Journal of Avian Biology

Journal of Avian Biology JAV-00814 Alvarez, S., salter, J. F., McCormack, J. E. and Milá, B. 2015. Speciation in mountain refugia: phylogeography and demographic history of the pine and blackcapped complex. J. Avian Biol. doi: 10.1111/ jav.00814 Supplementary material

Appendix 1 Table A1. Additional information on sampling localities of pine s (S. p. pinus, S. p. macropterus and S. p. perplexus), and black-capped s (S. atriceps). Taxon Country State/Province Locality Latitude/Longitude S. p. pinus USA Alaska Juneau 58 18'08''/-134 25'11'' S. p. pinus USA Arizona Pinaleño Mts. 32 39'56''/-109 52'29'' S. p. pinus USA California El Portal 37 45'59''/-119 45'37'' S. p. pinus USA Montana Holter Dam 46 56'01''/-111 54'55'' S. p. pinus USA Montana Flathead NF 47 52'00''/-113 48'30'' S. p. pinus USA New Jersey Bear Swamp 39 17'40''/-75 05'20'' S. p. pinus USA Oregon Willamette NF 44 11'57''/-121 57'22'' S. p. pinus USA Washington Wenatchee NF 47 01'19''/-121 08'15'' S. p. macropterus Mexico Durango La Flor 26 34'07''/-103 57'37'' S. p. macropterus Mexico Durango San Diego 24 56'48''/-105 55'13'' S. p. macropterus Mexico Michoacán Rosario 19 33'50''/-100 17'59'' S. p. perplexus Guatemala Huehuetenango Chichim 15 30'36''/-91 33'22'' S. p. perplexus Guatemala Huehuetenango Culchemal 15 31'17''/-91 28'47'' S. atriceps Guatemala Huehuetenango Chichim 15 30'36''/-91 33'22'' S. atriceps Guatemala Huehuetenango Culchemal 15 31'17''/-91 28'47'' 1

Figure A1. Photographs of the different taxa: Pine s S. p. pinus (A), S. p. macropterus (B), S. p. perplexus female (C) and male (D), and black-capped S. atriceps male (E). Photographs by BM. 2

Figure A2. Museum specimens of S. p. perplexus collected in Chiapas (region 2 in Fig. S3), Mexico, deposited at the Moore Laboratory of Zoology, shown from a ventral view (A), side view (B) and dorsal view (C). Due to DNA degradation, only small fragments of the target mtdna genes were sequenced from these specimens (see Fig. A4). A. B. C. 3

Figure A3. Distribution range and sampling regions of Spinus taxa in southern Mexico and Guatemala. Gray areas represent the species distribution. Region 1 extends from central Mexico through northern Mexico. Region 2 corresponds to the area around San Cristóbal de las Casas in Chiapas, Mexico, which is isolated from other highland regions. Region 3 corresponds to the highlands of Guatemala and a small region of SE Chiapas near the Tacaná volcano. The fresh tissue samples used in this study come from regions 1 and 3 (see Table 1). The few museum specimens of perplexus used in this study come from region 2, and the two macropterus specimens used as controls come from Durango and Jalisco in region 1. 4

Figure A4. Variable sites used to assign short sequences from 10 old museum specimens to major pine lineages. Identifiers for the old Mexican specimens are shown in red and include their respective catalog number from the Moore Laboratory of Zoology. They originate from Durango (DGO, n=1), Jalisco (JAL, n=1), and Chiapas (CHI, n=8), Mexico. Aligned sites within the gray boxes correspond to six variable sites found in a 93-bp fragment of ND2, and six variable sites found in a 41-bp fragment of ATPase 6. Hyphens represent shared nucleotides, and empty spaces represent missing data. Sites are numbered relative to the Carduelis pinus mitochondrial genome deposited in Genbank under accession KM078796.1, by Lerner et al. (2011). 5

Figure A5. Sampled individuals of S. p. perplexus from Huehuetenango (Guatemala). The pictures correspond to the following sample ID for females: 01N5980 (A), 01N5981 (B), 01N5994 (C), 01N6005 (D), 01N6019 (E), 01N6025 (F), and males: 01N5995 (G), 01N6017 (H), 01N6024 (I), 01N6027 (J), 01N6028 (K) and 01N6083 (L). Photographs for male number 01N6012 not available. Photographs by BM. 6

