Probability distributions on cladograms, Random discrete structures, pp.1-18, 1996. ,
Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today, Stat. Sci, vol.16, pp.23-34, 2001. ,
Quantifying agedependent extinction from species phylogenies, Syst. Biol, vol.65, pp.35-50, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01265486
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates, Proc. Natl. Acad. Sci. USA, vol.106, pp.13410-13414, 2009. ,
Global decline of bumblebees is phylogenetically structured and inversely related to species range size and pathogen incidence, Proc. Roy. Soc. Lond. B, vol.284, p.20170204, 2017. ,
A global species assessment, 2004. ,
Has the Earth's sixth mass extinction already arrived?, Nature, vol.471, pp.51-57, 2011. ,
Evolving entities: towards a unified framework for understanding diversity at the species and higher levels, Philos. Trans. R. Soc. Lond. B, vol.365, pp.1801-1813, 2010. ,
Variation in extinction risk among birds: chance or evolutionary predisposition?, Proc. R. Soc. Lond. B, vol.264, pp.401-408, 1997. ,
Self-similar fragmentations, Ann. I.H. Poincaré, vol.38, pp.319-340, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-00101984
Random fragmentation and coagulation processes, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00103015
Taxonomic selectivity in amphibians: ignorance, geography or biology?, Anim. Conserv, vol.9, pp.135-143, 2006. ,
Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance, Syst. Biol, vol.55, pp.685-691, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00370261
Testing for equal rates of cladogenesis in diverse taxa, Evolution, vol.57, pp.2469-2474, 2003. ,
Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow, Evolution, vol.71, pp.1149-1163, 2017. ,
,
apTreeshape: statistical analysis of phylogenetic tree shape, Bioinformatics, vol.22, pp.363-364, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00370265
Latent extinction risk and the future battlegrounds of mammal conservation, Proc. Roy. Soc. Lond. B, vol.103, pp.4157-4161, 2006. ,
Testing for latitudinal bias in diversification rates : an example using, New World birds. Ecology, vol.86, pp.2278-2287, 2005. ,
The mid-domain effect: geometric species richness, Trends Ecol. Evol, vol.15, pp.70-76, 2000. ,
Slowdowns in diversification rates from real phylogenies may not be real, Syst. Biol, vol.59, pp.458-464, 2010. ,
A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies, Syst. Biol, vol.61, pp.785-792, 2012. ,
Extinction risk and diversification are linked in a plant biodiversity hotspot, PLoS Biol, vol.9, pp.1-9, 2011. ,
Revisiting the impacts of non-random extinction on the tree-of-life, Biol. Lett, vol.9, 2013. ,
Is extinction age dependent?, Palaios, vol.21, pp.571-579, 2006. ,
Mathematical population genetics 1: theoretical introduction, 2012. ,
Conservation evaluation and phylogenetic diversity, Biol. Conserv, vol.61, pp.1-10, 1992. ,
Distribution of phylogenetic diversity under random extinction, J. Theor. Biol, vol.251, pp.286-296, 2008. ,
The Poisson-Dirichlet distribution and related topics: models and asymptotic behaviors, 2010. ,
Calibrating the tree of life: fossils, molecules and evolutionary timescales, Ann. Bot, vol.104, pp.789-794, 2009. ,
Loss of avian phylogenetic diversity in neotropical agricultural systems, Science, vol.345, pp.1343-1346, 2014. ,
Selectivity in mammalian extinction risk and threat types: a new measure of phylogenetic signal strength in binary traits, Conserv. Biol, vol.24, pp.1042-1051, 2010. ,
How ecology and landscape dynamics shape phylogenetic trees, Syst. Biol, vol.64, pp.590-607, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01176270
Birds, body size and the threat of extinction, Philos. Trans. R. Soc. Lond. B, vol.347, pp.205-212, 1995. ,
The sixth extinction: journeys among the lost and left behind, 2007. ,
Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages, Evolution, vol.45, pp.340-350, 1991. ,
Adaptive radiation and the topology of large phylogenies, Evolution, vol.47, pp.253-263, 1993. ,
Age-dependent speciation can explain the shape of empirical phylogenies, Syst. Biol, vol.64, pp.432-440, 2015. ,
Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees, Evolution, vol.46, pp.1818-1826, 1992. ,
Phylogenetically patterned speciation rates and extinction risks change the loss of evolutionary history during extinctions, Proc. R. Soc. Lond. B, vol.267, pp.613-620, 2000. ,
Taxon sampling and the accuracy of phylogenetic analyses, J. Syst. Evol, vol.46, pp.239-257, 2008. ,
The unified neutral theory of biodiversity and biogeography, 2001. ,
Differential human impact on the survival of genetically distinct avian lineages, Bird Conserv. Int, vol.9, pp.147-154, 1999. ,
Mammals on the EDGE: conservation priorities based on threat and phylogeny, PLoS One, vol.2, p.296, 2007. ,
IUCN red list categories and criteria: version 3.1, 2012. ,
The global diversity of birds in space and time, Nature, vol.491, pp.444-448, 2012. ,
Phylogeny and the selectivity of extinction in Australian marsupials, Anim. Conserv, vol.5, pp.135-142, 2002. ,
R package "cubature": adaptive multivariate integration over hypercubes, 2013. ,
Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas, Proc. Natl. Acad. Sci. USA, vol.109, pp.6620-6625, 2012. ,
R package "picante": R tools for integrating phylogenies and ecology, 2014. ,
The coalescent, Stoch. Proc. Appl, vol.13, pp.235-248, 1982. ,
Searching for evolutionary patterns in the shape of a phylogenetic tree, Evolution, vol.47, pp.1171-1181, 1993. ,
Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon), Proc. R. Soc. Lond. B, vol.273, pp.539-546, 2006. ,
Molecular clocks: four decades of evolution, Nat. Rev. Genet, vol.6, pp.654-662, 2005. ,
Birth-death models and coalescent point processes: the shape and probability of reconstructed phylogenies. Theor, Popul. Biol, vol.90, pp.113-128, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00936070
Predicting the loss of phylogenetic diversity under non-stationary diversification models, J. Theor. Biol, vol.337, pp.111-124, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00833585
Probabilistic models for the (sub) tree (s) of life, Braz. J. Probab. Stat, vol.31, pp.415-475, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01288230
The sixth extinction: patterns of life and the future of humankind, 1995. ,
Unravelling the structure of species extinction risk for predictive conservation science, Proc. Roy. Soc. Lond. B, vol.278, pp.1329-1338, 1710. ,
When can decreasing diversification rates be detected with molecular phylogenies and the fossil record?, Syst. Biol, vol.59, pp.646-659, 2010. ,
Explosive speciation in the New World Dendroica warblers, Proc. R. Soc. Lond. B, vol.266, pp.1629-1636, 1999. ,
Patterns of rarity and taxonomic group size in plants, Biol. Conserv, vol.126, pp.146-154, 2005. ,
The theory of island biogeography, 1967. ,
On the relative abundance of bird species, Proc. Natl. Acad. Sci. USA, vol.43, pp.293-295, 1957. ,
Estimating a binary character's effect on speciation and extinction, Syst. Biol, vol.56, pp.701-710, 2007. ,
Absolute diversification rates in Angiosperm clades, Evolution, vol.55, pp.1762-1780, 2001. ,
Rockfish (sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing, Biol. Conserv, vol.142, pp.1787-1796, 2009. ,
Phylogenies support outof-equilibrium models of biodiversity, Ecol. Lett, vol.18, pp.347-356, 2015. ,
Extinction vulnerability and selectivity: combining ecological and paleontological views, Annu. Rev. Ecol. Syst, vol.28, pp.495-516, 1997. ,
The ecological dynamics of clade diversification and community assembly, Am. Nat, vol.172, pp.270-284, 2008. ,
Clade age and not diversification rate explains species richness among animal taxa, Am. Nat, vol.169, pp.97-106, 2007. ,
Understanding how biodiversity unfolds through time under neutral theory, Philos. Trans. R. Soc. Lond. B, vol.371, pp.1-12, 2016. ,
Why does diversification slow down?, Trends Ecol. Evol, vol.29, pp.190-197, 2014. ,
Branch lengths on birth-death trees and the expected loss of phylogenetic diversity, Syst. Biol, vol.61, pp.195-203, 2012. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00715445
Inferring evolutionary process from phylogenetic tree shape, Q. Rev. Biol, vol.72, pp.31-54, 1997. ,
Tree balance and tree completeness, Evolution, vol.49, pp.379-384, 1995. ,
Holocene extinctions and the loss of feature diversity, Holocene extinctions, pp.279-338, 2009. ,
Reconciling molecular phylogenies with the fossil record, Proc. Natl. Acad. Sci, vol.108, pp.16327-16332, 2011. ,
Spatial patterns of phylogenetic diversity, Ecol. Lett, vol.14, pp.141-149, 2011. ,
Birth-death models in macroevolution, Annu. Rev. Ecol. Evol. Syst, vol.37, pp.1-17, 2006. ,
Extinction and the loss of evolutionary history, Science, vol.278, pp.692-694, 1997. ,
Tempo and mode of evolution revealed from molecular phylogenies, Proc. Natl. Acad. Sci, vol.89, pp.8322-8326, 1992. ,
The mean and variance of phylogenetic diversity under rarefaction, Methods Ecol. Evol, vol.4, pp.566-572, 2013. ,
APE: analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, pp.289-290, 2004. ,
URL : https://hal.archives-ouvertes.fr/ird-01887318
Phylogenetically clustered extinction risks do not substantially prune the tree of life, PLoS One, vol.6, p.23528, 2011. ,
Survivorship analysis of fossil taxa when realtime extinction rates vary: the paleogene planktonic foraminifera, Paleobiology, vol.18, pp.115-131, 1992. ,
Density-dependent cladogenesis in birds, PLoS Biol, vol.6, p.71, 2008. ,
The shape and temporal dynamics of phylogenetic trees arising from geographic speciation, Syst. Biol, vol.59, pp.660-673, 2010. ,
R package "sads": maximum likelihood models for species abundance distributions, 2015. ,
Dates from the molecular clock: how wrong can we be?, Trends Ecol. Evol, vol.22, pp.180-184, 2007. ,
Using interspecies phylogenies to test macroevolutionary hypotheses, New uses for new phylogenies, pp.153-168, 1996. ,
Phylogenetic approaches to the study of extinction, Annu. Rev. Ecol. Evol. Syst, vol.39, pp.301-319, 2008. ,
Nonrandom extinction and the loss of evolutionary history, Science, vol.288, pp.328-330, 2000. ,
Predicting extinction risk in declining species, Proc. Roy. Soc. Lond. B, vol.267, pp.1947-1952, 2000. ,
, Extinction. BioEssays, vol.22, pp.1123-1133, 2000.
