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1.
Figure 6

Figure 6. From: Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Information content. Posterior 95% credibility interval width is plotted against posterior mean divergence time using the results from Multidivtime on TOptimal. Here R2 indicates the amount of information present in the data matrix and the regression coefficient is an estimate of the expected uncertainty that is independent of sequence length.

Joseph W Brown, et al. BMC Biol. 2008;6:6-6.
2.
Figure 5

Figure 5. From: Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Estimated rates of molecular evolution over time, in assessment of possible episodic evolution. Standardized inferred rate of sequence evolution (per data partition) is plotted against inferred age for internal nodes on the optimal mtDNA tree reconstruction (TOptimal) using Multidivtime. Time is given in millions of years before present. No support is shown for an accelerated rate accompanying initial avian diversification or following the K-Pg boundary (vertical dashed line).

Joseph W Brown, et al. BMC Biol. 2008;6:6-6.
3.
Figure 2

Figure 2. From: Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Alternative tree topologies. TConsensus (left) represents a conservative consensus estimate of avian familial relationships [53] (AICc = 421460.9166). TOptimal (right) is our optimal topology derived from a partitioned model maximum likelihood search in RAxML (AICc = 414160.2536). Some topological constraints were implemented in this search (see additional file 1). Solid circles and numbers indicate the placement of calibration points (see Table 5 for ages). Letters denote nodes whose age estimates are provided in Table 3.

Joseph W Brown, et al. BMC Biol. 2008;6:6-6.
4.
Figure 4

Figure 4. From: Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

A timeline for early avian evolution. Maximum clade credibility (MCC) chronogram inferred using the non-autocorrelated model of rate evolution in BEAST while allowing topology to vary (TFlexible). Time is given in millions of years before present. The vertical dashed line indicates the K-Pg boundary. Error bars (blue and green) represent 95% posterior credibility intervals and are only given for nodes that were present on more than 50% of the posterior sampled trees. An unambiguous ancient diversification is indicated by 37 credibility intervals restricted to the Cretaceous (green bars).

Joseph W Brown, et al. BMC Biol. 2008;6:6-6.
5.
Figure 3

Figure 3. From: Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Comparative timing of divergences for avian orders and families based on four different 'relaxed clock' methods. Chronograms based on the optimal mtDNA tree reconstruction (TOptimal) using r8s (top left), Dating5 (bottom left), PATHd8 (top right) and Multidivtime (bottom right); see methods for explanation of differences between analytical approaches. For legibility, error bars are removed and trees are pruned to the family level. Filled circles denote major clades: orange, Paleognathae; purple, Neognathae; blue, Galloanserae; green, Neoaves; red, Passeriformes. Time is given in millions of years before present. The vertical dashed lines indicate the K-Pg boundary. r8s, Dating5 and Multidivtime reconstructions support Cretaceous origin and diversification. PATHd8 alone supports Cretaceous origin but Tertiary diversification.

Joseph W Brown, et al. BMC Biol. 2008;6:6-6.
6.
Figure 1

Figure 1. From: Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages.

Different ways that fossil and molecular data date lineages. Time intervals defined by the horizontal dashed lines and vertical arrows pertain to age estimates for the divergence between hypothetical lineages X and Y. Even with a complete fossil record and perfect molecular clock a discrepancy is expected between fossil (FA) and molecular (MA) age estimates. As diagnostic morphological characters generally evolve (TMorphology) after species divergence (TSpecies), the fossil record will always underestimate (by δDiagnostic character) the true speciation time. Genetic data, on the other hand, will overestimate speciation time (by δCoalescence), as polymorphisms present during species divergence will coalesce some time in the past (TGene; related to the ancestral species effective population size). The genuine difference between molecular and morphological divergence times will thus be δTrue MA-FA. With a less complete fossil record, the oldest known fossil is unlikely to temporally correspond precisely to the origination of a diagnostic character delimiting X and Y, further decreasing FA by δOldest fossil. Under the more realistic scenario of lineage-specific rate heterogeneity and limited taxon/character sampling, errors associated with molecular methods (δClock error) may result in overestimation or underestimation of the true speciation time, although underestimates are bounded by the fossil constraint (δFossil error). The observed discrepancy in age estimates, δRealized MA-FA, may be considerably larger than expectations (δTrue MA-FA).

Joseph W Brown, et al. BMC Biol. 2008;6:6-6.

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