Appendix 2. List of the 97 specimens used in the study, including specimen ID, species code (BCSI = black-capped, BHSI = black-headed, PISI = pine ), locality information, and haplotype designation for target molecular markers. Asterisks refer to the shorter fragments of mtdna genes amplified for old museum specimens from the Moore Laboratory of Zoology (see Fig. A4). For the Genbank accession of each haplotype see Appendix 3. Specimen ID Species State Country ND2 ATP BRM15 GAPDH AldoB 03N1055 BCSI 24 (Y2) 22 (Y1) 4 1, 2 5 03N1056 BCSI 23 (Y1) 23 (Y2) 4 2 5 01N6034 BCSI 24 (Y2) 22 (Y1) 4 1, 2 5 01N6050 BCSI 23 (Y1) 24 (Y3) 4 2, 3 5 03N1083 BHSI X2 X2 6, 7 7 2, 3 01N7017 BHSI Peten Guatemala X1 X1 5 5, 6 4 01N5994 PISI 21 (A1) 20 (A1) 1 1 5 01N5995 PISI 21 (A1) 20 (A1) 3 1 1 01N6005 PISI 21 (A1) 20 (A1) 1 1 5 01N6012 PISI 22 (A2) 20 (A1) 1, 3 1 1, 5 01N6017 PISI 21 (A1) 21 (A2) 1, 3 1 1, 5 01N6024 PISI 21 (A1) 01N6027 PISI 21 (A1) 20 (A1) 1, 3 1 01N6028 PISI 21 (A1) 21 (A2) 1, 3 1 01N5980 PISI 22 (A2) 20 (A1) 3 1, 4 1 01N5981 PISI 21 (A1) 21 (A2) 3 1 1 01N6025 PISI 21 (A1) 20 (A1) 3 1 1 01N6019 PISI 21 (A1) 01N6083 PISI 22 (A2) 20 (A1) 1, 3 1 01N5701 PISI Durango Mexico 1 (B) 4 (E) 2 1 1 01N5702 PISI Durango Mexico 1 (B) 1 (B) 1 1 1 01N5703 PISI Durango Mexico 18 (S) 1 (B) 1 1 01N5704 PISI Durango Mexico 1 (B) 1 (B) 1 1 1 01N5705 PISI Durango Mexico 1 (B) 1 (B) 1 1 1 01N5706 PISI Durango Mexico 1 (B) 1 (B) 1 1 1, 6 01N5707 PISI Durango Mexico 6 (G) 1 (B) 1 1 1 01N5708 PISI Durango Mexico 1 (B) 1 (B) 1 1 1 01N5712 PISI Durango Mexico 1 (B) 5 (F) 1 1 1 01N5718 PISI Durango Mexico 1 (B) 1 (B) 1 1 1 01N5721 PISI Durango Mexico 15 (P) 01N5722 PISI Durango Mexico 1 (B) 01N5723 PISI Durango Mexico 1 (B) 01N5728 PISI Durango Mexico 14 (O) 01N5732 PISI Durango Mexico 1 (B) 01N5743 PISI Durango Mexico 1 (B) 1 (B) 01N5744 PISI Durango Mexico 5 (F) 1 (B) 01N5745 PISI Durango Mexico 10 (K) 01N5746 PISI Durango Mexico 1 (B) 6 (G) 7

