Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

By Michael E. Alfaro, F. Santini, Chad D. Brock, Hugo Alamillo, A. Dornburg, D. Rabosky, G. Carnevale, Luke J. Harmon. Proceedings of the National Academy of Sciences of the United States of America, 2009

852 citations recorded by the source corpus.

The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85% of all species as well as 3 slowdowns that have produced “living fossils.” In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/c4a766b297bfd9f9220dcc7e30d5213527588806

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Citations in the corpus

Neotropical Plant Evolution: Assembling the Big Picture (2013, background): “There is also a need to apply and test the new and increasingly sophisticated methods more widely to estimate rates of diversification, detect shifts in diversification rates and potentially tease apart whether these are attributable to changes in speciation or extinction rates or both (Alfaro et al”
The Bipedal Stem Crocodilian Poposaurus gracilis: Inferring Function in Fossils and Innovation in Archosaur Locomotion (2011, background): “Thus clades with comparatively few species, such as the 313 extant species of crown turtles (Testudines) with unexceptional diversification rates for vertebrates (Alfaro et al. 2009), might still have evolutionary innovations.”
The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas (2015, methodology): “…rates derived from either extant or fossil data are currently available, like MEDUSA (Modeling Evolutionary Diversification Using Stepwise Akaike Information Criterion, Alfaro et al., 2009), fossilMEDUSA, BayesRate (Silvestro, Schnitzler & Zizka, 2011), and PyRate (Silvestro et al., 2014).”
Neotropical diversification seen through glassfrogs (2014, methodology): “…complexity with instantaneous shifts in the rate of diversification at a single breakpoint on one branch of the tree where the descendant clade from this branch has its own set of speciation and extinction rates, whereas the remainder of the tree has different rates (Alfaro et al., 2009).”
Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity (2015, background): “…for other shortfalls; these estimates can be used to compare estimated species geographic ranges with occurrence records (Meyer et al. 2015), for example, or to evaluate the congruence of estimated phylogenies with partial phylogenetic trees based on available data (see Antonelli et al. 2014).”
Diversitree: comparative phylogenetic analyses of diversification in R (2012, methodology): “This is similar to Medusa (modelling evolutionary diversiﬁcation under stepwise AIC: Alfaro et al. 2009) for diversiﬁcation and Auteur (Eastman et al. 2011) for continuous character evolution.”
A Bayesian approach for detecting the impact of mass‐extinction events on molecular phylogenies when rates of lineage diversification may vary (2016, methodology): “Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society, Methods in Ecology and Evolution, 7, 947–959 Chan & Moore 2005; Alfaro et al. 2009; Rabosky 2014).”
Error in Phylogenetic Estimation for Bushes in the Tree of Life (2013, methodology): “Methods to characterize shi!s in the rate of speciation have been developed [94] and it might be possible to use these methods to parameterize realistic model trees with shi!ing rates of speciation and extinction rather than our simple two-parameter bush model.”
Five hundred million years of extinction and recovery: a phanerozoic survey of large‐scale diversity patterns in fishes (2012, neutral): “Global correlation of the Hangenberg horizon, and therefore the Devonian–Carboniferous boundary, is an ongoing project (Kaiser et al. 2008; Brezinski et al. 2009, 2010) which could reveal further examples of vertebrate faunal hiatus or sudden taxonomic turnover in even conformable deposits. Abrupt v”
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees (2014, methodology): “In addition, by adopting a Bayesian approach, we can algorithmically explore a greater number of candidate models than is possible with incremental (e.g., stepwise) information-theoretic approaches [20].”
Odd man out: why are there fewer plant species in African rain forests? (2014, methodology): “…generic dated phylogeny of palms in combination with accurate knowledge of generic diversity, and using a clade specific diversification model (Alfaro et al. 2009; Morlon 2014), Baker and Couvreur (2013b) inferred that none of the African palm lineages underwent a significant decrease in…”
Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. II. Diversification history and origin of regional assemblages (2013, methodology): “A lack of significant rate changes leading up to a genus does not mean that subclades within the genus, which are not resolved in our tree, have not undergone rate shifts (Alfaro et al., 2009).”
rfishbase: exploring, manipulating and visualizing FishBase data from R. (2012, result): “For instance, recent studies have attempted to identify whether reef-associated clades experience greater species diversification rates than non-reef-associated groups (Alfaro et al., 2009).”
Functional distinctiveness of major plant lineages (2014, methodology): “The process was repeated, with new values of Di,i and Ii,j calculated based on the refined neighbourhoods of each clade; this is analogous to the algorithm used by Alfaro et al. (2009).”
Morphology, Taxonomy, and Phylogeny of Triassic Pholidophorid Fishes (Actinopterygii, Teleostei) (2013, background): “…that includes over half of all living vertebrate species, is underscored by continued use of the type species of the genus, †Pholidophorus latiusculus, as a temporal calibration point for molecular trees of Teleostei (e.g., Alfaro et al., 2009; Betancur-R. et al., 2013; Broughton et al., 2013).”
Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates? (2019, background): “& 505 Harmon, L.J. (2009). Nine exceptional radiations plus high turnover explain species 506 diversity in jawed vertebrates. Proceedings of the National Academy of Sciences, 106, 507 13410–13414. 508 Barker, F.K., Burns, K.J., Klicka, J., Lanyon, S.M. & Lovette, I.J. (2013). Going to extremes: 509 ”