D. Aldous, Probability distributions on cladograms, Random discrete structures, pp.1-18, 1996.

D. Aldous, Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today, Stat. Sci, vol.16, pp.23-34, 2001.

H. K. Alexander, A. Lambert, and T. Stadler, Quantifying agedependent extinction from species phylogenies, Syst. Biol, vol.65, pp.35-50, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01265486

M. Alfaro, F. Santini, C. Brock, H. Alamillo, A. Dornburg et al., Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates, Proc. Natl. Acad. Sci. USA, vol.106, pp.13410-13414, 2009.

M. P. Arbetman, G. Gleiser, C. L. Morales, P. Williams, and M. A. Aizen, 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.

J. E. Baillie, C. Hilton-taylor, and S. N. Stuart, A global species assessment, 2004.

A. D. Barnosky, N. Matzke, S. Tomiya, G. O. Wogan, B. Swartz et al., Has the Earth's sixth mass extinction already arrived?, Nature, vol.471, pp.51-57, 2011.

T. G. Barraclough, 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.

P. M. Bennett and I. P. Owens, Variation in extinction risk among birds: chance or evolutionary predisposition?, Proc. R. Soc. Lond. B, vol.264, pp.401-408, 1997.

J. Bertoin, Self-similar fragmentations, Ann. I.H. Poincaré, vol.38, pp.319-340, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00101984

J. Bertoin, Random fragmentation and coagulation processes, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00103015

J. Bielby, A. A. Cunningham, and A. Purvis, Taxonomic selectivity in amphibians: ignorance, geography or biology?, Anim. Conserv, vol.9, pp.135-143, 2006.

M. Blum and O. François, 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

F. Bokma, Testing for equal rates of cladogenesis in diverse taxa, Evolution, vol.57, pp.2469-2474, 2003.

A. Bonnet-lebrun, A. Manica, A. Eriksson, and A. S. Rodrigues, 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.

. Maliet and . Al,

N. Bortolussi, E. Durand, M. Blum, and O. François, apTreeshape: statistical analysis of phylogenetic tree shape, Bioinformatics, vol.22, pp.363-364, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00370265

M. Cardillo, G. M. Mace, J. L. Gittleman, and A. Purvis, Latent extinction risk and the future battlegrounds of mammal conservation, Proc. Roy. Soc. Lond. B, vol.103, pp.4157-4161, 2006.

M. Cardillo, C. D. Orme, and I. P. Owens, Testing for latitudinal bias in diversification rates : an example using, New World birds. Ecology, vol.86, pp.2278-2287, 2005.

R. K. Colwell and D. C. Lees, The mid-domain effect: geometric species richness, Trends Ecol. Evol, vol.15, pp.70-76, 2000.

N. Cusimano and S. S. Renner, Slowdowns in diversification rates from real phylogenies may not be real, Syst. Biol, vol.59, pp.458-464, 2010.

N. Cusimano, T. Stadler, and S. S. Renner, 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.

T. J. Davies, G. F. Smith, D. U. Bellstedt, J. S. Boatwright, B. Bytebier et al., Extinction risk and diversification are linked in a plant biodiversity hotspot, PLoS Biol, vol.9, pp.1-9, 2011.

T. J. Davies and K. Yessoufou, Revisiting the impacts of non-random extinction on the tree-of-life, Biol. Lett, vol.9, 2013.

N. A. Doran, A. J. Arnold, W. C. Parker, and F. W. Huffer, Is extinction age dependent?, Palaios, vol.21, pp.571-579, 2006.

W. J. Ewens, Mathematical population genetics 1: theoretical introduction, 2012.

D. P. Faith, Conservation evaluation and phylogenetic diversity, Biol. Conserv, vol.61, pp.1-10, 1992.

B. Faller, F. Pardi, and M. Steel, Distribution of phylogenetic diversity under random extinction, J. Theor. Biol, vol.251, pp.286-296, 2008.

S. Feng, The Poisson-Dirichlet distribution and related topics: models and asymptotic behaviors, 2010.

F. Forest, Calibrating the tree of life: fossils, molecules and evolutionary timescales, Ann. Bot, vol.104, pp.789-794, 2009.

L. O. Frishkoff, D. S. Karp, L. K. M'gonigle, C. D. Mendenhall, J. Zook et al., Loss of avian phylogenetic diversity in neotropical agricultural systems, Science, vol.345, pp.1343-1346, 2014.

S. A. Fritz and A. Purvis, 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.

F. Gascuel, R. Ferrière, R. Aguilée, and A. Lambert, How ecology and landscape dynamics shape phylogenetic trees, Syst. Biol, vol.64, pp.590-607, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01176270

K. J. Gaston and T. M. Blackburn, Birds, body size and the threat of extinction, Philos. Trans. R. Soc. Lond. B, vol.347, pp.205-212, 1995.

T. Glavin, The sixth extinction: journeys among the lost and left behind, 2007.

C. Guyer and J. B. Slowinski, Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages, Evolution, vol.45, pp.340-350, 1991.

C. Guyer and J. B. Slowinski, Adaptive radiation and the topology of large phylogenies, Evolution, vol.47, pp.253-263, 1993.

O. Hagen, K. Hartmann, M. Steel, and T. Stadler, Age-dependent speciation can explain the shape of empirical phylogenies, Syst. Biol, vol.64, pp.432-440, 2015.

S. B. Heard, Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees, Evolution, vol.46, pp.1818-1826, 1992.

S. B. Heard and A. O. Mooers, 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.

T. A. Heath, S. M. Hedtke, and D. M. Hillis, Taxon sampling and the accuracy of phylogenetic analyses, J. Syst. Evol, vol.46, pp.239-257, 2008.

S. Hubbell, The unified neutral theory of biodiversity and biogeography, 2001.

A. L. Hughes, Differential human impact on the survival of genetically distinct avian lineages, Bird Conserv. Int, vol.9, pp.147-154, 1999.

N. J. Isaac, S. T. Turvey, B. Collen, C. Waterman, and J. E. Baillie, Mammals on the EDGE: conservation priorities based on threat and phylogeny, PLoS One, vol.2, p.296, 2007.

. Iucn, IUCN red list categories and criteria: version 3.1, 2012.

W. Jetz, G. Thomas, J. Joy, K. Hartmann, and A. Mooers, The global diversity of birds in space and time, Nature, vol.491, pp.444-448, 2012.

C. N. Johnson, S. Delean, and A. Balmford, Phylogeny and the selectivity of extinction in Australian marsupials, Anim. Conserv, vol.5, pp.135-142, 2002.

S. G. Johnson and B. Narasimhan, R package "cubature": adaptive multivariate integration over hypercubes, 2013.

K. A. Jønsson, P. Fabre, S. A. Fritz, R. S. Etienne, R. E. Ricklefs et al., Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas, Proc. Natl. Acad. Sci. USA, vol.109, pp.6620-6625, 2012.

S. W. Kembel, D. D. Ackerly, S. P. Blomberg, W. K. Cornwell, P. D. Cowan et al., R package "picante": R tools for integrating phylogenies and ecology, 2014.