01N5747 PISI Durango Mexico 1 (B) 1 (B) 01N5748 PISI Durango Mexico 13 (N) 01N5750 PISI Durango Mexico 16 (Q) 7 (H) 01N5751 PISI Durango Mexico 8 (I) 8 (I) 01N5752 PISI Durango Mexico 1 (B) 9 (J) 01N5754 PISI Durango Mexico 19 (T) 10 (K) 01N5755 PISI Durango Mexico 6 (G) 1 (B) 01N5756 PISI Durango Mexico 1 (B) 11 (L) 01N5757 PISI Durango Mexico 1 (B) 1 (B) 99N0026 PISI Michoacan Mexico 1 (B) 1 (B) 99N0071 PISI Michoacan Mexico 1 (B) 2 (C ) 99N0095 PISI Michoacan Mexico 1 (B) 99N0096 PISI Michoacan Mexico 4 3 (D) 99N0101 PISI Michoacan Mexico 1 (B) 1 (B) 02N7319 PISI Alaska USA 13 (N) 1 (B) 02N7320 PISI Alaska USA 1 (B) 02N7321 PISI Alaska USA 1 (B) 1 (B) 02N7322 PISI Alaska USA 1 (B) 1 (B) 02N7323 PISI Alaska USA 6 (G) 1 (B) 00N6678 PISI California USA 1 (B) 1 (B) 1 1 1 00N6679 PISI California USA 19 (T) 16 (Q) 1 1 00N6680 PISI California USA 1 (B) 1 (B) 1 1 1 00N6681 PISI California USA 3 (D) 1 1 1 00N6682 PISI California USA 15 (P) 1 (B) 1 1 1 00N6683 PISI California USA 6 (G) 1 (B) 00N6685 PISI California USA 12 (M) 1 (B) 00N6687 PISI California USA 16 (Q) 17 (R ) 00N6694 PISI California USA 1 (B) 00N6695 PISI California USA 6 (G) 1 (B) 00N5185 PISI Montana USA 1 (B) 00N5189 PISI Montana USA 13 (N) 15 (P) 1 1 1 01N7776 PISI Montana USA 1 (B) 18 (T) 1 1 01N7779 PISI Montana USA 16 (Q) 17 (R ) 1 1 1 01N7793 PISI Montana USA 1 (B) 6 (G) 1 1 1 01N7798 PISI Montana USA 5 (F) 1 (B) 1 1 1 01N9446 PISI Montana USA 2 ( C) 15 (P) 01N9447 PISI Montana USA 6 (G) 01N9448 PISI Montana USA 19 (T) 19 01N7500 PISI New Jersey USA 1 (B) 1 (B) 01N7501 PISI New Jersey USA 7 (H) 1 (B) 01N7502 PISI New Jersey USA 20 (V) 1 (B) 99N7290 PISI Oregon USA 17 (R ) 1 (B) 99N7762 PISI Oregon USA 11 (L) 13 99N7763 PISI Oregon USA 1 (B) 14 99N7764 PISI Oregon USA 1 (B) 1 (B) 8

99N7196 PISI Washington USA 1 (B) 12 99N7200 PISI Washington USA 9 (J) 1 (B) 99N7202 PISI Washington USA 1 (B) 1 (B) MLZ- 50012 PISI Chiapas Mexico * * MLZ- 50013 PISI Chiapas Mexico * * MLZ- 50014 PISI Chiapas Mexico * * MLZ- 56848 PISI Chiapas Mexico * * MLZ- 56892 PISI Chiapas Mexico * * MLZ- 56895 PISI Chiapas Mexico * * MLZ- 57018 PISI Chiapas Mexico * * MLZ- 57023 PISI Chiapas Mexico * * MLZ- 57025 PISI Chiapas Mexico * * MLZ- 20566 PISI Durango Mexico * * MLZ- 26769 PISI Jalisco Mexico * * 9

