to explore human gut community dynamics: we established a synthetic community composed of three representative human gut isolates (Roseburia intestinalis L1-82, Faecalibacterium prausnitzii A2-165 and Blautia hydrogenotrophica S5a33) and explored their interactions under well-controlled conditions in vitro. Systematic mono- and pair-wise fermentation experiments confirmed competition for fructose and cross-feeding of formate. We quantified...

Data from: Symmetry breaking and inter-clonal behavioural variability in slime molds

David Vogel, Audrey Dussutour & Jean-Louis Deneubourg
Cells are dynamic systems capable of switching from an isotropic growth to a polarized growth even in the absence of any pre-existing external asymmetry. Here, we study this process of symmetry breaking in the acellular slime mold Physarum polycephalum. In the experiments slime molds could grow on two identical opposed sources of calcium. We highlighted a positive correlation between growth dynamic, level of symmetry breaking and calcium concentration. We identified three populations of slime molds...

Data from: DNA taxonomy in the timber genus Milicia: evidence of unidirectional introgression in the West African contact zone

Kasso Daïnou, Jean-François Flot, Bernd Degen, Céline Blanc-Jolivet, Jean-Louis Doucet, Ludivine Lassois & Olivier J. Hardy
DNA-based techniques are helpful in characterising hybridisation patterns in plant species. To be efficient in disentangling species boundaries and interspecific gene flow, it is recommended to combine various methodologies and types of markers. Here, we used different analytical tools (algorithms implemented in Structure, Tess, NewHybrids and HIest, and the haploweb approach) and three nuclear genetic markers (7 nuclear simple sequence repeat loci (SSRs), 62 single-nucleotide polymorphism loci (SNPs) and a single-copy gene region, At103) to...

Observational data and model output for sediment nutrient cycling at Patagonian fjords

Hong Chin Ng, Jon R. Hawkings, Jemma L. Wadham, Katharine R. Hendry, Tim M. Conway, Sebastien Bertrand, Matthias Sieber, Brent A. Summers, Felipe S. Freitas, James P.J. Ward, Helena V. Pryer & Sandra Arndt
Glacier meltwater supplies a significant amount of silicon (Si) and iron (Fe) sourced from weathered bedrock to downstream ecosystems. However, the extent to which these essential nutrients reach the ocean is regulated by the nature of the benthic cycling of dissolved Si and Fe within fjord systems, given the rapid deposition of reactive particulate fractions at fjord heads. The dataset is used to examine the benthic cycling of the two nutrients at Patagonian fjord heads...

Data from: Extensive seed and pollen dispersal and assortative mating in the rain forest tree Entandrophragma cylindricum (Meliaceae) inferred from indirect and direct analyses

Franck Kameni Monthe, Olivier J. Hardy, Jean-Louis Doucet, Judy Loo, Jérôme Duminil & Jean-Louis Doucet
Pollen and seed dispersal are key processes affecting the demographic and evolutionary dynamics of plant species and are also important considerations for the sustainable management of timber trees. Through direct and indirect genetic analyses, we studied the mating system and the extent of pollen and seed dispersal in an economically important timber species, Entandrophragma cylindricum (Meliaceae). We genotyped adult trees, seeds and saplings from a 400-ha study plot in a natural forest from East Cameroon...

Data from: Relationships between population density, fine-scale genetic structure, mating system and pollen dispersal in a timber tree from African rainforests.

Jérôme Duminil, Kasso Daïnou, David Kombi Kaviriri, Pauline Gillet, Judy Loo, Jean-Louis Doucet & Olivier J. Hardy
Due to the reduction of population density and/or the environmental changes it induces, selective logging could affect the demography, reproductive biology and evolutionary potential of forest trees. This is particularly relevant in tropical forests where natural population densities can be low and isolated trees may be subject to outcross pollen limitation and/or produce low quality selfed seeds that exhibit inbreeding depression. Comparing reproductive biology processes and genetic diversity of populations at different densities can provide...

Data from: Short-term changes in the structure of termite assemblages associated with slash-and-burn agriculture in Côte d'Ivoire

Kanvaly Dosso, Yves Roisin, Seydou Tiho, Souleymane Konaté & Kolo Yéo
Termites are major decomposers in tropical regions and play critical roles in many soil-related processes. Studies conducted in Asia and the Neotropics suggest that habitat modification can strongly affect termite assemblages, but data on termite communities from forests in Africa, especially West Africa, are scarce. Here, we measured the short-term impact of slash-and-burn agriculture on termite assemblages in an agricultural region of central Côte d'Ivoire. We assessed termite diversity and relative abundance in four habitat...

Data from: The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

Myriam Heuertz, Katharina B. Budde, Santiago C. González-Martínez & Olivier J. Hardy
Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f....

