Supplementary Materials

Home , Columbimorphae, Coraciimorphae, Mesite

S1. Ne estimates from Indels on TENT, with comparisons to MP-EST* tree.

S2. Ne estimates from Gene Trees.

S3. Generation Length Sensitivity Analysis

Figures

Figure S1. Estimated Ne of size partitioned indels plotted on MP-EST* timetree time scale.

Figure S2. Estimated Ne of size partitioned indels plotted on TENT timetree time scale.

Figure S3. Estimated Ne of nucleotide gene trees plotted on MP-EST* timetree time scale.

Figure S4. Estimated Ne of indel gene trees plotted on MP-EST* timetree time scale.

Figure S5. Estimated Ne of nt+indel gene trees plotted on MP-EST* timetree time scale.

Figure S6. Estimated Ne of nucleotide gene trees plotted on TENT timetree time scale.

Figure S7. Estimated Ne of indel gene trees plotted on TENT timetree time scale.

Figure S8. Estimated Ne of nt+indel gene trees plotted on TENT timetree time scale.

Tables

Table S1. Ancestral state reconstruction of generation length.

Table S2. Generation lengths of species studied.

Table S3. Species sampled with clade names.

Table S4. Estimated Ne on TENT.

Table S5. Rank ordered Ne estimates >100 bp indels.

Table S6. Rank ordered Ne estimates >50 bp indels.

Table S7. Rank ordered Ne estimates >10 bp indels.

Table S8. Rank ordered Ne estimates >2 bp indels.

Table S9. Rank ordered Ne estimates all indels.

Table S10. Gene tree estimated Ne of nucleotide and indel data using MP-EST* tree.

Table S11. Gene tree estimated Ne of nucleotide and indel data using TENT.

Table S12. Upper quartile and median Ne estimates of TENT indel and gene trees.

Table S13. Rank ordered gene tree Ne estimates 1938 loci nucleotides MP-EST* vs TENT. Table S14. Rank ordered gene tree Ne estimates 1938 loci unwt indels MP-EST* vs TENT.

Table S15. Rank ordered gene tree Ne estimates 1938 loci wt25 indels MP-EST* vs TENT.

Table S16. Rank ordered gene tree Ne estimates 1938 loci nts+unwt Indels MP-EST* vs TENT.

Table S17. Rank ordered gene tree Ne estimates 1938 loci nts+wt25 Indels MP-EST* vs TENT.

Table S18. Rank ordered gene tree Ne estimates 2515 loci nucleotides MP-EST* vs TENT.

Table S19. Rank ordered gene tree Ne estimates 2515 loci unwt indels MP-EST* vs TENT.

Table S20. Rank ordered gene tree Ne estimates 2515 loci nts+unwt Indels MP-EST* vs TENT.

Table S21. Sensitivity analysis of generation length on MP-EST* tree.

Table S22. Sensitivity analysis of generation length on TENT.

S1. Ne estimates from Indels on TENT, with comparisons to MP-EST* tree.

The highest estimated Ne values ranged from 3,258, 842 to 26,127,434 in the TENT, with higher estimates in more size inclusive partitions (Table S4). Lowest estimated Ne values ranged from 110,471 to 329,562, with higher estimates in more size inclusive partitions. Ne estimates were generally similar in both absolute magnitude and relative rank order in the MP-EST* tree and TENT for those nodes branches that were present in both trees (Tables S5-S9). Notable exceptions, however, include the hoatzin+Cursorimorphae+waterbirds+Telluraves branch which differed by an order of magnitude between the MP-EST* tree and TENT within each indel partition and the Coraciimorphae branch which differed two-fold in most indel size partitions. All of the five highest estimated Ne’s were the same branches in both trees, with the exception of hoatzin+Cursorimorphae+waterbirds+Telluraves and Coraciimorphae. The highest Ne estimates common to both trees and across all indel size partitions was the Columbimorphae branch. Others that tended to rank high, however inconsistently across partitions, included bee-eater+woodpecker, Cursorimorphae, and turaco+bustard. Five branches in each of the MP- EST* tree and TENT are not present in the other; thus, cannot be compared. The lack of congruence in these trees involve rearrangement of very short internal branches and nearly equal levels of gene tree concordance/discordance with respect to these particular branches.

S2. Ne estimates from Gene Trees.