Appendix 3. Genbank accessions and associated specimens. Accession Locus Haplotype Sample ID Species State Country KT358733 ND2 B (1) 02N7322 Pine Alaska USA KT358734 ND3 C (2) 01N9446 Pine Montana USA KT358735 ND4 D (3) 00N6681 Pine California USA KT358736 ND5 E (4) 99N0096 Pine Michoacan Mexico KT358737 ND6 F (5) 01N5744 Pine Durango Mexico KT358738 ND7 G (6) 00N6683 Pine California USA KT358739 ND8 H (7) 01N7501 Pine New Jersey USA KT358740 ND9 I (8) 01N5751 Pine Durango Mexico KT358741 ND10 J (9) 99N7200 Pine Washington USA KT358742 ND11 K (10) 01N5745 Pine Durango Mexico KT358743 ND12 L (11) 99N7762 Pine Oregon USA KT358744 ND13 M (12) 00N6685 Pine California USA KT358745 ND14 N (13) 00N5189 Pine Montana USA KT358746 ND15 O (14) 01N5728 Pine Durango Mexico KT358747 ND16 P (15) 00N6682 Pine California USA KT358748 ND17 Q (16) 00N6687 Pine California USA KT358749 ND18 R (17) 99N7290 Pine Oregon USA KT358750 ND19 S (18) 01N5703 Pine Durango Mexico KT358751 ND20 T (19) 01N9448 Pine Montana USA KT358752 ND21 V (20) 01N7502 Pine New Jersey USA KT358753 ND22 A1 (21) 01N5981 Pine KT358754 ND23 A2 (22) 01N6012 Pine KT358755 ND24 Y1 (23) 03N1056 KT358756 ND25 Y2 (24) 01N6034 KT358757 ND26 X1 01N7017 KT358758 ND27 X2 03N1083 Peten Guatemala KT358759 ATPase8&6 B (1) 99N0026 Pine Michoacan Mexico KT358760 ATPase8&6 C (2) 99N0071 Pine Michoacan Mexico KT358761 ATPase8&6 D (3) 99N0096 Pine Michoacan Mexico KT358762 ATPase8&6 E (4) 01N5701 Pine Durango Mexico 10

KT358763 ATPase8&6 F (5) 01N5712 Pine Durango Mexico KT358764 ATPase8&6 G (6) 01N5746 Pine Durango Mexico KT358765 ATPase8&6 H (7) 01N5750 Pine Durango Mexico KT358766 ATPase8&6 I (8) 01N5751 Pine Durango Mexico KT358767 ATPase8&6 J (9) 01N5752 Pine Durango Mexico KT358768 ATPase8&6 K (10) 01N5754 Pine Durango Mexico KT358769 ATPase8&6 L (11) 01N5756 Pine Durango Mexico KT358770 ATPase8&6 M (12) 99N7196 Pine Washington USA KT358771 ATPase8&6 N (13) 99N7762 Pine Oregon USA KT358772 ATPase8&6 O (14) 99N7763 Pine Oregon USA KT358773 ATPase8&6 P (15) 00N5189 Pine Montana USA KT358774 ATPase8&6 Q (16) 00N6679 Pine California USA KT358775 ATPase8&6 R (17) 00N6687 Pine California USA KT358776 ATPase8&6 T (18) 01N7776 Pine Montana USA KT358777 ATPase8&6 U (19) 01N9448 Pine Montana USA KT358778 ATPase8&6 A1 (20) 01N5980 Pine KT358779 ATPase8&6 A2 (21) 01N5981 Pine KT358780 ATPase8&6 Y1 (22) 03N1055 KT358781 ATPase8&6 Y2 (23) 03N1056 KT358782 ATPase8&6 Y3 (24) 01N6050 KT358783 ATPase8&6 X1 01N7017 KT358784 ATPase8&6 X2 03N1083 Peten Guatemala KT358785 BRM 1 01N5702 Pine Durango Mexico KT358786 BRM 2 01N5701 Pine Durango Mexico KT358787 BRM 3 01N5995 Pine KT358788 BRM 4 01N6050 KT358789 BRM 5 01N7017 KT358790 BRM 6 03N1083 KT358791 BRM 7 03N1083 Peten Guatemala 11

KT358792 GAPDH 1 01N5702 Pine Durango Mexico KT358793 GAPDH 1 01N6034 KT358794 GAPDH 2 03N1056 KT358795 GAPDH 3 01N6050 KT358796 GAPDH 4 01N5980 Pine KT358797 GAPDH 5 01N7017 KT358798 GAPDH 6 01N7017 KT358799 GAPDH 7 03N1083 Peten Guatemala Peten Guatemala KT358800 AldoB 1 01N5702 Pine Durango Mexico KT358801 AldoB 2 03N1083 KT358802 AldoB 3 03N1083 KT358803 AldoB 4 01N7017 Peten Guatemala KT358804 AldoB 5 01N6012 Pine KT358805 AldoB 5 03N1056 KT358806 AldoB 6 01N5706 Pine Durango Mexico 12