J. F. Kingman, The coalescent, Stoch. Proc. Appl, vol.13, pp.235-248, 1982.

M. Kirkpatrick and M. Slatkin, Searching for evolutionary patterns in the shape of a phylogenetic tree, Evolution, vol.47, pp.1171-1181, 1993.

K. H. Kozak, D. W. Weisrock, and A. Larson, 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.

S. Kumar, Molecular clocks: four decades of evolution, Nat. Rev. Genet, vol.6, pp.654-662, 2005.

A. Lambert and T. Stadler, 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

A. Lambert and M. Steel, 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

A. Lambert, 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

R. E. Leakey and R. Lewin, The sixth extinction: patterns of life and the future of humankind, 1995.

T. M. Lee and W. Jetz, Unravelling the structure of species extinction risk for predictive conservation science, Proc. Roy. Soc. Lond. B, vol.278, pp.1329-1338, 1710.

L. H. Liow, T. B. Quental, and C. R. Marshall, When can decreasing diversification rates be detected with molecular phylogenies and the fossil record?, Syst. Biol, vol.59, pp.646-659, 2010.

I. J. Lovette and E. Bermingham, Explosive speciation in the New World Dendroica warblers, Proc. R. Soc. Lond. B, vol.266, pp.1629-1636, 1999.

F. D. Lozano and M. W. Schwartz, Patterns of rarity and taxonomic group size in plants, Biol. Conserv, vol.126, pp.146-154, 2005.

R. Macarthur and E. Wilson, The theory of island biogeography, 1967.

R. H. Macarthur, On the relative abundance of bird species, Proc. Natl. Acad. Sci. USA, vol.43, pp.293-295, 1957.

W. P. Maddison, P. E. Midford, and S. P. Otto, Estimating a binary character's effect on speciation and extinction, Syst. Biol, vol.56, pp.701-710, 2007.

S. Magallon and M. J. Sanderson, Absolute diversification rates in Angiosperm clades, Evolution, vol.55, pp.1762-1780, 2001.

K. Magnuson-ford, T. Ingram, D. W. Redding, and A. Ø. Mooers, Rockfish (sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing, Biol. Conserv, vol.142, pp.1787-1796, 2009.

M. Manceau, A. Lambert, and H. Morlon, Phylogenies support outof-equilibrium models of biodiversity, Ecol. Lett, vol.18, pp.347-356, 2015.

M. L. Mckinney, Extinction vulnerability and selectivity: combining ecological and paleontological views, Annu. Rev. Ecol. Syst, vol.28, pp.495-516, 1997.

M. A. Mcpeek, The ecological dynamics of clade diversification and community assembly, Am. Nat, vol.172, pp.270-284, 2008.

M. A. Mcpeek and J. M. Brown, Clade age and not diversification rate explains species richness among animal taxa, Am. Nat, vol.169, pp.97-106, 2007.

O. Missa, C. Dytham, and H. Morlon, Understanding how biodiversity unfolds through time under neutral theory, Philos. Trans. R. Soc. Lond. B, vol.371, pp.1-12, 2016.

D. Moen and H. Morlon, Why does diversification slow down?, Trends Ecol. Evol, vol.29, pp.190-197, 2014.

A. Mooers, O. Gascuel, T. Stadler, H. Li, and M. Steel, 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

A. Mooers and S. Heard, Inferring evolutionary process from phylogenetic tree shape, Q. Rev. Biol, vol.72, pp.31-54, 1997.

A. O. Mooers, Tree balance and tree completeness, Evolution, vol.49, pp.379-384, 1995.

A. Ø. Mooers, S. J. Goring, S. T. Turvey, and T. S. Kuhn, Holocene extinctions and the loss of feature diversity, Holocene extinctions, pp.279-338, 2009.

H. Morlon, T. L. Parsons, and J. B. Plotkin, Reconciling molecular phylogenies with the fossil record, Proc. Natl. Acad. Sci, vol.108, pp.16327-16332, 2011.

H. Morlon, D. W. Schwilk, J. A. Bryant, P. A. Marquet, A. G. Rebelo et al., Spatial patterns of phylogenetic diversity, Ecol. Lett, vol.14, pp.141-149, 2011.

S. Nee, Birth-death models in macroevolution, Annu. Rev. Ecol. Evol. Syst, vol.37, pp.1-17, 2006.

S. Nee and R. M. May, Extinction and the loss of evolutionary history, Science, vol.278, pp.692-694, 1997.

S. Nee, A. O. Mooers, and P. H. Harvey, Tempo and mode of evolution revealed from molecular phylogenies, Proc. Natl. Acad. Sci, vol.89, pp.8322-8326, 1992.

D. A. Nipperess and F. A. Matsen, The mean and variance of phylogenetic diversity under rarefaction, Methods Ecol. Evol, vol.4, pp.566-572, 2013.

E. Paradis, J. Claude, and K. Strimmer, APE: analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, pp.289-290, 2004.
URL : https://hal.archives-ouvertes.fr/ird-01887318

R. K. Parhar and A. Ø. Mooers, Phylogenetically clustered extinction risks do not substantially prune the tree of life, PLoS One, vol.6, p.23528, 2011.

P. N. Pearson, Survivorship analysis of fossil taxa when realtime extinction rates vary: the paleogene planktonic foraminifera, Paleobiology, vol.18, pp.115-131, 1992.

A. B. Phillimore and T. D. Price, Density-dependent cladogenesis in birds, PLoS Biol, vol.6, p.71, 2008.

A. L. Pigot, A. B. Phillimore, I. P. Owens, and C. D. Orme, The shape and temporal dynamics of phylogenetic trees arising from geographic speciation, Syst. Biol, vol.59, pp.660-673, 2010.

P. I. Prado, M. D. Miranda, and A. Chalom, R package "sads": maximum likelihood models for species abundance distributions, 2015.

M. J. Pulquério and R. A. Nichols, Dates from the molecular clock: how wrong can we be?, Trends Ecol. Evol, vol.22, pp.180-184, 2007.

A. Purvis, P. Harvey, A. Leigh-brown, J. Maynard-smith, and S. Nee, Using interspecies phylogenies to test macroevolutionary hypotheses, New uses for new phylogenies, pp.153-168, 1996.

A. Purvis, Phylogenetic approaches to the study of extinction, Annu. Rev. Ecol. Evol. Syst, vol.39, pp.301-319, 2008.

A. Purvis, P. Agapow, J. L. Gittleman, and G. M. Mace, Nonrandom extinction and the loss of evolutionary history, Science, vol.288, pp.328-330, 2000.

A. Purvis, J. L. Gittleman, G. Cowlishaw, and G. M. Mace, Predicting extinction risk in declining species, Proc. Roy. Soc. Lond. B, vol.267, pp.1947-1952, 2000.

A. Purvis, K. E. Jones, and G. M. Mace, Extinction. BioEssays, vol.22, pp.1123-1133, 2000.

O. G. Pybus and P. H. Harvey, Testing macro-evolutionary models using incomplete molecular phylogenies, Proc. R. Soc. Lond. B, vol.267, pp.2267-2272, 2000.

R. Development-core and . Team, R: a language and environment for statistical computing, R Foundation for Statistical Computing, 2012.