All gene tree analyses showed a distinct spike in estimated Ne near the K-Pg boundary when plotted against MP-EST* and TENT timetrees (Figures S3-S8; Tables S11-S12). Gene tree Ne estimates tended to be higher than indel Ne estimates whether or not they included indels. Indel gene trees yielded higher upper quartile and median Ne estimates than nucleotide gene trees (Table S10) but the difference was not consistent on any given branch, and nucleotide gene trees yielded the highest estimates overall. The highest gene tree Ne estimates were consistently higher using 1938 loci than with 2515 loci (Tables S11, S12). The highest gene tree Ne estimates were slightly higher when made on the MP-EST* tree than on the TENT when the highest scores were branches shared by both trees (Tables S13-S20). Gene trees tended to favor turaco-bustard as the highest estimated Ne when CBL was positive, or Columbimorphae when it was not. Cursorimorphae and bee-eater+woodpecker were also among the highest Ne estimates. Other branches such as hoatzin+Cursorimorphae+waterbirds+Telluraves, Otidimorphae+Columbimorphae, and waterbird+Telluraves, were high on one tree or the other but not comparable due either to zero CBL or non-recovered on both trees.

S3. Generation Length Sensitivity Analysis

We report the ancestral generation length that would be required to reduce our Ne estimates for each branch into the median and upper quartile of each size partition using the MP-EST* tree and the TENT (Tables S21, S22). The MP-EST* results are reported in the main text so only the TENT results are summarized here. Longer generation lengths were typically implied using short indels, which are characterized by shorter CBL. Among the clades with the highest estimated Ne, Columbimorphae required a generation length of 26.6-69.8 years (yrs) for the upper quartile and 46.4-143.3 yrs. Values for hoatzin+Cursorimorphae+waterbirds+Telluraves ranged from 7.2-52.3 yrs for the upper quartile and 13.0- 107.4 yrs for the median. Although turaco+bustard had among the highest estimated Ne in many size partitions, its implied generation lengths were lower: 20.6-24.8 yrs for the upper quartile and 33.6-45.0 yrs for the median.

a b >100 bp indels >100 bp indels

8.E+06 1.E+07

7.E+06

6.E+06

5.E+06

4.E+06 Ne 1.E+06 log Ne 3.E+06

2.E+06

1.E+06

0.E+00 1.E+05 70 60 50 40 30 20 10 0 70 60 50 40 30 20 10 0 MYBP MYBP c d >50 bp indels >50 bp indels

1.4E+07 1.0E+07 1.2E+07

1.0E+07

8.0E+06 Ne 1.0E+06 log Ne 6.0E+06

4.0E+06

2.0E+06

0.0E+00 1.0E+05 70 60 50 40 30 20 10 0 70 60 50 40 30 20 10 0 MYBP MYBP

e >10 bp indels f >10 bp indels

4.5E+07 4.0E+07 3.5E+07 1.E+07 3.0E+07 2.5E+07 Ne log Ne 2.0E+07 1.E+06 1.5E+07 1.0E+07 5.0E+06 0.0E+00 1.E+05 70 60 50 40 30 20 10 0 70 60 50 40 30 20 10 0 MYBP MYBP

g h >2 bp indels >2 bp indels

2.0E+07

1.0E+07

1.5E+07

1.0E+07 Ne log Ne 1.0E+06

5.0E+06

0.0E+00 1.0E+05 70 60 50 40 30 20 10 0 70 60 50 40 30 20 10 0 MYBP MYBP i j all indels all indels 3.0E+07

2.5E+07 1.E+07

2.0E+07

1.5E+07 Ne log Ne 1.E+06 1.0E+07

5.0E+06

0.0E+00 1.E+05 70 60 50 40 30 20 10 0 70 60 50 40 30 20 10 0 MYBP MYBP

Figure S1. Estimated Ne of size partitioned intronic indels plotted on MP-EST* timetree time scale. (a, b) >100 bp indel size class; (c, d) >50 bp indel size class; (e, f) >10 bp indel size class; (g, h) >12 bp indel size class; (i, j) all indels size class; (a, c, e, g, i) Ne in linear scale; (b, d, f, h, j) Ne in log scale. Symbols as in Figure 3 of main text. MYBP = million years before present.

Figure S2. Estimated Ne of size partitioned intronic indels plotted on TENT timetree time scale. (a, b) >100 bp indel size class; (c, d) >50 bp indel size class; (e, f) >10 bp indel size class; (g, h) >12 bp indel size class; (i, j) all indels size class; (a, c, e, g, i) Ne in linear scale; (b, d, f, h, j) Ne in log scale. MYBP = million years before present. Figure S3. Estimated Ne of nucleotide gene trees plotted on MP-EST* timetree. a, b, dataset of 1938 intronic loci with at least one >100 bp indel (chosen to match indel and combined nt+indel gene tree datasets, but indels not included in these gene trees) ; c, d, complete dataset of 2,515 intronic loci; a, c, Ne in linear scale; b, d, Ne in log scale. MYBP = million years before present.