Testing macro-evolutionary models using incomplete molecular phylogenies, Proc. R. Soc. Lond. B, vol.267, pp.2267-2272, 2000. ,
R: a language and environment for statistical computing, R Foundation for Statistical Computing, 2012. ,
Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions, Ecol. Lett, vol.12, pp.735-743, 2009. ,
Density-dependent diversification in North American wood warblers, Proc. R. Soc. Lond. B, vol.275, pp.2363-2371, 2008. ,
Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?, Evolution, vol.62, pp.1866-1875, 2008. ,
Clade age and species richness are decoupled across the eukaryotic tree of life, PLoS Biol, vol.10, p.1001381, 2012. ,
Stochastic models of phylogeny and the evolution of diversity, J. Geol, vol.81, pp.525-542, 1973. ,
Incorporating evolutionary measures into conservation prioritization, Conserv. Biol, vol.20, pp.1670-1678, 2006. ,
Speciation, extinction and diversity, Speciation and patterns of diversity, pp.257-277, 2009. ,
Global variation in the diversification rate of passerine birds, Ecology, vol.87, pp.2468-78, 2006. ,
History and diversity: explorations at the intersection of ecology and evolution, Am. Nat, vol.170, pp.56-70, 2007. ,
Rapid cladogenesis in marine fishes revisited, Evolution, vol.59, pp.1119-1127, 2005. ,
Present and future taxonomic selectivity in bird and mammal extinctions, Conserv. Biol, vol.12, pp.1365-1376, 1998. ,
A beta-splitting model for evolutionary trees, R. Soc. Open Sci, vol.3, p.160016, 2016. ,
Uncovering highertaxon diversification dynamics from clade age and species-richness data, Syst. Biol, vol.66, pp.367-378, 2016. ,
Taxon size predicts rates of rarity in vascular plants, Ecol. Lett, vol.4, issue.5, pp.464-469, 2001. ,
Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks, BMC Evol. Biol, vol.10, pp.1-21, 2010. ,
African cichlid fish: a model system in adaptive radiation research, Proc. R. Soc. Lond. B, vol.273, pp.1987-1998, 2006. ,
Testing whether certain traits have caused amplified diversification-an improved method based on a model of random speciation and extinction, Am. Nat, vol.142, pp.1019-1024, 1993. ,
Recovering speciation and extinction dynamics based on phylogenies, J. Evol. Biol, vol.26, pp.1203-1219, 2013. ,
On age and species richness of higher taxa, Am. Nat, vol.184, pp.447-455, 2014. ,
Global patterns and drivers of avian extinctions at the species and subspecies level, PLoS One, vol.7, p.47080, 2012. ,
Nonrandom extinction leads to elevated loss of angiosperm evolutionary history, Ecol. Lett, vol.11, pp.1047-1053, 2008. ,
Ecological species, multispecies, and oaks, Taxon, vol.25, pp.233-239, 1976. ,
Biodiversity conservation: does phylogeny matter?, Curr. Biol, vol.8, pp.379-381, 1998. ,
Phylogenies reveal new interpretation of speciation and the Red Queen, Nature, vol.463, pp.349-352, 2010. ,
Predicting loss of evolutionary history: where are we?, Biol. Rev, vol.0, pp.0-0, 2015. ,
Selective extinction and rapid loss of evolutionary history in the bird fauna, Proc. R. Soc. Lond. B, vol.268, pp.127-130, 2001. ,
Are we in the midst of the sixth mass extinction? A view from the world of amphibians, Proc. Natl. Acad. Sci. USA, vol.105, pp.11466-11473, 2008. ,
Divergent timing and patterns of species accumulation in lowland and highland neotropical birds, Evolution, vol.60, pp.842-855, 2006. ,
Molecular dating when rates vary, Trends Ecol. Evol, vol.20, pp.320-327, 2005. ,
A mathematical theory of evolution, based on the conclusions of, Trans. R. Soc. Lond. B, vol.213, pp.402-410, 1925. ,
Evidence from molecular systematics for decreased avian diversification in the Pleistocene Epoch, Proc. Natl. Acad. Sci, vol.92, pp.5832-5835, 1995. ,
Are rates of species diversification correlated with rates of morphological evolution?, Proceedings of the Royal Society of London B: Biological Sciences Pages rspb, 2009. ,
Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis, Systematic biology, vol.51, pp.866-872, 2002. ,
Evidence for adaptive radiation from a phylogenetic study of plant defenses, Proceedings of the National Academy of Sciences, vol.106, pp.18067-18072, 2009. ,
Probability distributions on cladograms. Pages 1-18 in Random discrete structures, 1996. ,
Stochastic models and descriptive statistics for phylogenetic trees, from yule to today, Statistical Science Pages, pp.23-34, 2001. ,
Quantifying age-dependent extinction from species phylogenies, Systematic biology, vol.65, pp.35-50, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01265486
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates, Proceedings of the National Academy of Sciences, vol.106, pp.13410-13414, 2009. ,
Do reefs drive diversification in marine teleosts? evidence from the pufferfish and their allies (order tetraodontiformes), Evolution, vol.61, pp.2104-2126, 2007. ,
Evolutionary food web model based on body masses gives realistic networks with permanent species turnover, Scientific reports, vol.5, p.10955, 2015. ,
A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement, Oikos, vol.117, pp.1227-1239, 2008. ,
A straightforward computational approach for measuring nestedness using quantitative matrices, Environmental Modelling & Software, vol.26, pp.173-178, 2011. ,
Classes of small-world networks, Proceedings of the national academy of sciences, vol.97, pp.11149-11152, 2000. ,
Associations between floral specialization and species diversity: cause, effect, or correlation?, Evolutionary Ecology, vol.23, p.159, 2009. ,
The measure of order and disorder in the distribution of species in fragmented habitat, Oecologia, vol.96, pp.373-382, 1993. ,
Pleistocene phylogeographic effects on avian populations and the speciation process, Proceedings of the Royal Society of London B: Biological Sciences, vol.265, pp.457-463, 1998. ,
Fast demographic traits promote high diversification rates of amazonian trees, Ecology Letters, vol.17, pp.527-536, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01555612
Age and rate of diversification of the hawaiian silversword alliance (compositae), Proceedings of the National Academy of Sciences, vol.95, pp.9402-9406, 1998. ,
Emergence of scaling in random networks, science, vol.286, pp.509-512, 1999. ,