D. L. Rabosky, 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.

D. L. Rabosky and I. J. Lovette, Density-dependent diversification in North American wood warblers, Proc. R. Soc. Lond. B, vol.275, pp.2363-2371, 2008.

D. L. Rabosky and I. J. Lovette, Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?, Evolution, vol.62, pp.1866-1875, 2008.

D. L. Rabosky, G. J. Slater, and M. E. Alfaro, Clade age and species richness are decoupled across the eukaryotic tree of life, PLoS Biol, vol.10, p.1001381, 2012.

D. M. Raup, S. J. Gould, T. J. Schopf, and D. S. Simberloff, Stochastic models of phylogeny and the evolution of diversity, J. Geol, vol.81, pp.525-542, 1973.

D. W. Redding and A. Ø. Mooers, Incorporating evolutionary measures into conservation prioritization, Conserv. Biol, vol.20, pp.1670-1678, 2006.

R. Ricklefs, R. Butlin, J. Bridle, and D. Schluter, Speciation, extinction and diversity, Speciation and patterns of diversity, pp.257-277, 2009.

R. E. Ricklefs, Global variation in the diversification rate of passerine birds, Ecology, vol.87, pp.2468-78, 2006.

R. E. Ricklefs, History and diversity: explorations at the intersection of ecology and evolution, Am. Nat, vol.170, pp.56-70, 2007.

L. Rüber and R. Zardoya, Rapid cladogenesis in marine fishes revisited, Evolution, vol.59, pp.1119-1127, 2005.

G. J. Russell, T. M. Brooks, M. M. Mckinney, and C. G. Anderson, Present and future taxonomic selectivity in bird and mammal extinctions, Conserv. Biol, vol.12, pp.1365-1376, 1998.

R. Sainudiin and A. Véber, A beta-splitting model for evolutionary trees, R. Soc. Open Sci, vol.3, p.160016, 2016.

L. L. Sánchez-reyes, H. Morlon, and S. Magallón, Uncovering highertaxon diversification dynamics from clade age and species-richness data, Syst. Biol, vol.66, pp.367-378, 2016.

M. W. Schwartz and D. Simberloff, Taxon size predicts rates of rarity in vascular plants, Ecol. Lett, vol.4, issue.5, pp.464-469, 2001.

R. S. Schwartz and R. L. Mueller, Branch length estimation and divergence dating: estimates of error in Bayesian and maximum likelihood frameworks, BMC Evol. Biol, vol.10, pp.1-21, 2010.

O. Seehausen, African cichlid fish: a model system in adaptive radiation research, Proc. R. Soc. Lond. B, vol.273, pp.1987-1998, 2006.

J. Slowinski and C. Guyer, 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.

T. Stadler, Recovering speciation and extinction dynamics based on phylogenies, J. Evol. Biol, vol.26, pp.1203-1219, 2013.

T. Stadler, D. L. Rabosky, R. E. Ricklefs, and F. Bokma, On age and species richness of higher taxa, Am. Nat, vol.184, pp.447-455, 2014.

J. K. Szabo, N. Khwaja, S. T. Garnett, and S. H. Butchart, Global patterns and drivers of avian extinctions at the species and subspecies level, PLoS One, vol.7, p.47080, 2012.

J. C. Vamosi and J. R. Wilson, Nonrandom extinction leads to elevated loss of angiosperm evolutionary history, Ecol. Lett, vol.11, pp.1047-1053, 2008.

L. Van-valen, Ecological species, multispecies, and oaks, Taxon, vol.25, pp.233-239, 1976.

D. P. Vazquez and J. L. Gittleman, Biodiversity conservation: does phylogeny matter?, Curr. Biol, vol.8, pp.379-381, 1998.

C. Venditti, A. Meade, and M. Pagel, Phylogenies reveal new interpretation of speciation and the Red Queen, Nature, vol.463, pp.349-352, 2010.

S. Veron, T. J. Davies, M. W. Cadotte, P. Clergeau, and S. Pavoine, Predicting loss of evolutionary history: where are we?, Biol. Rev, vol.0, pp.0-0, 2015.

V. Euler and F. , Selective extinction and rapid loss of evolutionary history in the bird fauna, Proc. R. Soc. Lond. B, vol.268, pp.127-130, 2001.

D. B. Wake and V. T. Vredenburg, 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.

J. T. Weir, Divergent timing and patterns of species accumulation in lowland and highland neotropical birds, Evolution, vol.60, pp.842-855, 2006.

J. J. Welch and L. Bromham, Molecular dating when rates vary, Trends Ecol. Evol, vol.20, pp.320-327, 2005.

Y. G. , A mathematical theory of evolution, based on the conclusions of, Trans. R. Soc. Lond. B, vol.213, pp.402-410, 1925.

R. Zink and J. Slowinski, Evidence from molecular systematics for decreased avian diversification in the Pleistocene Epoch, Proc. Natl. Acad. Sci, vol.92, pp.5832-5835, 1995.

D. C. Adams, C. M. Berns, K. H. Kozak, and J. J. Wiens, Are rates of species diversification correlated with rates of morphological evolution?, Proceedings of the Royal Society of London B: Biological Sciences Pages rspb, 2009.

P. Agapow and A. Purvis, 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.

A. A. Agrawal, M. Fishbein, R. Halitschke, A. P. Hastings, D. L. Rabosky et al., Evidence for adaptive radiation from a phylogenetic study of plant defenses, Proceedings of the National Academy of Sciences, vol.106, pp.18067-18072, 2009.

D. Aldous, Probability distributions on cladograms. Pages 1-18 in Random discrete structures, 1996.

D. J. Aldous, Stochastic models and descriptive statistics for phylogenetic trees, from yule to today, Statistical Science Pages, pp.23-34, 2001.

H. K. Alexander, A. Lambert, and T. Stadler, Quantifying age-dependent extinction from species phylogenies, Systematic biology, vol.65, pp.35-50, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01265486

M. E. Alfaro, F. Santini, C. Brock, H. Alamillo, A. Dornburg et al., 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.

M. E. Alfaro, F. Santini, and C. D. Brock, Do reefs drive diversification in marine teleosts? evidence from the pufferfish and their allies (order tetraodontiformes), Evolution, vol.61, pp.2104-2126, 2007.

K. T. Allhoff, D. Ritterskamp, B. C. Rall, B. Drossel, and C. Guill, Evolutionary food web model based on body masses gives realistic networks with permanent species turnover, Scientific reports, vol.5, p.10955, 2015.

M. Almeida-neto, P. Guimaraes, P. R. Guimarães, R. D. Loyola, and W. Ulrich, A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement, Oikos, vol.117, pp.1227-1239, 2008.

M. Almeida-neto and W. Ulrich, A straightforward computational approach for measuring nestedness using quantitative matrices, Environmental Modelling & Software, vol.26, pp.173-178, 2011.

L. A. Amaral, A. Scala, M. Barthelemy, and H. E. Stanley, Classes of small-world networks, Proceedings of the national academy of sciences, vol.97, pp.11149-11152, 2000.

W. S. Armbruster and N. Muchhala, Associations between floral specialization and species diversity: cause, effect, or correlation?, Evolutionary Ecology, vol.23, p.159, 2009.

