Appendix from S. Kleindorfer et al., Species Collapse via Hybridization in Darwin s Tree Finches (Am. Nat., vol. 183, no. 3, p.

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1 2014 by The University of Chicago. All rights reserved. DOI: / Appendix from S. Kleindorfer et al., Species Collapse via ization in Darwin s Tree Finches (Am. Nat., vol. 183, no. 3, p. 325) 1

2 Appendix from S. Kleindorfer et al., Species Collapse Via ization Supplementary Figures and Tables A B C Figure A1: Images of three sympatric tree finches from Floreana Island in that were retrospectively assigned to the following populations: A, genetic population 1 ( 2-year-old male); B, hybrid tree finch ( 4-year-old male); and C, genetic population 2 (yearling male). At the time of measurement in the field, the birds were categorized as small (A), intermediate (B), or large (C) tree finches. 2

3 Appendix from S. Kleindorfer et al., Species Collapse Via ization Ln Probability of the data (mean of 10 runs) A Number of genetic clusters (K) B 20 Delta K Number of genetic clusters (K) Figure A2: Estimates of the logarithm of probability of the data (A) and delta K (B), for K p 1 6 under the standard admixture model in STRUCTURE. 3

4 Appendix from S. Kleindorfer et al., Species Collapse Via ization Ln Probability of the data (mean of 10 runs) A Number of genetic clusters (K) B Delta K Number of genetic clusters (K) Figure A3: Estimates of the logarithm of probability of the data (A) and delta K (B), for K p 1 6 under the LOCPRIOR model in STRUCTURE. Table A1. Allelic variation at 10 microsatellite loci across two years ( and ) Locus N N A H E H O : Small-bodied finch: Gf Gf Gf Gf Gf Gf Gf Gf Gf Gf

5 Appendix from S. Kleindorfer et al., Species Collapse Via ization Table A1 (Continued) Locus N N A H E H O Intermediate finch: Gf Gf Gf Gf Gf Gf Gf Gf Gf Gf Large-bodied finch: Gf Gf Gf Gf Gf Gf Gf Gf Gf Gf : Small-bodied finch: Gf Gf Gf Gf Gf Gf Gf Gf Gf Gf Intermediate finch: Gf Gf Gf Gf Gf Gf Gf Gf Gf Gf Large-bodied finch: Gf Gf Gf Gf Gf Gf Gf Gf Gf Gf Note: Loci that depart significantly from Hardy-Weinberg equilibrium are indicated in bold. N p sample size; N A p number of alleles; H E p observed heterozygosity; and H O p expected heterozygosity. 5

6 Appendix from S. Kleindorfer et al., Species Collapse Via ization Table A2. Morphological trait values for putative species and year, prior to molecular genetic analysis Small tree finch (small-bodied) mean SD (N) Medium tree finch (intermediate) mean SD (N) Large tree finch (large-bodied) mean SD (N) Year Species Interaction F F F Beak-head (42) (30) (19) (26) (5) (24) 11.28*** *** 14.47*** Beak-feather (42) (30) (19) (26) (5) (24) 6.45** *** 9.80*** Beak-naris (42) (31) (19) (26) (5) (24) 16.90*** *** 10.60*** Naris diameter (42) (28) (19) (24) (5) (23) 22.68*** 6.30** 1.01 Beak depth (42) (31) (19) (26) (5) (24) *** 9.60*** Beak width (42) (31) (19) (26) (5) (24) *** 6.80*** Tarsus (42) (30) (19) (26) (5) (24) 5.58* *** Mass (9) (30) (4) (24) 19.4 (5) (24) Note: Shown are mean values and standard deviations for males (females excluded). Results of MANOVA show the effects of year, species, and the interaction term year # species for male morphology. The F values are shown. *P!.05. **P!.01. ***P!.001. Table A3. Details of MCLUST models with the highest Bayesian Information Criteria (BIC) from analyses of and data Model 1 (best) Model 2 Model : Model name EEE VEV EEV BIC value 1, , (DBIC p.08) 1, (DBIC p 4.20) Clusters : Model name EEV VEV EEE BIC value (DBIC p.13) (DBIC p.49) Clusters : Model name EEE VVV VEV BIC value (DBIC p 2.54) (DBIC p 2.57) Clusters Note: Absolute values of the BIC have no interpretation, but larger numbers indicate that the best model fit in terms of cluster size, shape, and orientation. Models within 2 BIC units of the best model are considered to have substantial support, whereas models with BIC values between 2 and 7 can be said to have some support. All models were of ellipsoidal distribution, with equal (E), or variable (V) volume, shape, and orientation, respectively (Fraley and Raftery 2006). Table A4. Allele frequency table for microsatellite loci for each genetic cluster and year identified using STRUCTURE Locus, allele/n 6 Gf01: N a a b b

7 Appendix from S. Kleindorfer et al., Species Collapse Via ization Table A4 Locus, allele/n (Continued) a a a Gf03: N a a Gf04: N Gf05: N a a Gf06: N Gf07: N a a a Gf12: N a b b 7

8 Appendix from S. Kleindorfer et al., Species Collapse Via ization Table A4 (Continued) Locus, allele/n Gf13: N a a a a b b Note: N p sample size. was composed predominantly of small morphs, cluster 2 was comprised predominantly of large morphs, and the hybrid cluster was composed mainly of individuals with intermediate morphology. a Private alleles for a single year. b Private alleles in both years. Table A5. Comparison of male morphology for tree finches on Floreana Island David Lack: historical species Kleindorfer and O Connor: contemporary genetic population ANOVA results Species (historical)/genetic population (contemporary) N Mean SD (range) N Mean SD (range) F, P Beak depth: Small tree finch/genetic population ( ) ( ) 22.70,!.001 Medium tree finch/hybrid cluster ( ) ( ) 83.87,!.001 Large tree finch/hybrid ( ) ( ) 88.86,!.001 Beak-naris: Small tree finch/genetic population ( ) ( ) 1.86,.17 Medium tree finch/hybrid cluster ( ) ( ) ,!.001 Large tree finch/genetic population ,!.001 Wing: Small tree finch/genetic population (60 68) (56 70) 40.80,!.001 Medium tree finch/hybrid cluster (66 74) (60 71) 55.63,!.001 Large tree finch/genetic population (70 74) (62 72) 13.40,!.001 Note: The table shows a comparison of measurements taken by D. Lack (for birds collected between 1888 and 1906) and S. Kleindorfer and J. O Connor ( and ). The species categories (small, medium, and large tree finch) refer to the historical classifications ( ), whereas the genetic population categories (genetic population 1 or 2 or hybrid) refer to contemporary populations (, ). The statistical results are for ANOVA analyses with male morphological traits as the dependent variables, and species/genetic population and sampling year as fixed factors. Literature Cited Only in Appendix Fraley, C., and A. E. Raftery MCLUST version 3 for R: normal mixture modeling and model-based clustering. Department of Statistics, University of Washington, Seattle. 8