Modularity and community detection in bipartite networks, Physical Review E, vol.76, p.66102, 2007. ,
Distinguishing the effects of the red queen and court jester on miocene mammal evolution in the northern rocky mountains, Journal of Vertebrate Paleontology, vol.21, pp.172-185, 2001. ,
Sister-group analysis in identifying correlates of diversification, Evol Ecol, vol.12, pp.751-754, 1998. ,
Revealing the factors that promote speciation, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.353, pp.241-249, 1998. ,
The nested assembly of plant-animal mutualistic networks, Proceedings of the National Academy of Sciences, vol.100, pp.9383-9387, 2003. ,
Extinction can be estimated from moderately sized molecular phylogenies, Evolution, vol.69, pp.1036-1043, 2015. ,
Detecting hidden diversification shifts in models of trait-dependent speciation and extinction, Systematic biology, vol.65, pp.583-601, 2016. ,
The red queen and the court jester: species diversity and the role of biotic and abiotic factors through time, science, vol.323, pp.728-732, 2009. ,
Speciation in the fossil record, Trends in Ecology & Evolution, vol.16, pp.405-411, 2001. ,
The signature of phylogenetic constraints on food-web structure, Ecological Complexity, vol.5, pp.132-139, 2008. ,
Self-similar fragmentations. Pages 319-340 in Annales de l, Institut Henri Poincare (B) Probability and Statistics, vol.38, 2002. ,
URL : https://hal.archives-ouvertes.fr/hal-00101984
Random fragmentation and coagulation processes vol, vol.102, 2006. ,
Which random processes describe the tree of life? a large-scale study of phylogenetic tree imbalance, Systematic Biology, vol.55, pp.685-691, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00370261
What do interaction network metrics tell us about specialization and biological traits, Ecology, vol.89, pp.3387-3399, 2008. ,
apTreeshape: statistical analysis of phylogenetic tree shape, Bioinformatics, vol.22, pp.363-364, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00370265
Environmental control of food web structure, Ecology, vol.64, pp.253-263, 1983. ,
Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom, Systematic Biology, vol.60, pp.410-419, 2011. ,
Detecting macroevolutionary self-destruction from phylogenies, Systematic biology, vol.65, pp.109-127, 2015. ,
Network topology: patterns and mechanisms in plantherbivore and host-parasitoid food webs, Journal of Animal Ecology, vol.80, pp.342-351, 2011. ,
Emergence of structural patterns in neutral trophic networks, PLoS One, vol.7, p.38295, 2012. ,
Empirical evaluation of neutral interactions in host-parasite networks, The American Naturalist, vol.183, pp.468-479, 2014. ,
Symmetree: whole-tree analysis of differential diversification rates, Bioinformatics, vol.21, pp.1709-1710, 2004. ,
Gunifrac: generalized unifrac distances. R package version 1, 2012. ,
A new time tree reveals earth history's imprint on the evolution of modern birds, Science Advances, vol.1, p.1501005, 2015. ,
Neutral community dynamics and the evolution of species interactions, The American Naturalist, vol.191, pp.421-434, 2018. ,
Phylogenetics: The theory and practice of phylogenetic systematics, 1982. ,
Macroevolutionary perspectives to environmental change, Ecology letters, vol.16, pp.72-85, 2013. ,
Deciphering the evolution of birdwing butterflies 150 years after alfred russel wallace, Scientific Reports, vol.5, p.11860, 2015. ,
Explosive radiation or cryptic mass extinction? interpreting signatures in molecular phylogenies, Evolution, vol.63, pp.2257-2265, 2009. ,
An extreme case of plant-insect codiversification: figs and figpollinating wasps, Systematic Biology, vol.61, pp.1029-1047, 2012. ,
Slowdowns in diversification rates from real phylogenies may not be real, Systematic biology, vol.59, pp.458-464, 2010. ,
A new method for handling missing species in diversification analysis applicable to randomly or nonrandomly sampled phylogenies, Systematic biology, vol.61, pp.785-792, 2012. ,
Neutral biodiversity theory can explain the imbalance of phylogenetic trees but not the tempo of their diversification, Evolution: International Journal of Organic Evolution, vol.65, pp.1841-1850, 2011. ,
Introducing the bipartite package: analysing ecological networks, vol.1, pp.0-2413793, 2008. ,
A method for detecting modules in quantitative bipartite networks, Methods in Ecology and Evolution, vol.5, pp.90-98, 2014. ,
Estimating the effect of competition on trait evolution using maximum likelihood inference, Systematic biology, vol.65, pp.700-710, 2016. ,
Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences, Molecular ecology resources, vol.15, pp.785-794, 2015. ,
Evolution restricts the coexistence of specialists and generalists: the role of trade-off structure, The American Naturalist, vol.163, pp.518-531, 2004. ,
Butterflies and plants: a study in coevolution, Evolution, vol.18, pp.586-608, 1964. ,
The dimensionality of ecological networks, Ecology letters, vol.16, pp.577-583, 2013. ,
Evolutionary history and ecological processes shape a local multilevel antagonistic network, Current Biology, vol.23, pp.1355-1359, 2013. ,
Species diversity can drive speciation, Nature, vol.434, p.1015, 2005. ,
A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence, The American Naturalist, vol.180, pp.75-89, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00859542
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record, Proc. R. Soc. B Page, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00859543
Estimating the duration of speciation from phylogenies, Evolution, vol.68, pp.2430-2440, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01108686
How reliably can we infer diversity-dependent diversification from phylogenies?, Methods in Ecology and Evolution, vol.7, pp.1092-1099, 2016. ,
Prolonging the past counteracts the pull of the present: protracted speciation can explain observed slowdowns in diversification, Systematic Biology, vol.61, pp.204-213, 2012. ,
Quantitative traits and diversification, Systematic biology, vol.59, pp.619-633, 2010. ,
Diversitree: comparative phylogenetic analyses of diversification in r, Methods in Ecology and Evolution, vol.3, pp.1084-1092, 2012. ,
Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies, Systematic biology, vol.58, pp.595-611, 2009. ,
Ecology: abundant equals nested, Nature, vol.500, p.411, 2013. ,
The ecological and evolutionary implications of merging different types of networks, Ecology letters, vol.14, pp.1170-1181, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01938647
Comparing the conservatism of ecological interactions in plant-pollinator and plant-herbivore networks, Population Ecology, vol.57, pp.29-36, 2015. ,
Host shifts and evolutionary radiations of butterflies, Proceedings of the Royal Society of London B: Biological Sciences, vol.277, pp.3735-3743, 2010. ,
Abundance and generalisation in mutualistic networks: solving the chicken-and-egg dilemma, Ecology letters, vol.19, pp.4-11, 2016. ,
Nestedness versus modularity in ecological networks: two sides of the same coin, Journal of Animal Ecology, vol.79, pp.811-817, 2010. ,
Relating traits to diversification: a simple test, The American Naturalist, vol.172, pp.102-115, 2008. ,
Macroevolution and the biological diversity of plants and herbivores, Proceedings of the National Academy of Sciences, vol.106, pp.18054-18061, 2009. ,
Local adaptation and the geometry of host-parasite coevolution, Ecology Letters, vol.5, pp.246-256, 2002. ,
How ecology and landscape dynamics shape phylogenetic trees, Systematic biology, vol.64, pp.590-607, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01176270
Patterns of parapatric speciation, Evolution, vol.54, pp.1126-1134, 2000. ,
, Bayesian data analysis, vol.2, 2014.
Posterior predictive assessment of model fitness via realized discrepancies, Statistica sinica, pp.733-760, 1996. ,
Sampling method influences the structure of plant-pollinator networks, Oikos, vol.120, pp.822-831, 2011. ,
Phylogenetic signal in plant pathogen-host range, Proceedings of the National Academy of Sciences, vol.104, pp.4979-4983, 2007. ,
Coevolution in multidimensional trait space favours escape from parasites and pathogens, Nature, vol.483, p.328, 2012. ,
Tempo and mode in plant breeding system evolution, Evolution, vol.66, pp.3701-3709, 2012. ,
Species selection maintains self-incompatibility, Science, vol.330, pp.493-495, 2010. ,
Phylogenetic inference of reciprocal effects between geographic range evolution and diversification, Systematic Biology, vol.60, pp.451-465, 2011. ,
Ecological interactions are evolutionarily conserved across the entire tree of life, Nature, vol.465, p.918, 2010. ,
Statistical challenges in null model analysis, Oikos, vol.121, pp.171-180, 2012. ,
The phylogenetic regression, Phil. Trans. R. Soc. Lond. B, vol.326, pp.119-157, 1989. ,
Reversible jump markov chain monte carlo computation and bayesian model determination, Biometrika, vol.82, pp.711-732, 1995. ,
Feasibility and coexistence of large ecological communities, Nature communications, vol.8, p.0, 2017. ,
Emergence of complexity in evolving niche-model food webs, Journal of theoretical biology, vol.251, pp.108-120, 2008. ,
Age-dependent speciation can explain the shape of empirical phylogenies, Systematic biology, vol.64, pp.432-440, 2015. ,
The generalized time variable reconstructed birth-death process, Journal of theoretical biology, vol.300, pp.265-276, 2012. ,
Continuous traits and speciation rates: Alternatives to statedependent diversification models, Methods in Ecology and Evolution, 2017. ,
, Phylogenies without fossils. Evolution, vol.48, pp.523-529, 1994.
Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees, Evolution, vol.46, pp.1818-1826, 1992. ,
Tree of life reveals clock-like speciation and diversification, Molecular biology and evolution, vol.32, pp.835-845, 2015. ,
Looking for trees in the forest: summary tree from posterior samples, BMC evolutionary biology, vol.13, p.221, 2013. ,
Coevolution and the diversification of life, The American Naturalist, vol.184, pp.425-438, 2014. ,
Time dependency of molecular rate estimates and systematic overestimation of recent divergence times, Molecular biology and evolution, vol.22, pp.1561-1568, 2005. ,
The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events, Journal of theoretical biology, vol.380, pp.321-331, 2015. ,
Inferring speciation and extinction rates under different sampling schemes, Molecular biology and evolution, vol.28, pp.2577-2589, 2011. ,
The shape of modern tree reconstruction methods, Systematic biology, vol.63, pp.436-441, 2014. ,
Phylometrics: an r package for detecting macroevolutionary patterns, using phylogenetic metrics and backward tree simulation, Methods in Ecology and Evolution, vol.7, pp.806-810, 2016. ,
The unified neutral theory of biodiversity and biogeography (mpb-32)(monographs in population biology), 2001. ,
Do phylogenetic methods produce trees with biased shapes?, Evolution, vol.50, pp.1418-1424, 1996. ,
A compound poisson process for relaxing the molecular clock, Genetics, vol.154, pp.1879-1892, 2000. ,
The likelihood node density effect and consequences for evolutionary studies of molecular rates, Evolution, vol.61, pp.2293-2307, 2007. ,
Key innovations and the ecology of macroevolution, Trends in ecology & evolution, vol.13, pp.31-36, 1998. ,
Individual-based models for adaptive diversification in high-dimensional phenotype spaces, Journal of theoretical biology, vol.390, pp.97-105, 2016. ,
Phylogenetic analysis of trophic associations, The American Naturalist, vol.168, pp.1-14, 2006. ,
Heritability at the species level: analysis of geographic ranges of cretaceous mollusks, Science, vol.238, pp.360-363, 1987. ,
Bitrophic interactions shape biodiversity in space, Proceedings of the National Academy of Sciences, vol.109, pp.4521-4526, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00783210
Ehrlich and raven revisited: mechanisms underlying codiversification of plants and enemies. Annual review of ecology, p.42, 2011. ,
The global diversity of birds in space and time, Nature, vol.491, p.444, 2012. ,
Invariant properties in coevolutionary networks of plant-animal interactions, Ecology letters, vol.6, pp.69-81, 2003. ,
Symbiosis catalyses niche expansion and diversification, Proceedings of the Royal Society of London B: Biological Sciences, vol.280, 2013. ,