W. Atmar and B. D. Patterson, The measure of order and disorder in the distribution of species in fragmented habitat, Oecologia, vol.96, pp.373-382, 1993.

J. C. Avise, 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.

T. R. Baker, R. T. Pennington, S. Magallon, E. Gloor, W. F. Laurance et al., 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

B. G. Baldwin and M. J. Sanderson, Age and rate of diversification of the hawaiian silversword alliance (compositae), Proceedings of the National Academy of Sciences, vol.95, pp.9402-9406, 1998.

A. Barabási and R. Albert, Emergence of scaling in random networks, science, vol.286, pp.509-512, 1999.

M. J. Barber, Modularity and community detection in bipartite networks, Physical Review E, vol.76, p.66102, 2007.

A. D. Barnosky, 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.

T. G. Barraclough, Sister-group analysis in identifying correlates of diversification, Evol Ecol, vol.12, pp.751-754, 1998.

T. G. Barraclough, A. P. Vogler, and P. H. Harvey, Revealing the factors that promote speciation, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.353, pp.241-249, 1998.

J. Bascompte, P. Jordano, C. J. Melián, and J. M. Olesen, The nested assembly of plant-animal mutualistic networks, Proceedings of the National Academy of Sciences, vol.100, pp.9383-9387, 2003.

J. M. Beaulieu and B. C. O'meara, Extinction can be estimated from moderately sized molecular phylogenies, Evolution, vol.69, pp.1036-1043, 2015.

J. M. Beaulieu and B. C. O'meara, Detecting hidden diversification shifts in models of trait-dependent speciation and extinction, Systematic biology, vol.65, pp.583-601, 2016.

M. J. Benton, 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.

M. J. Benton and P. N. Pearson, Speciation in the fossil record, Trends in Ecology & Evolution, vol.16, pp.405-411, 2001.

L. Bersier and P. Kehrli, The signature of phylogenetic constraints on food-web structure, Ecological Complexity, vol.5, pp.132-139, 2008.

J. Bertoin, 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

J. Bertoin, Random fragmentation and coagulation processes vol, vol.102, 2006.

M. G. Blum and O. François, 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

N. Blüthgen, J. Fründ, D. P. Vázquez, and F. Menzel, What do interaction network metrics tell us about specialization and biological traits, Ecology, vol.89, pp.3387-3399, 2008.

N. Bortolussi, E. Durand, M. Blum, and O. François, apTreeshape: statistical analysis of phylogenetic tree shape, Bioinformatics, vol.22, pp.363-364, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00370265

F. Briand, Environmental control of food web structure, Ecology, vol.64, pp.253-263, 1983.

C. D. Brock, L. J. Harmon, and M. E. Alfaro, Testing for temporal variation in diversification rates when sampling is incomplete and nonrandom, Systematic Biology, vol.60, pp.410-419, 2011.

L. Bromham, X. Hua, and M. Cardillo, Detecting macroevolutionary self-destruction from phylogenies, Systematic biology, vol.65, pp.109-127, 2015.

L. Cagnolo, A. Salvo, and G. Valladares, Network topology: patterns and mechanisms in plantherbivore and host-parasitoid food webs, Journal of Animal Ecology, vol.80, pp.342-351, 2011.

E. Canard, N. Mouquet, L. Marescot, K. J. Gaston, D. Gravel et al., Emergence of structural patterns in neutral trophic networks, PLoS One, vol.7, p.38295, 2012.

E. Canard, N. Mouquet, D. Mouillot, M. Stanko, D. Miklisova et al., Empirical evaluation of neutral interactions in host-parasite networks, The American Naturalist, vol.183, pp.468-479, 2014.

K. M. Chan and B. R. Moore, Symmetree: whole-tree analysis of differential diversification rates, Bioinformatics, vol.21, pp.1709-1710, 2004.

J. Chen, Gunifrac: generalized unifrac distances. R package version 1, 2012.

S. Claramunt and J. Cracraft, A new time tree reveals earth history's imprint on the evolution of modern birds, Science Advances, vol.1, p.1501005, 2015.

M. T. Coelho and T. F. Rangel, Neutral community dynamics and the evolution of species interactions, The American Naturalist, vol.191, pp.421-434, 2018.

D. H. Colless, Phylogenetics: The theory and practice of phylogenetic systematics, 1982.

F. L. Condamine, J. Rolland, and H. Morlon, Macroevolutionary perspectives to environmental change, Ecology letters, vol.16, pp.72-85, 2013.

F. L. Condamine, E. F. Toussaint, A. Clamens, G. Genson, F. A. Sperling et al., Deciphering the evolution of birdwing butterflies 150 years after alfred russel wallace, Scientific Reports, vol.5, p.11860, 2015.

M. D. Crisp and L. G. Cook, Explosive radiation or cryptic mass extinction? interpreting signatures in molecular phylogenies, Evolution, vol.63, pp.2257-2265, 2009.

A. Cruaud, N. Rønsted, B. Chantarasuwan, L. S. Chou, W. L. Clement et al., An extreme case of plant-insect codiversification: figs and figpollinating wasps, Systematic Biology, vol.61, pp.1029-1047, 2012.

N. Cusimano and S. S. Renner, Slowdowns in diversification rates from real phylogenies may not be real, Systematic biology, vol.59, pp.458-464, 2010.

N. Cusimano, T. Stadler, and S. S. Renner, 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.

T. J. Davies, A. P. Allen, L. Borda-de-Água, J. Regetz, and C. J. Melián, 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.

C. F. Dormann, B. Gruber, and J. Fründ, Introducing the bipartite package: analysing ecological networks, vol.1, pp.0-2413793, 2008.

C. F. Dormann and R. Strauss, A method for detecting modules in quantitative bipartite networks, Methods in Ecology and Evolution, vol.5, pp.90-98, 2014.

J. Drury, J. Clavel, M. Manceau, and H. Morlon, Estimating the effect of competition on trait evolution using maximum likelihood inference, Systematic biology, vol.65, pp.700-710, 2016.

D. Duchêne, S. Duchêne, and S. Y. Ho, Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences, Molecular ecology resources, vol.15, pp.785-794, 2015.

M. Egas, U. Dieckmann, and M. W. Sabelis, Evolution restricts the coexistence of specialists and generalists: the role of trade-off structure, The American Naturalist, vol.163, pp.518-531, 2004.

P. R. Ehrlich and P. H. Raven, Butterflies and plants: a study in coevolution, Evolution, vol.18, pp.586-608, 1964.

A. Eklöf, U. Jacob, J. Kopp, J. Bosch, R. Castro-urgal et al., The dimensionality of ecological networks, Ecology letters, vol.16, pp.577-583, 2013.

M. Elias, C. Fontaine, and F. F. Van-veen, Evolutionary history and ecological processes shape a local multilevel antagonistic network, Current Biology, vol.23, pp.1355-1359, 2013.

