Methods

General approach

Our tree construction approach combines relaxed clock molecular trees of well-supported avian clades with a fossil calibrated backbone with representatives from each clade. It is neither a typical supertree (i.e. a combination of existing trees) nor a supermatrix approach (a single analysis applied to the entire genetic data matrix). We follow four steps:

1. Each species is assigned to one of 158 clades;
2. Relaxed-clock trees are generated for each clade;
3. Species without genetic information are partially constrained within their clade based on a combination of consensus trees from step 2 and taxonomic information. Placement of these species is then consistent with the partial constraints and a pure birth model of diversification;
4. Steps 2 and 3 generate trees for each clade that are based either on only species with genetic data (step 2) or on all species including those with and without genetic data (step 3). Construction of final trees is achieved by combining trees from either step 2 or step 3 with time-calibrated relaxed molecular clock backbone trees.

Expanded methods: Jetz et al. 2012, Supplementary Methods section 1.1.1

Backbone trees

We constructed and dated distributions of “backbone” trees each containing 158 tips. Each tip represents a crown clade in the complete avian tree. A portion of the topology of these backbone trees is highly constrained on the basis of strong support (posterior probabilities => 0.95) from studies by either Hackett et al. (2008) or Ericson et al. (2006). The remaining nodes with posterior probabilities <0.95 were not constrained (41 nodes based on Hackett et al. 2008 and 37 based on Ericson et al. 2006). The backbone contains 129 avian crown clades with more than four species and 29 smaller clades with four or fewer species.

Expanded methods: Jetz et al. 2012, Supplementary Methods section 1.1.2

Tree versions: Overview:

Version	Paper	Summary of changes	Change type
V1	Jetz et al. 2012	-	-
V2.i	Jetz et al. 2014	Crown psittaciform (Mopsitta tanta) calibration replaced with the younger stem psittaciform Avolatavis tenens	Backbone calibration
V2.ii	Jetz et al. 2014	Psittaciform Mopsitta tanta and debated charadriiform Morsoravis sedilis removed	Backbone calibration
V2.iii	Jetz et al. 2014	As in (ii), but with additional removal of the calibration for Anseriformes and altering the soft maximum age on the root of the tree	Backbone calibration

Tree versions: detailed:

V1 : Trees are taken from Jetz et al. 2012 and follow all methods described therein (see summary and links above).

V2 : Following Global Distribution and Conservation of Evolutionary Distinctness in Birds (Current Biology 2014; doi: http://dx.doi.org/10.1016/j.cub.2014.03.011). The trees developed for this study follow the same structure and taxonomy as Jetz et al (2012), but have different fossil calibrations. Revisions were made to the fossil calibration in the light of criticism from Mayr (2013). Mayrs suggested that four of the calibrations used in Jetz et al (2012) were problematic: the minimum ages of stem Cacatuidae + Psittacidae (or crown Psittaciformes), crown Charadriiformes, crown Anseriformes, and the soft maximum age for Neornithes.

V2.i Crown psittaciform (Mopsitta tanta) calibration replaced with the younger stem psittaciform Avolatavis tenens [Parrot_decisive]

For this version we removed the psittaciform Mopsitta tanta (Waterhouse et al. 2008) because it is represented by fragmentary remains and its affinities are uncertain with recent analyses suggesting that it may belong to the Threskiorinithae (Mayr and Bertelli 2011). We replaced the crown psittaciform calibration with the younger stem psittaciform, _Avolatavis tenens, _from the Fossil Butte member of the Green River Formation (Ksepka and Clarke 2012). Revising the psittaciform calibration allows (but does not enforce) a potentially younger (more recent) age for the Psittaciformes. Since it is also the closest calibration to the Passeriformes, it also allows a more recent origin for this major radiation.

V2.ii Psittaciform Mopsitta tanta and debated charadriiform Morsoravis sedilis removed [MayrParSho_decisive]

In addition to the removal (here without replacement) of _Mopsitta _we also removed the putative charadriiform _Morsoravis sedilis. _The affinities of this exceptionally well-preserved fossilhave been questioned, suggesting that it may not be a charadriiform (Mayr 2011, 2013). Indeed, phylogenetic evidence appears uncertain and challenges the perspective of Dyke and van Tuinen (Dyke and Van Tuinen 2004) and Bertelli et al. (Bertelli et al. 2010). Exclusion of _Morsoravis _allows a more recent origin for crown Charadriiformes.

V2.iii As in (ii), but with additional removal of the calibration for Anseriformes and altering the soft maximum age on the root of the tree [MayrAll_decisive]

This final calibration approach extended the changes detailed in (ii) by additionally removing the calibration for Anseriformes and altering the soft maximum age on the root of the tree. Mayr (2013) suggested that the placement of the putative Anseriform Vegavis iaai is “not unambiguous” and questioned specific anatomical features but did not provide explicit phylogenetic evidence to refute the conclusions of (Clarke et al. 2005). The apparently robust phylogenetic evidence in support of an Anseriform affiliation for Vegavis (Clarke et al. 2005) has led to its acceptance as a robust fossil calibration (e.g.Slack et al. 2006, Brown et al. 2007).However, Mayr’s concerns have since been corroborated by analyses suggesting that while Vegavis belongs to the crown Neornithes its position within the clade, and specifically as an Anseriform are not well supported (Lee et al. 2014). We originally (Jetz et al. 2012) used the Ornithurae fossil Gansus yumensis _(You et al. 2006)to provide a soft maximum age on the root of the tree. The justification was based on an extension of the logic of Benton and Donoghue (Benton and Donoghue 2007) who propose using the abundant Ornithurae taxa _Hesperornis, Baptornis _and _Ichthyornis from the Niobrara Chalk Formation of Kansus as a soft maximum age constraint. Ganus yumensis _falls within the Ornithurae grade (You et al. 2006)but heralds from much older deposits thus extending the maximum age constraint into the Early Cretaceous. The calibration density apportions only a 5% probability that the root age of the tree would be older than _Ganus yumensis. Mayr (2013) suggests that the choice of _Ganus yumensis _is arbitrary so here we revert to the original recommendation of Benton and Donoghue.

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