Figure S4. Estimated Ne of indel gene trees plotted on MP-EST* timetree time scale. a, b, unweighted dataset of 1938 intronic loci with at least one >100 bp indel; c, d, complete dataset of 2,515 intronic loci with >100bp indels weighted 25x; e, f, dataset of 1938 loci with >100bp indels weighted 25x; a, c, e, g, i, Ne in linear scale; b, d, f, h, j, Ne in log scale. MYBP = million years before present.

Figure S5. Estimated Ne of gene trees composed of combined nucleotide and indel data plotted on the MP-EST* timetree time scale. a, b, unweighted dataset of 1938 intronic loci with at least one >100 bp indel; c, d, complete unweighted dataset of 2,515 intronic loci with >100bp indels weighted 25x; e, f, dataset of 1938 loci with >100bp indels weighted 25x; a, c, e, g, i, Ne in linear scale; b, d, f, h, j, Ne in log scale. MYBP = million years before present.

Figure S6. Estimated Ne of nucleotide gene trees plotted on TENT timetree. (a, b) dataset of 1938 intronic loci with at least one >100 bp indel (chosen to match indel and combined nt+indel gene tree datasets, but indels not included in these gene trees); (c, d) complete dataset of 2,515 intronic loci; (a, c) Ne in linear scale; (b, d) Ne in log scale. MYBP = million years before present. Figure S7. Estimated Ne of indel gene trees plotted on TENT timetree time scale. (a, b) unweighted dataset of 1938 intronic loci with at least one >100 bp indel; (c, d) complete dataset of 2,515 intronic loci with >100bp indels weighted 25x; (e, f) dataset of 1938 loci with >100bp indels weighted 25x; (a, c, e, g, i) Ne in linear scale; (b, d, f, h, j) Ne in log scale. MYBP = million years before present.

Figure S7. Estimated Ne of indel gene trees plotted on TENT timetree time scale. (a, b) unweighted dataset of 1938 intronic loci with at least one >100 bp indel; (c, d) complete dataset of 2,515 intronic loci with >100bp indels weighted 25x; (e, f) dataset of 1938 loci with >100bp indels weighted 25x; (a, c, e, g, i) Ne in linear scale; (b, d, f, h, j) Ne in log scale. MYBP = million years before present.

Figure S8. Estimated Ne of gene trees comosed of combined nucleotide and indel data plotted on the TENT timetree time scale. (a, b) unweighted dataset of 1938 intronic loci with at least one >100 bp indel; (c, d) complete unweighted dataset of 2,515 intronic loci with >100bp indels weighted 25x; (e, f) dataset of 1938 loci with >100bp indels weighted 25x; (a, c, e, g, i) Ne in linear scale; (b, d, f, h, j) Ne in log scale. MYBP = million years before present.