B. C. Emerson and N. Kolm, Species diversity can drive speciation, Nature, vol.434, p.1015, 2005.

R. S. Etienne and B. Haegeman, 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

R. S. Etienne, B. Haegeman, T. Stadler, T. Aze, P. N. Pearson et al., 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

R. S. Etienne, H. Morlon, and A. Lambert, Estimating the duration of speciation from phylogenies, Evolution, vol.68, pp.2430-2440, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01108686

R. S. Etienne, A. L. Pigot, and A. B. Phillimore, How reliably can we infer diversity-dependent diversification from phylogenies?, Methods in Ecology and Evolution, vol.7, pp.1092-1099, 2016.

R. S. Etienne and J. Rosindell, 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.

R. G. Fitzjohn, Quantitative traits and diversification, Systematic biology, vol.59, pp.619-633, 2010.

R. G. Fitzjohn, Diversitree: comparative phylogenetic analyses of diversification in r, Methods in Ecology and Evolution, vol.3, pp.1084-1092, 2012.

R. G. Fitzjohn, W. P. Maddison, and S. P. Otto, Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies, Systematic biology, vol.58, pp.595-611, 2009.

C. Fontaine, Ecology: abundant equals nested, Nature, vol.500, p.411, 2013.

C. Fontaine, P. R. Guimarães, S. Kéfi, N. Loeuille, J. Memmott et al., 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

C. Fontaine and E. Thébault, Comparing the conservatism of ecological interactions in plant-pollinator and plant-herbivore networks, Population Ecology, vol.57, pp.29-36, 2015.

J. A. Fordyce, Host shifts and evolutionary radiations of butterflies, Proceedings of the Royal Society of London B: Biological Sciences, vol.277, pp.3735-3743, 2010.

H. Fort, D. P. Vázquez, and B. L. Lan, Abundance and generalisation in mutualistic networks: solving the chicken-and-egg dilemma, Ecology letters, vol.19, pp.4-11, 2016.

M. A. Fortuna, D. B. Stouffer, J. M. Olesen, P. Jordano, D. Mouillot et al., Nestedness versus modularity in ecological networks: two sides of the same coin, Journal of Animal Ecology, vol.79, pp.811-817, 2010.

R. P. Freckleton, A. B. Phillimore, and M. Pagel, Relating traits to diversification: a simple test, The American Naturalist, vol.172, pp.102-115, 2008.

D. J. Futuyma and A. A. , Macroevolution and the biological diversity of plants and herbivores, Proceedings of the National Academy of Sciences, vol.106, pp.18054-18061, 2009.

S. Gandon, Local adaptation and the geometry of host-parasite coevolution, Ecology Letters, vol.5, pp.246-256, 2002.

F. Gascuel, R. Ferrière, R. Aguilée, and A. Lambert, How ecology and landscape dynamics shape phylogenetic trees, Systematic biology, vol.64, pp.590-607, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01176270

S. Gavrilets, H. Li, and M. D. Vose, Patterns of parapatric speciation, Evolution, vol.54, pp.1126-1134, 2000.

A. Gelman, J. B. Carlin, H. S. Stern, D. B. Dunson, A. Vehtari et al., Bayesian data analysis, vol.2, 2014.

A. Gelman, H. X.-l.-meng, and . Stern, Posterior predictive assessment of model fitness via realized discrepancies, Statistica sinica, pp.733-760, 1996.

R. H. Gibson, B. Knott, T. Eberlein, and J. Memmott, Sampling method influences the structure of plant-pollinator networks, Oikos, vol.120, pp.822-831, 2011.

G. S. Gilbert and C. O. Webb, Phylogenetic signal in plant pathogen-host range, Proceedings of the National Academy of Sciences, vol.104, pp.4979-4983, 2007.

R. T. Gilman, S. L. Nuismer, and D. Jhwueng, Coevolution in multidimensional trait space favours escape from parasites and pathogens, Nature, vol.483, p.328, 2012.

E. E. Goldberg and B. Igi?, Tempo and mode in plant breeding system evolution, Evolution, vol.66, pp.3701-3709, 2012.

E. E. Goldberg, J. R. Kohn, R. Lande, K. A. Robertson, S. A. Smith et al., Species selection maintains self-incompatibility, Science, vol.330, pp.493-495, 2010.

E. E. Goldberg, L. T. Lancaster, and R. H. Ree, Phylogenetic inference of reciprocal effects between geographic range evolution and diversification, Systematic Biology, vol.60, pp.451-465, 2011.

J. M. Gómez, M. Verdú, and F. Perfectti, Ecological interactions are evolutionarily conserved across the entire tree of life, Nature, vol.465, p.918, 2010.

N. J. Gotelli and W. Ulrich, Statistical challenges in null model analysis, Oikos, vol.121, pp.171-180, 2012.

A. Grafen, The phylogenetic regression, Phil. Trans. R. Soc. Lond. B, vol.326, pp.119-157, 1989.

P. J. Green, Reversible jump markov chain monte carlo computation and bayesian model determination, Biometrika, vol.82, pp.711-732, 1995.

J. Grilli, M. Adorisio, S. Suweis, G. Barabás, J. R. Banavar et al., Feasibility and coexistence of large ecological communities, Nature communications, vol.8, p.0, 2017.

C. Guill and B. Drossel, Emergence of complexity in evolving niche-model food webs, Journal of theoretical biology, vol.251, pp.108-120, 2008.

O. Hagen, K. Hartmann, M. Steel, and T. Stadler, Age-dependent speciation can explain the shape of empirical phylogenies, Systematic biology, vol.64, pp.432-440, 2015.

N. Hallinan, The generalized time variable reconstructed birth-death process, Journal of theoretical biology, vol.300, pp.265-276, 2012.

M. G. Harvey and D. L. Rabosky, Continuous traits and speciation rates: Alternatives to statedependent diversification models, Methods in Ecology and Evolution, 2017.

P. H. Harvey, R. M. May, and S. Nee, Phylogenies without fossils. Evolution, vol.48, pp.523-529, 1994.

S. B. Heard, Patterns in tree balance among cladistic, phenetic, and randomly generated phylogenetic trees, Evolution, vol.46, pp.1818-1826, 1992.

S. B. Hedges, J. Marin, M. Suleski, M. Paymer, and S. Kumar, Tree of life reveals clock-like speciation and diversification, Molecular biology and evolution, vol.32, pp.835-845, 2015.

J. Heled and R. R. Bouckaert, Looking for trees in the forest: summary tree from posterior samples, BMC evolutionary biology, vol.13, p.221, 2013.

D. H. Hembry, J. B. Yoder, and K. R. Goodman, Coevolution and the diversification of life, The American Naturalist, vol.184, pp.425-438, 2014.

S. Y. Ho, M. J. Phillips, A. Cooper, and A. J. Drummond, Time dependency of molecular rate estimates and systematic overestimation of recent divergence times, Molecular biology and evolution, vol.22, pp.1561-1568, 2005.

S. Höhna, The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events, Journal of theoretical biology, vol.380, pp.321-331, 2015.

S. Höhna, T. Stadler, F. Ronquist, and T. Britton, Inferring speciation and extinction rates under different sampling schemes, Molecular biology and evolution, vol.28, pp.2577-2589, 2011.

T. A. Holton, M. Wilkinson, and D. Pisani, The shape of modern tree reconstruction methods, Systematic biology, vol.63, pp.436-441, 2014.

X. Hua and L. Bromham, 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.

S. P. Hubbell, The unified neutral theory of biodiversity and biogeography (mpb-32)(monographs in population biology), 2001.