Data from: Closing a gap in tropical forest biomass estimation: taking crown mass variation into account in pantropical allometries

Pierre Ploton, Nicholas Barbier, Stéphane Takoudjou Momo, Maxime Réjou-Méchain, Faustin Boyemba Bosela, Georges Chuyong, Gilles Dauby, Vincent Droissart, Adeline Fayolle, Rosa Calisto Goodman, Mathieu Henry, Narcisse Guy Kamdem, John Katembo Mukirania, David Kenfack, Moses Libalah, Alfred Ngomanda, Vivien Rossi, Bonaventure Sonké, Nicolas Texier, Duncan Thomas, Donatien Zebaze, Pierre Couteron, Uta Berger & Raphaël Pélissier
Accurately monitoring tropical forest carbon stocks is an outstanding challenge. Allometric models that consider tree diameter, height and wood density as predictors are currently used in most tropical forest carbon studies. In particular, a pantropical biomass model has been widely used for approximately a decade, and its most recent version will certainly constitute a reference in the coming years. However, this reference model shows a systematic bias for the largest trees. Because large trees are...

Data from: Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

Kasso Dainou, Grégory Mahy, Jérôme Duminil, Christopher W. Dick, Jean-Louis Doucet, Armel S. L. Donkpégan, Michaël Pluijgers, Brice Sinsin, Philippe Lejeune & Olivier J. Hardy
The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological...

Data from: Do people imitate when making decisions? - evidence from a spatial prisoners dilemma experiment

Jelena Grujic & Tom Lenaerts
How do people decide which action to take? This question is best answered using Game Theory, which has proposed a series of decision mechanisms that people potentially use. In network simulations, wherein games are repeated and payoff differences can be observed, those mechanisms rely often on imitation of successful behavior. Surprisingly, little to no evidence has been provided about whether, how and what people actually use to alter their actions in that context. By comparing...

Solving the coral species delimitation conundrum

Catalina Ramírez-Portilla, Andrew Baird, Peter Cowman, Andrea Quattrini, Saki Harii, Frederic Sinniger & Jean-François Flot
Distinguishing coral species is not only crucial for physiological, ecological and evolutionary studies, but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that inter-specific hybridization might be responsible for...

Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil

Darlan S. Candido, Ingra M. Claro, Jaqueline G. De Jesus, William M. Souza, Filipe R. R. Moreira, Simon Dellicour, Thomas A. Mellan, Louis Du Plessis, Rafael H. M. Pereira, Flavia C. S. Sales, Erika R. Manuli, Julien Thézé, Luiz Almeida, Mariane T. Menezes, Carolina M. Voloch, Marcilio J. Fumagalli, Thaís M. Coletti, Camila A. M. Da Silva, Mariana S. Ramundo, Mariene R. Amorim, Henrique H. Hoeltgebaum, Swapnil Mishra, Mandev S. Gill, Luiz M. Carvalho, Lewis F. Buss … & Nuno R. Faria
Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1–1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil....

Microsatellite genotypes and ITS2 DNA sequence data for Seriatopora hystrix

Rosa Maria Van Der Ven, Jean-François Flot, Carol Buitrago-López & Marc Kochzius
Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral, Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. Seriatopora hystrix showed high differentiation,...

Data from: The shepherds' tale: a genome-wide study across 9 dog breeds implicates two loci in the regulation of fructosamine serum concentration in Belgian shepherds

Simon K. G. Forsberg, Marcin Kierczak, Ingrid Ljungvall, Anne-Christine Merveille, Vassiliki Gouni, Maria Wiberg, Jakob Lundgren Willesen, Sofia Hanås, Anne-Sophie Lequarré, Louise Mejer Sørensen, Laurent Tiret, Kathleen McEntee, Eija Seppälä, Jørgen Koch, Géraldine Battaille, Hannes Lohi, Merete Fredholm, Valerie Chetboul, Jens Häggström, Örjan Carlborg, Kerstin Lindblad-Toh & Katja Höglund
Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated hemoglobin (HbA1c) are two major biomarkers of glycaemia where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds....

Data from: Determinants and dynamics of banded vegetation pattern migration in arid climates

Vincent Deblauwe, Pierre Couteron, Jan Bogaert & Nicolas Barbier
Dense vegetation bands aligned parallel to contour levels and alternating at regular intervals with relatively barren interbands have been reported at the margins of all tropical deserts. Since their discovery in the 1950s, it has been suspected that these vegetation bands migrate upslope, forming a space-time cyclic pattern. Evidence to date has been relatively sparse and indirect, and observations have remained conflicting. Unequivocal photographic evidence of upslope migration (a few dm yr-1) is provided here...

Data from: Impact of past climatic changes and resource availability on the population demography of three food-specialist bees

Simon Dellicour, Denis Michez, Jean-Yves Rasplus & Patrick Mardulyn
Past climate change is known to have strongly impacted current patterns of genetic variation of animals and plants in Europe. However, ecological factors also have the potential to influence demographic history, and thus patterns of genetic variation. In this study, we investigated the impact of past climate, and also the potential impact of host plant species abundance, on intraspecific genetic variation in three co-distributed and related specialized solitary bees of the genus Melitta with very...

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