NA NA 9.83 3.75-15.92 8.58 5.37-11.79 8.67 6.42-10.93 9.25 6.98-11.53 7.89 5.03-10.75 6.47 2.00-10.94 7.66 4.34-10.98 5.43 2.14-8.72 9.05 4.88-13.22 8.99 3.27-14.72 9.14 5.91-12.37 8.38 3.69-13.08 8.31 6.02-10.61 7.62 4.23-11.01 7.578.26 3.91-11.23 5.76-10.76 5.97 2.21-9.72 7.64 3.53-11.75 14.99 11.10-18.88 10.40 7.44-13.36 10.33 7.20-13.45 a 2.09-8.72 2.11-9.65 3.78-16.03 5.14-12.10 5.18-11.54 6.19-10.78 7.08-11.84 5.25-10.79 2.05-11.05 4.79-13.47 3.16-14.64 6.13-12.54 3.57-13.06 5.83-10.58 6.04-10.61 4.08-10.81 7.58-13.51 3.86-11.17 5.64-10.70 3.46-11.69 7.31-13.60 4.49-11.06 11.50-18.90 Clade NA Palaeognathae 9.90 NA turaco+bustard 7.77 NA Passerea minusOtidimorphae 8.33 8.398.40 5.68-11.11 5.53-11.27 owl+Accipitrimorphae owl+Coraciimorphae 8.62 NA 8.55 6.04-11.05 7.45 2.14-12.76 Telluraves+waterbirds NA 8.92 6.77-11.06 8.81 5.33-12.30 7.91 4.82-11.01 Otidimorphae+Caprimulgimorphae NA 8.07 5.57-10.58 6.39 2.02-10.76 Telluraves 8.49 8.61 6.39-10.82 waterbirds 9.46 8.21 5.54-10.88 Otidimorphae 8.02 7.70 4.51-10.90 Oscines 5.41 7.76 3.66-11.86 Neornithes 8.90 4.22 1.62-6.81 Phaethontimorphae 9.34 8.19 5.35-11.03 penguins 15.20 8.46 5.95-10.97 Neognathae 8.31 5.70 2.08-9.33 Pelecaniformes 10.55 8.67 5.92-11.42 Passerea 8.20 9.93 7.42-12.43 mesite+sandgrouse 7.51 9.07 6.17-11.97 ibis+egret+pelican 10.46 10.50 7.84-13.15 ("Apodiformes") swift+hummingbird 6.55 11.09 8.17-14.01 Phoenicopterimorphae 9.13 10.21 6.76-13.66 Passerimorphae 7.44 16.92 14.74-19.10 Passeriformes 5.88 1.59-6.84 1.99-9.30 5.87-10.62 6.65-11.11 5.48-10.77 5.33-10.98 2.09-12.81 6.07-11.18 4.70-10.95 1.94-10.85 6.49-10.82 5.44-10.81 7.94-13.36 4.90-11.00 8.22-14.10 3.49-11.77 6.89-11.49 5.06-10.74 5.55-10.66 6.92-13.77 6.43-12.08 7.48-12.61 5.96-12.08 14.36-19.24 Table S1. Ancestral State Reconstruction of Generation Length. MP-EST* TENT ExaML MP-EST* TENT ExaML NA NA parrots 7.58 Gen Len 95% CI Gen Len 95%CI GenLen 95%CI Gen Len 95%CI ¥ recovered by ASTRAL; not in MP-EST* or TENT ExaML trees ExaML TENT or MP-EST* in not ASTRAL; by recovered cuckoo+bustard Coraciimorphae+Australaves 8.25 hoatzin+Cursorimorphae NA 8.60 6.18-11.03 8.36 trogon+hornbill+bee-eater+woodpecker hoatzin+Cursorimorphae+waterbirds 8.88 Coraciimorphae 8.12 Coraciimorphae minus mousebird 8.16 Galloanseres 7.45 hornbill+bee-eater+woodpecker 8.62 Columbimorphae 7.83 Galliformes 6.39 hoatzin+Cursorimorphae+waterbirds+Telluraves 8.65 Columbea 8.13 fulmar+penguins+Pelecaniformes 10.65 Caprimulgimorphae 7.95 fulmar+penguins 11.16 finch+zebrafinch 4.22 bee-eater+woodpecker 7.63 Cursorimorphae+waterbirdsEupasseriformes 9.19 5.65 falcon+Passerimorphae 7.90 AfroavesAustralaves NA 8.10 8.69 6.35-11.03 Neoaves 8.17 eaglesegret+pelican 10.34 16.80 Cursorimorphae 9.25 Aequornithia 10.05 Clade Accipitrimorphae 9.02 ¥

Table S2. Generation Lengths of Species Studied1. species years species years species years Acanthisitta chloris 3.5 Cuculus canorus 7 Nestor notabilis 12 Anas platyrhynchos 6.6 Dryobates pubescens 4.7 Nipponia nippon 10.1 Antrostomus carolinensis 5.6 Egretta garzetta 6.6 Opisthocomus hoazin 5.5 Apaloderma vittatum 7.3 Eurypyga helias 5.7 Pelecanus crispus 11 Aptenodytes forsteri 20.4 Falco peregrinus 6.8 Phaethon lepturus 11.1 Balearica regulorum 15.1 Gallus gallus 5 Phalacrocorax carbo 11.3 Buceros rhinoceros 18.4 Gavia stellata 9.8 Phoenicopterus ruber 15 Calypte anna 4.8 Geospiza fortis 4.3 Podiceps cristatus 7.1 Cariama cristata 6.7 Haliaeetus albicilla 17.5 Pterocles gutturalis 5.6 Cathartes aura 9.9 Haliaeetus leucocephalus 17.2 Pygoscelis adeliae 12 Chaetura pelagica 5.35 Leptosomus discolor 5.6 Struthio camelus 16.8 Charadrius vociferus 5.2 Manacus vitellinus 5.2 Taeniopygia guttata 3 Chlamydotis macqueenii 6.6 Meleagris gallopavo 7 Tauraco erythrolophus 3.3 Colius striatus 2.7 Melopsittacus undulatus 3.3 Tinamus guttatus 6.8 Columba livia 5.8 Merops nubicus 6.2 Tyto alba 6.2 Corvus brachyrhynchos 7.3 Mesitornis unicolor 4.2 1 source: International Union for Conservation of Nature and Natural Resources 2019; accessed 11/26/2019