J. P. Huelsenbeck and M. Kirkpatrick, Do phylogenetic methods produce trees with biased shapes?, Evolution, vol.50, pp.1418-1424, 1996.

J. P. Huelsenbeck, B. Larget, and D. Swofford, A compound poisson process for relaxing the molecular clock, Genetics, vol.154, pp.1879-1892, 2000.

A. F. Hugall and M. S. Lee, The likelihood node density effect and consequences for evolutionary studies of molecular rates, Evolution, vol.61, pp.2293-2307, 2007.

J. P. Hunter, Key innovations and the ecology of macroevolution, Trends in ecology & evolution, vol.13, pp.31-36, 1998.

I. Ispolatov, V. Madhok, and M. Doebeli, Individual-based models for adaptive diversification in high-dimensional phenotype spaces, Journal of theoretical biology, vol.390, pp.97-105, 2016.

A. Ives and H. Godfray, Phylogenetic analysis of trophic associations, The American Naturalist, vol.168, pp.1-14, 2006.

D. Jablonski, Heritability at the species level: analysis of geographic ranges of cretaceous mollusks, Science, vol.238, pp.360-363, 1987.

F. Jabot and J. Bascompte, 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

N. Janz, Ehrlich and raven revisited: mechanisms underlying codiversification of plants and enemies. Annual review of ecology, p.42, 2011.

W. Jetz, G. Thomas, J. Joy, K. Hartmann, and A. Mooers, The global diversity of birds in space and time, Nature, vol.491, p.444, 2012.

P. Jordano, J. Bascompte, and J. M. Olesen, Invariant properties in coevolutionary networks of plant-animal interactions, Ecology letters, vol.6, pp.69-81, 2003.

J. B. Joy, Symbiosis catalyses niche expansion and diversification, Proceedings of the Royal Society of London B: Biological Sciences, vol.280, 2013.

R. E. Kass and A. E. Raftery, Bayes factors, Journal of the american statistical association, vol.90, pp.773-795, 1995.

K. M. Kay, Reproductive isolation between two closely related hummingbird-pollinated neotropical gingers, Evolution, vol.60, pp.538-552, 2006.

K. M. Kay and R. D. Sargent, The role of animal pollination in plant speciation: integrating ecology, geography, and genetics, Evolution, and Systematics, vol.40, pp.637-656, 2009.

T. H. Keitt and H. E. Stanley, Dynamics of north american breeding bird populations, Nature, vol.393, p.257, 1998.

J. F. Kingman, The coalescent, Stoch. Proc. Appl, vol.13, pp.235-248, 1982.

M. Kondoh, Foraging adaptation and the relationship between food-web complexity and stability, Science, vol.299, pp.1388-1391, 2003.

M. Kopp and S. Gavrilets, Multilocus genetics and the coevolution of quantitative traits, Evolution, vol.60, pp.1321-1336, 2006.

K. H. Kozak, D. W. Weisrock, and A. Larson, 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.

B. R. Krasnov, M. A. Fortuna, D. Mouillot, I. S. Khokhlova, G. I. Shenbrot et al., Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks, The American Naturalist, vol.179, pp.501-511, 2012.

A. E. Krause, K. A. Frank, D. M. Mason, R. E. Ulanowicz, and W. W. Taylor, Compartments revealed in food-web structure, Nature, vol.426, p.282, 2003.

A. Krishna, P. R. Guimaraes, P. Jordano, and J. Bascompte, A neutral-niche theory of nestedness in mutualistic networks, Oikos, vol.117, pp.1609-1618, 2008.

T. Kubo and Y. Iwasa, Inferring the rates of branching and extinction from molecular phylogenies, Evolution, vol.49, pp.694-704, 1995.

A. Lambert, H. Morlon, and R. S. Etienne, 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

A. Lambert and T. Stadler, 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

A. Lambert and M. Steel, 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

A. Lambert, 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

N. Lartillot, M. J. Phillips, and F. Ronquist, A mixed relaxed clock model, Phil. Trans. R. Soc. B, vol.371, p.20150132, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02053611

T. M. Lewinsohn, P. Prado, P. Jordano, J. Bascompte, and J. Olesen, Structure in plantanimal interaction assemblages, Oikos, vol.113, pp.174-184, 2006.

E. Lewitus and H. Morlon, Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02408778

L. H. Liow, T. B. Quental, and C. R. Marshall, When can decreasing diversification rates be detected with molecular phylogenies and the fossil record?, Systematic Biology, vol.59, pp.646-659, 2010.

N. Loeuille and M. Loreau, Evolutionary emergence of size-structured food webs, Proceedings of the National Academy of Sciences, vol.102, pp.5761-5766, 2005.

I. J. Lovette and E. Bermingham, Explosive speciation in the new world dendroica warblers. Proceedings of the, Royal Society of London B: Biological Sciences, vol.266, pp.1629-1636, 1999.

C. A. Lozupone, M. Hamady, S. T. Kelley, and R. Knight, 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.

W. P. Maddison, Confounding asymmetries in evolutionary diversification and character change, Evolution, vol.60, pp.1743-1746, 2006.

W. P. Maddison, P. E. Midford, and S. P. Otto, Estimating a binary character's effect on speciation and extinction, Systematic biology, vol.56, pp.701-710, 2007.

W. P. Maddison and M. Slatkin, Null models for the number of evolutionary steps in a character on a phylogenetic tree, Evolution, vol.45, pp.1184-1197, 1991.

S. Magallón and M. J. Sanderson, Absolute diversification rates in angiosperm clades, Evolution, vol.55, pp.1762-1780, 2001.

D. L. Mahler, L. J. Revell, R. E. Glor, and J. B. Losos, 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.

O. Maliet, F. Gascuel, and A. Lambert, Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity, 2018.

M. Manceau and A. Lambert, The species problem from the modeler's point of view, 2017.

M. Manceau, A. Lambert, and H. Morlon, Phylogenies support out-of-equilibrium models of biodiversity, Ecology letters, vol.18, pp.347-356, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01176247

M. Manceau, A. Lambert, and H. Morlon, A unifying comparative phylogenetic framework including traits coevolving across interacting lineages, Systematic biology, vol.66, pp.551-568, 2016.

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer research, vol.27, pp.209-220, 1967.

M. R. May, S. Höhna, and B. R. Moore, 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.

M. R. May and B. R. Moore, 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.

R. M. May, Will a large complex system be stable, Nature, vol.238, p.413, 1972.

M. Smith and J. , A comment on the red queen, The American Naturalist, vol.110, pp.325-330, 1976.

B. Mcgill, Strong and weak tests of macroecological theory, Oikos, vol.102, pp.679-685, 2003.

M. A. Mcpeek, The ecological dynamics of clade diversification and community assembly, The American Naturalist, vol.172, pp.270-284, 2008.

M. A. Mcpeek and J. M. Brown, Clade age and not diversification rate explains species richness among animal taxa, The American Naturalist, vol.169, pp.97-106, 2007.

A. L. Meyer and J. J. Wiens, Estimating diversification rates for higher taxa: Bamm can give problematic estimates of rates and rate shifts, Evolution, vol.72, pp.39-53, 2018.