Bayes factors, Journal of the american statistical association, vol.90, pp.773-795, 1995. ,
Reproductive isolation between two closely related hummingbird-pollinated neotropical gingers, Evolution, vol.60, pp.538-552, 2006. ,
The role of animal pollination in plant speciation: integrating ecology, geography, and genetics, Evolution, and Systematics, vol.40, pp.637-656, 2009. ,
Dynamics of north american breeding bird populations, Nature, vol.393, p.257, 1998. ,
The coalescent, Stoch. Proc. Appl, vol.13, pp.235-248, 1982. ,
Foraging adaptation and the relationship between food-web complexity and stability, Science, vol.299, pp.1388-1391, 2003. ,
Multilocus genetics and the coevolution of quantitative traits, Evolution, vol.60, pp.1321-1336, 2006. ,
Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern north american woodland salamanders (plethodontidae: Plethodon), Proceedings of the Royal Society of London B: Biological Sciences, vol.273, pp.539-546, 2006. ,
Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks, The American Naturalist, vol.179, pp.501-511, 2012. ,
Compartments revealed in food-web structure, Nature, vol.426, p.282, 2003. ,
A neutral-niche theory of nestedness in mutualistic networks, Oikos, vol.117, pp.1609-1618, 2008. ,
Inferring the rates of branching and extinction from molecular phylogenies, Evolution, vol.49, pp.694-704, 1995. ,
The reconstructed tree in the lineage-based model of protracted speciation, Journal of mathematical biology, vol.70, pp.367-397, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01122781
Birth-death models and coalescent point processes: The shape and probability of reconstructed phylogenies, Theoretical population biology, vol.90, pp.113-128, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00936070
Predicting the loss of phylogenetic diversity under non-stationary diversification models, Journal of theoretical biology, vol.337, pp.111-124, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00833585
Probabilistic models for the (sub) tree (s) of life, Brazilian Journal of Probability and Statistics, vol.31, pp.415-475, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01288230
A mixed relaxed clock model, Phil. Trans. R. Soc. B, vol.371, p.20150132, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-02053611
Structure in plantanimal interaction assemblages, Oikos, vol.113, pp.174-184, 2006. ,
Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02408778
When can decreasing diversification rates be detected with molecular phylogenies and the fossil record?, Systematic Biology, vol.59, pp.646-659, 2010. ,
Evolutionary emergence of size-structured food webs, Proceedings of the National Academy of Sciences, vol.102, pp.5761-5766, 2005. ,
Explosive speciation in the new world dendroica warblers. Proceedings of the, Royal Society of London B: Biological Sciences, vol.266, pp.1629-1636, 1999. ,
Quantitative and qualitative ? diversity measures lead to different insights into factors that structure microbial communities, Applied and environmental microbiology, vol.73, pp.1576-1585, 2007. ,
Confounding asymmetries in evolutionary diversification and character change, Evolution, vol.60, pp.1743-1746, 2006. ,
Estimating a binary character's effect on speciation and extinction, Systematic biology, vol.56, pp.701-710, 2007. ,
Null models for the number of evolutionary steps in a character on a phylogenetic tree, Evolution, vol.45, pp.1184-1197, 1991. ,
Absolute diversification rates in angiosperm clades, Evolution, vol.55, pp.1762-1780, 2001. ,
Ecological opportunity and the rate of morphological evolution in the diversification of greater antillean anoles, Evolution: International Journal of Organic Evolution, vol.64, pp.2731-2745, 2010. ,
Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity, 2018. ,
The species problem from the modeler's point of view, 2017. ,
Phylogenies support out-of-equilibrium models of biodiversity, Ecology letters, vol.18, pp.347-356, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01176247
A unifying comparative phylogenetic framework including traits coevolving across interacting lineages, Systematic biology, vol.66, pp.551-568, 2016. ,
The detection of disease clustering and a generalized regression approach, Cancer research, vol.27, pp.209-220, 1967. ,
A bayesian approach for detecting the impact of massextinction events on molecular phylogenies when rates of lineage diversification may vary, Methods in Ecology and Evolution, vol.7, pp.947-959, 2016. ,
How well can we detect lineage-specific diversification-rate shifts? a simulation study of sequential aic methods, Systematic biology, vol.65, pp.1076-1084, 2016. ,
Will a large complex system be stable, Nature, vol.238, p.413, 1972. ,
A comment on the red queen, The American Naturalist, vol.110, pp.325-330, 1976. ,
Strong and weak tests of macroecological theory, Oikos, vol.102, pp.679-685, 2003. ,
The ecological dynamics of clade diversification and community assembly, The American Naturalist, vol.172, pp.270-284, 2008. ,
Clade age and not diversification rate explains species richness among animal taxa, The American Naturalist, vol.169, pp.97-106, 2007. ,
Estimating diversification rates for higher taxa: Bamm can give problematic estimates of rates and rate shifts, Evolution, vol.72, pp.39-53, 2018. ,
Some ecologic and morphologic considerations in the evolution of higher taxonomic categories, Ornithologie als biologische Wissenschaft Pages, pp.84-88, 1949. ,
Understanding how biodiversity unfolds through time under neutral theory, Phil. Trans. R. Soc. B, vol.371, p.20150226, 2016. ,
Bayesian model selection with bamm: effects of the model prior on the inferred number of diversification shifts, Methods in Ecology and Evolution, vol.8, pp.37-46, 2017. ,
The phylogenetic study of adaptive zones: has phytophagy promoted insect diversification?, The American Naturalist, vol.132, pp.107-128, 1988. ,
Why does diversification slow down?, Trends in Ecology & Evolution, vol.29, pp.190-197, 2014. ,
Ecological networks and their fragility, Nature, vol.442, p.259, 2006. ,
Branch lengths on birth-death trees and the expected loss of phylogenetic diversity, Systematic biology, vol.61, pp.195-203, 2011. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00715445