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Table S3. Species Sampled with Clade Names. g

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Tin XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXX Struth clade Neoaves Galloanseres Galliformes Columbea Phoenicopterimorphae Columbimorphae mesite+sandgrouse Passerea Passerea minusOtidimorphae Otidimorphae turaco+bustard Caprimulgimorphae swift+hummingbird ("Apodiformes") hoatzin+Cursorimorphae+waterbirds+Telluraves hoatzin+Cursorimorphae+waterbirds Cursorimorphae+waterbirds Cursorimorphae waterbirds Phaethontimorphae Aequornithia fulmar+penguins+Pelecaniformes fulmar+penguins penguins Pelecaniformes ibis+egret+pelican egret+pelican Telluraves owl+Accipitrimorphae Accipitrimorphae eagles Coraciimorphae+Australaves Coraciimorphae mousebird minus Coraciimorphae trogon+hornbill+bee-eater+woodpecker hornbill+bee-eater+woodpecker bee-eater+woodpecker Australaves falcon+Passerimorphae Passerimorphae parrots Passeriformes Eupasseriformes oscines finch+zebrafinch

Table S5. Rank Ordered Ne Estimates >100 bp Indels MP-EST* MP-EST* TENT TENT 7,577,755 waterbirds Columbimorphae 3,258,842 3,397,326 Columbimorphae bee-eater+woodpecker 2,637,162 2,719,920 bee-eater+woodpecker Passerimorphae 2,401,615 2,547,649 Passerea minus Otidimorphae egret+pelican 2,097,806 2,477,913 Coraciimorphae+Australaves Australaves 1,530,834 2,415,922 Australaves Galloanseres 1,133,702 2,211,450 Passerimorphae Coraciimorphae 1,051,512 1,771,397 egret+pelican finch+zebrafinch 1,001,174 1,429,457 Cursorimorphae Columbea 969,276 1,391,856 Coraciimorphae Cursorimorphae 967,672 1,203,937 hoatzin+Cursorimorphae+waterbirds trogon+hornbill+bee-eater+woodpecker 904,287 1,072,286 Galloanseres Eupasseriformes 864,740 990,644 finch+zebrafinch swift+hummingbird ("Apodiformes") 766,158 874,551 Columbea Passerea 673,244 859,505 Eupasseriformes Otidimorphae 665,161 851,569 trogon+hornbill+bee-eater+woodpecker Galliformes 664,589 805,096 swift+hummingbird ("Apodiformes") mesite+sandgrouse 638,278 758,394 Otidimorphae Afroaves 568,605 675,283 Galliformes Phaethontimorphae 555,971 649,572 Passerea Neoaves 455,878 646,358 owl+Accipitrimorphae oscines 397,277 591,358 mesite+sandgrouse parrots 391,061 469,189 Phaethontimorphae Caprimulgimorphae 390,216 468,816 Neoaves Passeriformes 387,433 407,088 parrots falcon+Passerimorphae 359,868 405,168 Caprimulgimorphae eagles 336,240 402,051 oscinespenguins 331,223 396,584 Passeriformes hornbill+bee-eater+woodpecker 324,854 349,603 penguins ibis+egret+pelican 320,021 343,977 Phoenicopterimorphae Phoenicopterimorphae 289,472 340,398 ibis+egret+pelican Coraciimorphae minus mousebird 231,747 333,925 hornbill+bee-eater+woodpecker Pelecaniformes 219,043 328,344 falcon+Passerimorphae Aequornithia 213,440 328,240 eagles Accipitrimorphae 210,724 244,745 Coraciimorphae minus mousebird Telluraves 174,476 221,203 Accipitrimorphae fulmar+penguins 141,239 196,051 Telluraves fulmar+penguins+Pelecaniformes 110,471 189,686 Aequornithia Otidimorphae+Caprimulgimorphae undef 184,213 Pelecaniformes hoatzin+Cursorimorphae+waterbirds+Telluravesundef 120,354 fulmar+penguins hoatzin+Cursorimorphae undef 118,644 fulmar+penguins+Pelecaniformes waterbirds+Telluraves undef undefhoatzin+Cursorimorphae+waterbirds+Telluraveswaterbirds undef undef turaco+bustard turaco+bustardundef undef Cursorimorphae+waterbirds owl+Coraciimorphae undef red highlighted values - within UQ of size partition green highlighted values - within 3rd quartile of size partition blue highlighted text - branches not present in other tree undef - cannot be calculated due to zero CBL