phoretic dispersal influences parasite population genetic...

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Supplemental Information for:

Phoretic dispersal influences parasite

population genetic structure

Emily DiBlasi, Kevin P. Johnson, Sydney A. Stringham,

Angela N. Hansen, Andrew B. Beach, Dale H. Clayton and Sarah E. Bush

Table of Contents: Table S1 Page 1 Table S2 Page 2 Table S3 Page 3 Table S4 Page 4 Table S5 Page 5 Table S6 Page 6 Table S7 Page 7 Table S8 Page 8 Table S9 Page 9 Figure S1 Page 10 Figure S2 Page 11 Figure S3 Page 12 Figure S4 Page 13 Figure S5 Page 14 R code Page 15

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Tables Table S1. Microsatellite loci developed for this study. We developed 17 primer sets specific to wing lice (Columbicola columbae) and 13 primer sets specific to body lice (Campanulotes compar).

# Repeat Forward Primer Reverse Primer Length

Body Lice Campanulotes compar

2B (AG) * 19 M13_GACAAGTGACCGTCTCTATCGCG AGTATGGCCGGTGACTTTCG 351 5B (ACT) * 23 M13_GACCGGCTCGAAGTCAAGAAACC GCACTCTGACAGGCGTTC 423

6B (ACT) * 16 M13_GACAAGTCAGTTCGCTCCCTTTG TCCACCTCCACAACTTTCCG 373

9B (AC) * 8 M13_GACTCTCGAAATTTCCACGTGCC TTGTGTGGCCAAACTCTTCG 318

10B (AAG) * 7 M13_GACTTCCTCTCAGAACGCTCAGG AAGCTTCCAGTTCCCTCTCG 167

11B (AG) * 18 M13_GACGAACCGGTTCGAGGAATGTC AGGAGCGATTAATGCCAAGC 416

12B (AGC) * 6 M13_GACAAAGGGAGTGGAGGGTACGG CGCGATCCAGGTCATTTCAC 277

13B (AT) * 7 M13_GACAGTAAGCAGTGGTCAGCAGG CGTCTTTCCGCGTTAAGTTTG 414

Wing Lice 3W (AG) * 14 M13_GACGGAGAGATAGGACGGGCTTG AAACAAGGACCTCGGACCC 417

Columbicola columbae 6W (AAG) * 7 M13_GACGGCGGTGGATGATTGAACAG TCACGTATGGATCCGGACAG 376

9W (AG) * 9 M13_GACTCACACTGGAGGCAAGGAAG GCACATTTGGACGAGTGGAG 327

10W (ATC) * 6 M13_GACTTGAAACTGAGAGGAGTGCC TCAATTTGACGATCCTGCTGG 443

12W (AG) * 9 M13_GACAAAGTCTGGGAGAGGTCAGC GTTGGTCGAGCAGGAATGAC 300

13W (AG) * 13 M13_GACGGTAACTTGTGCGTCCGTAAG ATCTTCATTTCCGGTTGCGG 376

15W (ACAG) * 6 M13_GACGTCTTCTCTTGAGTGTTGCAAC AATCGTGTGTAGCGTGCAAG 406

16W (AG) * 12 M13_GACTTATTCACAGCCTCCCTCCG ACGGGTCATAAGTGGCAAAG 422

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Table S2. Comparison of body and wing lice prevalence and abundance on pigeons at each site. Prevalence is the percent of pigeons sampled with at least one parasite. Abundance is the mean (± standard error) number of lice removed from each fumigated pigeon by ruffling (including parasite free birds).

Flock # Site # # pigeons sampled Parasite prevalence Parasite abundance

Flock 1 Site 1 83 Body lice Wing lice Body lice Wing lice

71.1 100.0 6.0 ± 0.9 31.5 ± 3.4 Flock 2 Site 2 70 72.9 98.6 6.4 ± 1.3 33.8 ± 4.8 Flock 3 Site 3 72 70.8 83.3 8.7 ± 3.2 21.9 ± 3.5

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Table S3. Indices of genetic diversity and subpopulation size for body and wing lice subpopulations on each host individual. The mean number of alleles observed (NA), observed heterozygosity (HO), expected heterozygosity (HS), subpopulation size (NC) and the inbreeding coefficient (FIS) with lower and upper 95% CIs in brackets are reported.

