Universal Artifacts Affect the Branching of Phylogenetic Trees, Not Universal Scaling Laws

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1

Density dependence in a recovering osprey population: demographic and behavioural processes

1.Understanding how density-dependent and independent processes influence demographic parameters, and hence regulate population size, is fundamental within population ecology. We investigated density dependence in growth rate and fecundity in a recovering population of a semicolonial raptor, the osprey Pandion haliaetus [Linnaeus, 1758], using 31 years of count and demographic data in Corsica. 2.The study population increased from three pairs in 1974 to an average of 22 pairs in the late 1990s, with two distinct phases during the recovery (increase followed by stability) and contrasted trends in breeding parameters in each phase. 3.We show density dependence in population growth rate in the second phase, indicating that the stabilized population was regulated. We also show density dependence in productivity (fledging success between years and hatching success within years). 4.Using long-term data on behavioural interactions at nest sites, and on diet and fish provisioning rate, we evaluated two possible mechanisms of density dependence in productivity, food depletion and behavioural interference. 5.As density increased, both provisioning rate and the size of prey increased, contrary to predictions of a food-depletion mechanism. In the time series, a reduction in fledging success coincided with an increase in the number of non-breeders. Hatching success decreased with increasing local density and frequency of interactions with conspecifics, suggesting that behavioural interference was influencing hatching success. 6.Our study shows that, taking into account the role of non-breeders, in particular in species or populations where there are many floaters and where competition for nest sites is intense, can improve our understanding of density-dependent processes and help conservation actions.Partial financial support was made available by Parc Naturel Régionnal de la Corse and the Ministère de l’Ecologie et du Développement Durable. F.M. was supported by a NERC fellowship.Peer reviewe

Le rôle écologique des bonobos (service écologique de dispersion de graine en forêt du Congo)