Inferring evolutionary process from phylogenetic tree shape, The quarterly review of Biology, vol.72, pp.31-54, 1997. ,
Critically evaluating the theory and performance of bayesian analysis of macroevolutionary mixtures, Proceedings of the National Academy of Sciences, vol.113, pp.9569-9574, 2016. ,
Toward ecologically explicit null models of nestedness, Oecologia, vol.152, pp.763-777, 2007. ,
Phylogenetic approaches for studying diversification, Ecology letters, vol.17, pp.508-525, 2014. ,
Rpanda: an r package for macroevolutionary analyses on phylogenetic trees, Methods in Ecology and Evolution, vol.7, pp.589-597, 2016. ,
Reconciling molecular phylogenies with the fossil record, Proceedings of the National Academy of Sciences, vol.108, pp.16327-16332, 2011. ,
Extinction rates can be estimated from molecular phylogenies, Phil. Trans. R. Soc. Lond. B, vol.344, pp.77-82, 1994. ,
Extinction and the loss of evolutionary history, Science, vol.278, pp.692-694, 1997. ,
The reconstructed evolutionary process, Phil. Trans. R. Soc. Lond. B, vol.344, pp.305-311, 1994. ,
Tempo and mode of evolution revealed from molecular phylogenies, Proceedings of the National Academy of Sciences, vol.89, pp.8322-8326, 1992. ,
Analysis of weighted networks, Physical review E, vol.70, p.56131, 2004. ,
Ecological networks, nestedness and sampling effort, Journal of Ecology, vol.95, pp.1134-1141, 2007. ,
The temporal dimension of marine speciation, Evolutionary Ecology, vol.26, pp.393-415, 2012. ,
Coevolution and the architecture of mutualistic networks, Evolution, vol.67, pp.338-354, 2013. ,
The modularity of pollination networks, Proceedings of the National Academy of Sciences, vol.104, pp.19891-19896, 2007. ,
Frugivoryrelated traits promote speciation of tropical palms, Nature ecology & evolution, vol.1, 1903. ,
Trees of unusual size: biased inference of early bursts from large molecular phylogenies, PloS one, vol.7, p.43348, 2012. ,
Density-dependent cladogenesis in birds, PLoS biology, vol.6, p.71, 2008. ,
The shape and temporal dynamics of phylogenetic trees arising from geographic speciation, Systematic biology, vol.59, pp.660-673, 2010. ,
Metacommunity theory explains the emergence of food web complexity, Proceedings of the National Academy of Sciences, vol.108, pp.19293-19298, 2011. ,
How ecological networks evolve, 2016. ,
Testing macro-evolutionary models using incomplete molecular phylogenies, Proceedings of the Royal Society of London B: Biological Sciences, vol.267, pp.2267-2272, 2000. ,
, R: A Language and Environment for Statistical Computing. {R Foundation for Statistical Computing}, 2012.
Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions, Ecology letters, vol.12, pp.735-743, 2009. ,
Ecological limits on clade diversification in higher taxa, The American Naturalist, vol.173, pp.662-674, 2009. ,
Extinction rates should not be estimated from molecular phylogenies, Evolution, vol.64, pp.1816-1824, 2010. ,
Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees, PloS one, vol.9, p.89543, 2014. ,
Challenges in the estimation of extinction from molecular phylogenies: a response to beaulieu and o'meara, Evolution, vol.70, pp.218-228, 2016. ,
Reproductive isolation and the causes of speciation rate variation in nature, Biological Journal of the Linnean Society, vol.118, pp.13-25, 2016. ,
How to make any method" fail": Bamm at the kangaroo court of false equivalency, 2017. ,
Model inadequacy and mistaken inferences of trait-dependent speciation, Systematic Biology, vol.64, pp.340-355, 2015. ,
Fisse: A simple nonparametric test for the effects of a binary character on lineage diversification rates, Evolution, vol.71, pp.1432-1442, 2017. ,
A robust semi-parametric test for detecting trait-dependent diversification, Systematic Biology, vol.65, pp.181-193, 2015. ,
Density-dependent diversification in north american wood warblers, Proceedings of the Royal Society of London B: Biological Sciences, vol.275, pp.2363-2371, 2008. ,
Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?, Evolution, vol.62, pp.1866-1875, 2008. ,
Is bamm flawed? theoretical and practical concerns in the analysis of multi-rate diversification models, Systematic biology, vol.66, pp.477-498, 2017. ,
Clade age and species richness are decoupled across the eukaryotic tree of life, PLoS biology, vol.10, p.1001381, 2012. ,
Components of reproductive isolation between the monkeyflowers mimulus lewisii and m. cardinalis (phrymaceae), Evolution, vol.57, pp.1520-1534, 2003. ,
Incorporating evolutionary measures into conservation prioritization, Conservation Biology, vol.20, pp.1670-1678, 2006. ,
Under-parameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies, Systematic Biology, vol.54, pp.973-983, 2005. ,
Effects of phenotypic complementarity and phylogeny on the nested structure of mutualistic networks, Oikos, vol.116, pp.1919-1929, 2007. ,
The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species-level phylogenies, Molecular Ecology, vol.10, pp.721-735, 2001. ,
Estimating diversification rates from phylogenetic information, Trends in Ecology & Evolution, vol.22, pp.601-610, 2007. ,
History and diversity: explorations at the intersection of ecology and evolution, The American Naturalist, vol.170, pp.56-70, 2007. ,
Effects of sampling completeness on the structure of plant-pollinator networks, Ecology, vol.93, pp.1593-1603, 2012. ,
On the structural stability of mutualistic systems, Science, vol.345, p.1253497, 2014. ,
Species diversity gradients: we know more and less than we thought, Journal of mammalogy, vol.73, pp.715-730, 1992. ,
Protracted speciation revitalizes the neutral theory of biodiversity, Ecology Letters, vol.13, pp.716-727, 2010. ,
Unifying ecology and macroevolution with individualbased theory, Ecology letters, vol.18, pp.472-482, 2015. ,
The interplay between behavior and morphology in the evolutionary dynamics of resource specialization, The American Naturalist, vol.169, pp.34-52, 2006. ,
Nested species interactions promote feasibility over stability during the assembly of a pollinator community, Ecology and evolution, vol.6, pp.997-1007, 2016. ,
, phenograms. Systematic Biology, vol.21, pp.225-226, 1972.
