1. Volume 27, Issue 1, Pages 68-77 (January 2017)
Phylogenomics and Morphology of Extinct Paleognaths Reveal the Origin and Evolution of the Ratites 
Takahiro Yonezawa, Takahiro Segawa, Hiroshi Mori, Paula F. Campos, Yuichi Hongoh, Hideki Endo, Ayumi Akiyoshi, Naoki Kohno, Shin Nishida, Jiaqi Wu, Haofei Jin, Jun Adachi, Hirohisa Kishino, Ken Kurokawa, Yoshifumi Nogi, Hideyuki Tanabe, Harutaka Mukoyama, Kunio Yoshida, Armand Rasoamiaramanana, Satoshi Yamagishi, Yoshihiro Hayashi, Akira Yoshida, Hiroko Koike, Fumihito Akishinonomiya, Eske Willerslev, Masami Hasegawa 
Current Biology 
Volume 27, Issue 1, Pages (January 2017)
DOI: /j.cub
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2. Figure 1
Divergence Times of Aves as Inferred from Nuclear and Mitochondrial Genome Data of 873 kbp
(A) Divergence times were estimated using the Bayesian relaxed clock method. Tree topology was fixed in advance based on the phylogenomic tree (Figure S1). Nodal numbers indicate the divergence times (in mya), and nodal bars indicate 95% highest posterior densities. The nodes with gray error bars indicate the calibrated nodes (Table S2). The node with the green error bar and the node with the orange error bar indicate the first splits within the crown Aves and within the crown Palaeognathae, respectively. Detailed information of the Aepyornis maximums and Mullerornis used in this study are summarized in Table S1.
(B) Stability of divergence time estimates with respect to taxon sampling and fossil calibrations. Posterior means and 95% confidence intervals (indicated by error bars) of the first splits within the crown Aves (in green outline) and within the crown Palaeognathae (in orange outline) are shown, respectively (Figure S2; Table S3). “No calibrations” means that the root age of the crown Aves has no fossil constraint. “Ichthyornis (86.5 mya) as maximum bound” means the root age of the crown Aves was assumed to be younger than 86.5 mya. “Enaliornis (100.5 mya) as maximum bound” means the root age of the crown Aves was assumed to be younger than mya. “Excl. Tinamou” indicates tinamous were excluded from the analyses. “Excl. Neognaths” indicates neognaths were excluded from the analyses. “Aves” indicates the non-avian outgroup (reptiles) was excluded from the analyses. “All” indicates all taxa (ratites, tinamous, neognaths, and reptiles) were involved in the analyses.
See also Figure S1, Figure S2, Table S1, Table S2, and Table S3.
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3. Figure 2
Ancestral States Reconstruction by Molecular Evolutionary Rates
(A) Correlation between body mass (BM) and egg weight (EW) among Palaeognathae. The regression line (log10EW = 0.669 × log10BM −0.2174: R2 = 0.983) was estimated from extant Palaeognathae, excluding kiwis. Gray dashed lines indicate 95% CI (Tables S4 and S5). Kiwis and Aepyornis are outliers (orange dots). Body mass and egg weight of the common ancestor of kiwis and Aepyornis (red dot) was estimated as described in the main text; it is suggested that the common ancestor was also an outlier.
(B) Comparison of mitochondrial substitution rates among Aves (Table S5). The boxplots indicate the medians, the lower and upper quartiles, and the minimum and the maximum values. The dots on the left side of each boxplot indicate estimated mitochondrial substitution rates of respective branches. There are statistically significant differences between the substitution rates of the flightless birds (ratites and penguins) and those of the volant birds, and between those of the flightless birds and the ancestral Palaeognathae. However, there was no significant difference between the substitution rates of the volant birds and the ancestral Palaeognathae. ∗∗p < 0.01.
(C) Correlation between avian body weight and mitochondrial substitution rate. The regression line as inferred from the extant crown Aves (see taxonomy at upper right for explanation of dot colors) is log10BM = −0.0208x  (R2 = ) (Table S5). The estimated mitochondrial substitution rates of the ancestral paleognaths (black dots) were plotted on this regression line. The width of the vertical green shaded bar corresponds to the range of the estimated mitochondrial substitution rates in 3rd codon positions of the ancestral paleognaths. The height of the horizontal blue shaded bar indicates the estimated body masses based on the regression line. The body masses of the ancestral paleognaths predicted by this procedure are 1,500–2,800 g.
(A) and (C) are shown in detail in DataBaseFig1 and DataBaseFig2 at respectively. Illustrations by Takashi Oda. See also Tables S4 and S5.
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4. Figure 3
Phylogenetic Positions of Fossil Palaeognathae and Evolution of Their Geographic Distribution
(A) Maximum-likelihood tree as inferred from the morphologic data matrix originally summarized by Mayr [16]. The thick black branches indicate the backbone of the constrained tree. The phylogenetic positions of the fossil species (indicated †) without molecular data were examined in these constraints. Clades indicated by red branches consist of fossil species only. Asterisks indicate species distributed in the Southern Hemisphere. The nodal numbers indicate ML bootstrap probability/Bayesian posterior probability.
(B) Maximum-likelihood trees as inferred from the reconstructed morphologic data matrix from Houde [5]. Figure conventions are as in (A).
(C) Maximum-likelihood trees as inferred from the morphologic data matrix from Worthy et al. [17]. Figure conventions are as in (A). Nodal support values for 92 and 68 morphological characters without homoplasy (the characters coded as “missing data” convergently acquired in the flightless birds were included and excluded, respectively) are shown below and above the branches.
(D) Reconstruction of the ancestral geographic distribution areas. The species indicated in orange are distributed in the Northern Hemisphere (Laurasia-derived landmasses). The species indicated in blue are distributed in the Southern Hemisphere (Gondwana-derived landmasses). Fossil species without molecular data are indicated †. Species indicated by circles were used for the reconstruction of the ancestral geographic distribution. The pie charts in these circles are proportional to the posterior probabilities of the distribution areas. Species indicated by squares are fossil species and were not involved in the analysis. Phylogenetic positions of fossil species were based on (A)–(C). The phylogenetic relationship among Lithornis, Palaeotis, and crown Palaeognathae was assumed as a trifurcation. Although Houde [5]’s data preferred a sister relationship between Palaeotis and ostrich [74/0.91], the phylogenetic position of Palaeotis is unclear because of many missing data. The possible alternative positions of Palaeotis are shown on the tree based on Mayr [16]’s data (blue arrows in A). The divergence times of the fossil species in this figure are arbitrary. The phylogenetic positions of fossil species without branches (e.g., Remiornis) are unknown.
See also Figure S3.
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5. Figure 4 Palaeognathae Genomic Time Tree and Body Size
Size of a circle on a given node is proportional to estimated body weight (Table S5). The phylogenetic positions of fossil species are indicated by dashed lines (their divergence times are arbitrary). The colors of the branches indicate geographic distribution. Hypothetical ancestral distribution and fossil records of the paleognaths are indicated on the paleomaps (triangles indicate volant birds; squares indicate ratites; detailed information on fossil records is shown in DataBaseTable1 and DataBaseFig4 ( The thick red vertical line indicates the K–Pg boundary. The paleomaps were downloaded from Illustrations by Takashi Oda. See also Figure S3 and Table S5.
Current Biology  , 68-77DOI: ( /j.cub )
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