Les bonobos (Pan paniscus) sont menacés d extinction. Ils sont les plus grands primates et les seuls grands singes de la rive sud du bassin du Congo. Ils sont nos plus proches parents avec les chimpanzés et sont étudiés dans l urgence par les anthropologues pour comprendre nos origines Hominidé. Mais qu en est-il de leur rôle fonctionnel dans la forêt ? Leur disparition aurait-elle des conséquences graves sur l écologie forestière ? Telles sont les questions de ce projet inédit, dont les réponses sont apportées par plusieurs années d observations d un groupe en liberté habitué au site de recherche LuiKotale (RD Congo). Dans cette forêt tropicale humide, la très grande majorité des plantes a besoin des animaux pour se reproduire et disperser leurs graines. Les bonobos sont les plus grands frugivores après les éléphants. Au cours de sa vie, chaque bonobo ingèrera et dispersera 9 tonnes de graines, de plus de 91 espèces de lianes, herbes, arbres et arbustes. Ces graines voyageront 24 heures dans le tube digestif des bonobos, qui les transporteront sur plusieurs kilomètres ( 1.3km; max : 4.5 km), loin de leur plante mère, où ils seront déposées intactes dans leurs fèces. Ces graines dispersées restent viables, germent mieux et plus rapidement que les graines non passées par le tube digestif d un bonobo. La diplochorie, impliquant les bousiers (Scarabaeidae), favorise leur survie post dispersion. Certaines plantes comme les Dialium pourraient même être dépendants du bonobo pour activer la germination de leurs graines en dormance tégumentaire. Les premiers paramètres de l efficacité des bonobos comme disperseurs de graines sont présents. Leurs comportements pourraient affecter la structure des populations végétales. La majorité de ces plantes zoochores ne peuvent recruter sans dispersion et la structure spatiale homogène des arbres laisse penser à un lien direct avec leur agent de dispersion. Peu d espèces remplaceraient les bonobos en terme de leur rôle fonctionnel, tout comme les bonobos ne remplacent pas les éléphants. Il y a peu de redondance fonctionnelle entre les mammifères frugivores très différents du Congo, qui doivent faire face aux pressions de chasse des hommes et disparaissent localement. La défaunation des forêts, résultant dans le syndrome des forêts vides, est un problème grave de biologie de la conservation illustré ici. La disparition des bonobos qui dispersent les graines de 65% des arbres de leur forêt, ou encore 11.6 millions de graines au cours de la vie d un bonobo, est liée à la conservation des forêts tropicales humides du CongoBonobos (Pan paniscus) are threatened with extinction. They are the largest primates, and the only apes (except human), of the southern bank of the Congo Basin. Along with chimpanzees, they are our closest living relatives and are studied by anthropologists to include/understand our hominid origins; but what about their functional role in the forest? Would their disappearance have serious consequences for forest ecology? Answering this question is the aim of this new project, with several years of observations of a free-ranging habituated group of bonobos on the LuiKotale research station (DR Congo). In this tropical rainforest, the very great majority of plants need animals to reproduce and disperse their seeds. Bonobos are the largest frugivorous animals in this region, after elephants. During its life, each bonobo will ingest and disperse nine tons of seeds, from more than 91 species of lianas, grass, trees and shrubs. These seeds will travel 24 hours in the bonobo digestive tract, which will transfer them over several kilometers (mean 1.3 km; max: 4.5 km), far from their parents, where they will be deposited intact in their feces. These dispersed seeds remain viable, germinate better and more quickly than unpassed seeds. For those seeds, diplochory with dung-beetles (Scarabaeidae) imrpoves post-dispersal survival. Certain plants such as Dialium may even be dependent on bonobos to activate the germination of their seeds, characterized by tegumentary dormancy. The first parameters of the effectiveness of seed dispersal by bonobos are present. Behavior of the bonobo could affect the population structure of plants whose seeds they disperse. The majority of these zoochorous plants cannot recruit without dispersal and the homogeneous spatial structure of the trees suggests a direct link with their dispersal agent. Few species could replace bonobos in terms of seed dispersal services, just as bonobos could not replace elephants. There is little functional redundancy between frugivorous mammals of the Congo, which face severe human hunting pressures and local exctinction. The defaunation of the forests, leading to the empty forest syndrome, is critical in conservation biology, as will be illustrated here. The disappearance of the bonobos, which disperse seeds of 65% of the tree species in these forests, or 11.6 million individual seeds during the life of each bonobo, will have consequences for the conservation of the Congo rainforestDIJON-BU Doc.électronique (212319901) / SudocSudocFranceF

Mise au point sur la présence de l'espèce Ambrosia artemisiifolia L. dans les départements de Côte-d'Or et de Sâone-et-Loire

National audienc

Détermination de la potentialité du stock de semences en messicoles rares d'une friche calcaire

National audienc

Configurational crop heterogeneity increases within-field plant diversity

Increasing landscape heterogeneity by restoring semi-natural elements to reverse farmland biodiversity declines is not always economically feasible or acceptable to farmers due to competition for land. We hypothesized that increasing the heterogeneity of the crop mosaic itself, hereafter referred to as crop heterogeneity, can have beneficial effects on within-field plant diversity. Using a unique multi-country dataset from a cross-continent collaborative project covering 1,451 agricultural fields within 432 landscapes in Europe and Canada, we assessed the relative effects of compositional and configurational crop heterogeneity on within-field plant diversity components. We also examined how these relationships were modulated by the position within the field. We found strong positive effects of configurational crop heterogeneity on within-field plant alpha and gamma diversity in field interiors. These effects were as high as the effect of semi-natural cover. In field borders, effects of crop heterogeneity were limited to alpha diversity. We suggest that a heterogeneous crop mosaic may overcome the high negative impact of management practices on plant diversity in field interiors, whereas in field borders, where plant diversity is already high, landscape effects are more limited. Synthesis and applications. Our study shows that increasing configurational crop heterogeneity is beneficial to within-field plant diversity. It opens up a new effective and complementary way to promote farmland biodiversity without taking land out of agricultural production. We therefore recommend adopting manipulation of crop heterogeneity as a specific, effective management option in future policy measures, perhaps adding to agri-environment schemes, to contribute to the conservation of farmland plant diversity