Uncovering higher-taxon diversification dynamics from clade age and species-richness data, Systematic biology, vol.66, pp.367-378, 2016. ,
Estimating rates of speciation and evolution: a bias due to homoplasy, Cladistics, vol.6, pp.387-391, 1990. ,
Linkage rules for plant-pollinator networks: trait complementarity or exploitation barriers?, PLoS biology, vol.5, p.31, 2007. ,
On the trophic relations of insects: a food-web approach, The American Naturalist, vol.137, pp.597-638, 1991. ,
, Tree balance. Systematic Zoology, vol.39, pp.266-276, 1990.
Testing whether certain traits have caused amplified diversification: an improved method based on a model of random speciation and extinction, The American Naturalist, vol.142, pp.1019-1024, 1993. ,
Pattern and timing of diversification in yucca (agavaceae): specialized pollination does not escalate rates of diversification, Proceedings of the Royal Society of London B: Biological Sciences, vol.275, pp.249-258, 2008. ,
Mammalian phylogeny reveals recent diversification rate shifts, Proceedings of the National Academy of Sciences, vol.108, pp.6187-6192, 2011. ,
On age and species richness of higher taxa, The American Naturalist, vol.184, pp.447-455, 2014. ,
The ghost of nestedness in ecological networks, Nature communications, vol.4, p.1391, 2013. ,
Coevolution in ecosystems: Red queen evolution or stasis?, Evolution, vol.38, pp.870-880, 1984. ,
Abrupt community transitions and cyclic evolutionary dynamics in complex food webs, Journal of theoretical biology, vol.337, pp.181-189, 2013. ,
A markov chain monte carlo version of the genetic algorithm differential evolution: easy bayesian computing for real parameter spaces, Statistics and Computing, vol.16, pp.239-249, 2006. ,
Stability of ecological communities and the architecture of mutualistic and trophic networks, Science, vol.329, pp.853-856, 2010. ,
Evaluating the dynamics of coevolution among geographically structured populations, Ecology, vol.78, pp.1619-1623, 1997. ,
Geographic structure and dynamics of coevolutionary selection, Nature, vol.417, p.735, 2002. ,
Estimating the rate of evolution of the rate of molecular evolution, Molecular biology and evolution, vol.15, pp.1647-1657, 1998. ,
A consumer's guide to nestedness analysis, Oikos, vol.118, pp.3-17, 2009. ,
Niche partitioning due to adaptive foraging reverses effects of nestedness and connectance on pollination network stability, Ecology letters, vol.19, pp.1277-1286, 2016. ,
Phylogenetic evidence for pollinator-driven diversification of angiosperms, Trends in Ecology & Evolution, vol.27, pp.353-361, 2012. ,
A new evolutionary law, Evol Theory, vol.1, pp.1-30, 1973. ,
Degree distribution in plant-animal mutualistic networks: forbidden links or random interactions?, Oikos, vol.108, pp.421-426, 2005. ,
Evaluating multiple determinants of the structure of plant-animal mutualistic networks, Ecology, vol.90, pp.2039-2046, 2009. ,
Species abundance and the distribution of specialization in host-parasite interaction networks, Journal of Animal Ecology, vol.74, pp.946-955, 2005. ,
Phylogenies reveal new interpretation of speciation and the red queen, Nature, vol.463, p.349, 2010. ,
The role of biotic forces in driving macroevolution: beyond the red queen, Proc. R. Soc. B, vol.282, p.20150186, 2015. ,
Diversity-dependent cladogenesis and trait evolution in the adaptive radiation of the auks (aves: Alcidae), Evolution: International Journal of Organic Evolution, vol.67, pp.403-416, 2013. ,
Searching for efficient markov chain monte carlo proposal kernels, Proceedings of the National Academy of Sciences, vol.110, pp.19307-19312, 2013. ,
When does coevolution promote diversification?, The American Naturalist, vol.176, pp.802-817, 2010. ,
A mathematical theory of evolution, based on the conclusions of, Trans. R. Soc. Lond. B, vol.213, pp.402-410, 1925. ,
Evidence from molecular systematics for decreased avian diversification in the pleistocene epoch, Proceedings of the National Academy of Sciences, vol.92, pp.5832-5835, 1995. ,