A. H. Miller, Some ecologic and morphologic considerations in the evolution of higher taxonomic categories, Ornithologie als biologische Wissenschaft Pages, pp.84-88, 1949.

O. Missa, C. Dytham, and H. Morlon, Understanding how biodiversity unfolds through time under neutral theory, Phil. Trans. R. Soc. B, vol.371, p.20150226, 2016.

J. S. Mitchell and D. L. Rabosky, 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.

C. Mitter, B. Farrell, and B. Wiegmann, The phylogenetic study of adaptive zones: has phytophagy promoted insect diversification?, The American Naturalist, vol.132, pp.107-128, 1988.

D. Moen and H. Morlon, Why does diversification slow down?, Trends in Ecology & Evolution, vol.29, pp.190-197, 2014.

J. M. Montoya, S. L. Pimm, and R. V. Solé, Ecological networks and their fragility, Nature, vol.442, p.259, 2006.

A. Mooers, O. Gascuel, T. Stadler, H. Li, and M. Steel, 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

A. O. Mooers and S. B. Heard, Inferring evolutionary process from phylogenetic tree shape, The quarterly review of Biology, vol.72, pp.31-54, 1997.

B. R. Moore, S. Höhna, M. R. May, B. Rannala, and J. P. Huelsenbeck, 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.

J. E. Moore and R. K. Swihart, Toward ecologically explicit null models of nestedness, Oecologia, vol.152, pp.763-777, 2007.

H. Morlon, Phylogenetic approaches for studying diversification, Ecology letters, vol.17, pp.508-525, 2014.

H. Morlon, E. Lewitus, F. L. Condamine, M. Manceau, J. Clavel et al., Rpanda: an r package for macroevolutionary analyses on phylogenetic trees, Methods in Ecology and Evolution, vol.7, pp.589-597, 2016.

H. Morlon, T. L. Parsons, and J. B. Plotkin, Reconciling molecular phylogenies with the fossil record, Proceedings of the National Academy of Sciences, vol.108, pp.16327-16332, 2011.

S. Nee, E. C. Holmes, R. M. May, and P. H. Harvey, Extinction rates can be estimated from molecular phylogenies, Phil. Trans. R. Soc. Lond. B, vol.344, pp.77-82, 1994.

S. Nee and R. M. , Extinction and the loss of evolutionary history, Science, vol.278, pp.692-694, 1997.

S. Nee, R. M. May, and P. H. Harvey, The reconstructed evolutionary process, Phil. Trans. R. Soc. Lond. B, vol.344, pp.305-311, 1994.

S. Nee, A. O. Mooers, and P. H. Harvey, Tempo and mode of evolution revealed from molecular phylogenies, Proceedings of the National Academy of Sciences, vol.89, pp.8322-8326, 1992.

M. E. Newman, Analysis of weighted networks, Physical review E, vol.70, p.56131, 2004.

A. Nielsen and J. Bascompte, Ecological networks, nestedness and sampling effort, Journal of Ecology, vol.95, pp.1134-1141, 2007.

R. D. Norris and P. M. Hull, The temporal dimension of marine speciation, Evolutionary Ecology, vol.26, pp.393-415, 2012.

S. L. Nuismer, P. Jordano, and J. Bascompte, Coevolution and the architecture of mutualistic networks, Evolution, vol.67, pp.338-354, 2013.

J. M. Olesen, J. Bascompte, Y. L. Dupont, and P. Jordano, The modularity of pollination networks, Proceedings of the National Academy of Sciences, vol.104, pp.19891-19896, 2007.

R. E. Onstein, W. J. Baker, T. L. Couvreur, S. Faurby, J. Svenning et al., Frugivoryrelated traits promote speciation of tropical palms, Nature ecology & evolution, vol.1, 1903.

M. W. Pennell, B. A. Sarver, and L. J. Harmon, Trees of unusual size: biased inference of early bursts from large molecular phylogenies, PloS one, vol.7, p.43348, 2012.

A. B. Phillimore and T. D. Price, Density-dependent cladogenesis in birds, PLoS biology, vol.6, p.71, 2008.

A. L. Pigot, A. B. Phillimore, I. P. Owens, and C. D. Orme, The shape and temporal dynamics of phylogenetic trees arising from geographic speciation, Systematic biology, vol.59, pp.660-673, 2010.

P. Pillai, A. Gonzalez, and M. Loreau, Metacommunity theory explains the emergence of food web complexity, Proceedings of the National Academy of Sciences, vol.108, pp.19293-19298, 2011.

T. Poisot and D. Stouffer, How ecological networks evolve, 2016.

O. G. Pybus and P. H. Harvey, 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. Development-core and . Team, R: A Language and Environment for Statistical Computing. {R Foundation for Statistical Computing}, 2012.

D. L. Rabosky, 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.

D. L. Rabosky, Ecological limits on clade diversification in higher taxa, The American Naturalist, vol.173, pp.662-674, 2009.

D. L. Rabosky, Extinction rates should not be estimated from molecular phylogenies, Evolution, vol.64, pp.1816-1824, 2010.

D. L. Rabosky, Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees, PloS one, vol.9, p.89543, 2014.

D. L. Rabosky, Challenges in the estimation of extinction from molecular phylogenies: a response to beaulieu and o'meara, Evolution, vol.70, pp.218-228, 2016.

D. L. Rabosky, Reproductive isolation and the causes of speciation rate variation in nature, Biological Journal of the Linnean Society, vol.118, pp.13-25, 2016.

D. L. Rabosky, How to make any method" fail": Bamm at the kangaroo court of false equivalency, 2017.

D. L. Rabosky and E. E. Goldberg, Model inadequacy and mistaken inferences of trait-dependent speciation, Systematic Biology, vol.64, pp.340-355, 2015.

D. L. Rabosky and E. E. Goldberg, Fisse: A simple nonparametric test for the effects of a binary character on lineage diversification rates, Evolution, vol.71, pp.1432-1442, 2017.

D. L. Rabosky and H. Huang, A robust semi-parametric test for detecting trait-dependent diversification, Systematic Biology, vol.65, pp.181-193, 2015.

D. L. Rabosky and I. J. Lovette, Density-dependent diversification in north american wood warblers, Proceedings of the Royal Society of London B: Biological Sciences, vol.275, pp.2363-2371, 2008.

D. L. Rabosky and I. J. Lovette, Explosive evolutionary radiations: decreasing speciation or increasing extinction through time?, Evolution, vol.62, pp.1866-1875, 2008.

D. L. Rabosky, J. S. Mitchell, and J. Chang, Is bamm flawed? theoretical and practical concerns in the analysis of multi-rate diversification models, Systematic biology, vol.66, pp.477-498, 2017.

D. L. Rabosky, G. J. Slater, and M. E. Alfaro, Clade age and species richness are decoupled across the eukaryotic tree of life, PLoS biology, vol.10, p.1001381, 2012.

J. Ramsey, H. Bradshaw, and D. W. Schemske, Components of reproductive isolation between the monkeyflowers mimulus lewisii and m. cardinalis (phrymaceae), Evolution, vol.57, pp.1520-1534, 2003.

D. W. Redding and A. Ø. Mooers, Incorporating evolutionary measures into conservation prioritization, Conservation Biology, vol.20, pp.1670-1678, 2006.

L. J. Revell, L. J. Harmon, and R. E. Glor, 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.

E. L. Rezende, P. Jordano, and J. Bascompte, Effects of phenotypic complementarity and phylogeny on the nested structure of mutualistic networks, Oikos, vol.116, pp.1919-1929, 2007.

I. Ribera, T. Barraclough, and A. Vogler, 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.

R. E. Ricklefs, Estimating diversification rates from phylogenetic information, Trends in Ecology & Evolution, vol.22, pp.601-610, 2007.

R. E. Ricklefs, History and diversity: explorations at the intersection of ecology and evolution, The American Naturalist, vol.170, pp.56-70, 2007.

A. Rivera-hutinel, R. Bustamante, V. Marín, and R. Medel, Effects of sampling completeness on the structure of plant-pollinator networks, Ecology, vol.93, pp.1593-1603, 2012.

R. P. Rohr, S. Saavedra, and J. Bascompte, On the structural stability of mutualistic systems, Science, vol.345, p.1253497, 2014.

M. L. Rosenzweig, Species diversity gradients: we know more and less than we thought, Journal of mammalogy, vol.73, pp.715-730, 1992.

J. Rosindell, S. J. Cornell, S. P. Hubbell, and R. S. Etienne, Protracted speciation revitalizes the neutral theory of biodiversity, Ecology Letters, vol.13, pp.716-727, 2010.

J. Rosindell, L. J. Harmon, and R. S. Etienne, Unifying ecology and macroevolution with individualbased theory, Ecology letters, vol.18, pp.472-482, 2015.

C. Rueffler, T. J. Van-dooren, and J. A. Metz, The interplay between behavior and morphology in the evolutionary dynamics of resource specialization, The American Naturalist, vol.169, pp.34-52, 2006.

S. Saavedra, R. P. Rohr, J. M. Olesen, and J. Bascompte, Nested species interactions promote feasibility over stability during the assembly of a pollinator community, Ecology and evolution, vol.6, pp.997-1007, 2016.

M. Sackin, phenograms. Systematic Biology, vol.21, pp.225-226, 1972.

L. L. Sánchez-reyes, H. Morlon, and S. Magallón, Uncovering higher-taxon diversification dynamics from clade age and species-richness data, Systematic biology, vol.66, pp.367-378, 2016.

M. J. Sanderson, Estimating rates of speciation and evolution: a bias due to homoplasy, Cladistics, vol.6, pp.387-391, 1990.

L. Santamaría and M. A. Rodríguez-gironés, Linkage rules for plant-pollinator networks: trait complementarity or exploitation barriers?, PLoS biology, vol.5, p.31, 2007.

K. Schoenly, R. Beaver, and T. Heumier, On the trophic relations of insects: a food-web approach, The American Naturalist, vol.137, pp.597-638, 1991.

K. Shao and R. R. Sokal, Tree balance. Systematic Zoology, vol.39, pp.266-276, 1990.

J. B. Slowinski and C. Guyer, 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.

C. I. Smith, O. Pellmyr, D. M. Althoff, M. Balcazar-lara, J. Leebens-mack et al., 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.

T. Stadler, Mammalian phylogeny reveals recent diversification rate shifts, Proceedings of the National Academy of Sciences, vol.108, pp.6187-6192, 2011.

T. Stadler, D. L. Rabosky, R. E. Ricklefs, and F. Bokma, On age and species richness of higher taxa, The American Naturalist, vol.184, pp.447-455, 2014.

P. P. Staniczenko, J. C. Kopp, and S. Allesina, The ghost of nestedness in ecological networks, Nature communications, vol.4, p.1391, 2013.

N. C. Stenseth and J. Smith, Coevolution in ecosystems: Red queen evolution or stasis?, Evolution, vol.38, pp.870-880, 1984.

D. Takahashi, Å. Brännström, R. Mazzucco, A. Yamauchi, and U. Dieckmann, Abrupt community transitions and cyclic evolutionary dynamics in complex food webs, Journal of theoretical biology, vol.337, pp.181-189, 2013.

C. J. Ter-braak, 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.

E. Thébault and C. Fontaine, Stability of ecological communities and the architecture of mutualistic and trophic networks, Science, vol.329, pp.853-856, 2010.

J. N. Thompson, Evaluating the dynamics of coevolution among geographically structured populations, Ecology, vol.78, pp.1619-1623, 1997.

J. N. Thompson and B. M. Cunningham, Geographic structure and dynamics of coevolutionary selection, Nature, vol.417, p.735, 2002.

J. L. Thorne, H. Kishino, and I. S. Painter, Estimating the rate of evolution of the rate of molecular evolution, Molecular biology and evolution, vol.15, pp.1647-1657, 1998.

W. Ulrich, M. Almeida-neto, and N. J. Gotelli, A consumer's guide to nestedness analysis, Oikos, vol.118, pp.3-17, 2009.

F. S. Valdovinos, B. J. Brosi, H. M. Briggs, P. Moisset-de-espanés, R. Ramos-jiliberto et al., Niche partitioning due to adaptive foraging reverses effects of nestedness and connectance on pollination network stability, Ecology letters, vol.19, pp.1277-1286, 2016.

T. Van-der-niet and S. D. Johnson, Phylogenetic evidence for pollinator-driven diversification of angiosperms, Trends in Ecology & Evolution, vol.27, pp.353-361, 2012.

L. Van-valen, A new evolutionary law, Evol Theory, vol.1, pp.1-30, 1973.

D. P. Vázquez, Degree distribution in plant-animal mutualistic networks: forbidden links or random interactions?, Oikos, vol.108, pp.421-426, 2005.

D. P. Vázquez, N. P. Chacoff, and L. Cagnolo, Evaluating multiple determinants of the structure of plant-animal mutualistic networks, Ecology, vol.90, pp.2039-2046, 2009.

D. P. Vázquez, R. Poulin, B. R. Krasnov, and G. I. Shenbrot, Species abundance and the distribution of specialization in host-parasite interaction networks, Journal of Animal Ecology, vol.74, pp.946-955, 2005.

C. Venditti, A. Meade, and M. Pagel, Phylogenies reveal new interpretation of speciation and the red queen, Nature, vol.463, p.349, 2010.

K. L. Voje, Ø. H. Holen, L. H. Liow, and N. C. Stenseth, The role of biotic forces in driving macroevolution: beyond the red queen, Proc. R. Soc. B, vol.282, p.20150186, 2015.

J. T. Weir and S. Mursleen, 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.

Z. Yang and C. E. Rodríguez, Searching for efficient markov chain monte carlo proposal kernels, Proceedings of the National Academy of Sciences, vol.110, pp.19307-19312, 2013.

J. B. Yoder and S. L. Nuismer, When does coevolution promote diversification?, The American Naturalist, vol.176, pp.802-817, 2010.

Y. and G. , A mathematical theory of evolution, based on the conclusions of, Trans. R. Soc. Lond. B, vol.213, pp.402-410, 1925.

R. M. Zink and J. B. Slowinski, 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.