Body Lice

Camanulotes compar Wing Lice

Columbicola columbae Sampling

Site Host Bird

Host Field ID

NC NA HO HS

FIS

NC NA HO HS

FIS

Flock 1 Bird1 1SLC4235 34 4.714 0.470 0.514 0.252 [0.142, 0.381] 50 4.500 0.707 0.685 -0.087 [-0.238, 0.039]

Bird2 1SLC42 14 4.500 0.475 0.560 0.101 [-0.076, 0.253] 27 4.875 0.675 0.668 -0.063 [-0.202, 0.032]

Bird3 1SLC67 29 4.500 0.549 0.616 0.056 [-0.112, 0.181] 84 3.875 0.556 0.608 0.029 [-0.166, 0.188]

Bird4 1SLC72 43 2.750 0.500 0.459 -0.132 [-0.290, -0.000] 79 3.750 0.537 0.545 -0.039 [-0.248, 0.126]

Bird5 1SLC50 17 3.750 0.475 0.489 -0.024 [-0.267, 0.239] 21 4.125 0.483 0.678 0.228 [0.019, 0.403]

Bird6 1SLC78 13 4.625 0.562 0.565 -0.049 [-0.211, 0.050] 34 5.000 0.575 0.683 0.107 [-0.022, 0.194]

Bird7 1SLC82 81 5.375 0.565 0.568 -0.049 [-0.214, 0.089] 145 4.250 0.556 0.604 0.021 [-0.112, 0.110]

Bird8 1SLC56 10 4.375 0.415 0.546 0.189 [-0.142, 0.527] 66 4.000 0.532 0.569 0.006 [-0.165, 0.156]

Bird9 1SLC77 42 4.000 0.615 0.550 -0.1704 [-0.338, -0.010] 43 4.000 0.584 0.678 0.085 [-0.098, 0.255]

Bird10 1SLC4229 11 4.000 0.519 0.566 -0.008 [-0.245, 0.174] 71 4.250 0.507 0.620 0.130 [-0.020, 0.245]

Flock 2 Bird1 2SLC4290 20 5.000 0.581 0.570 0.151 [0.076, 0.210] 48 4.375 0.534 0.647 0.118 [-0.032, 0.244]

Bird2 2SLC50 27 2.500 0.264 0.320 0.123 [-0.106, 0.315] 62 3.500 0.488 0.539 0.043 [-0.204, 0.288]

Bird3 2SLC51 14 5.125 0.575 0.597 -0.013 [-0.154, 0.106] 43 4.625 0.583 0.641 0.037 [-0.101, 0.146]

Bird4 2SLC56 65 4.250 0.519 0.522 -0.048 [-0.204, 0.078] 241 3.875 0.494 0.561 0.065 [-0.094, 0.189]

Bird5 2SLC69 20 4.625 0.450 0.527 0.094 [-0.065, 0.250] 43 4.875 0.562 0.626 0.050 [-0.079, 0.145]

Bird6 2SLC68 15 5.125 0.465 0.535 0.078 [-0.078, 0.194] 105 4.500 0.513 0.589 0.078 [-0.080, 0.207]

Bird7 2SLC63 14 3.375 0.513 0.481 -0.119 [-0.426, 0.162] 28 3.750 0.460 0.532 0.084 [-0.083, 0.226]

Bird8 2SLC53 16 2.125 0.339 0.271 -0.300 [-0.488, -0.081] 30 4.500 0.632 0.651 -0.025 [-0.167, 0.105]

Bird9 2SLC57 45 2.375 0.263 0.318 0.123 [-0.277, 0.470] 35 3.750 0.625 0.569 -0.151 [-0.288, -0.025]

Bird10 2SLC54 16 3.750 0.356 0.457 0.161 [-0.069, 0.312] 35 4.625 0.643 0.648 -0.047 [-0.207, 0.100]

Flock 3 Bird1 3SLC4316 203 5.143 0.481 0.574 0.295 [0.125, 0.450] 146 3.250 0.529 0.558 -0.002 [-0.218, 0.196]

Bird2 3SLC46 91 3.250 0.444 0.516 0.085 [-0.122, 0.260] 82 4.250 0.625 0.611 -0.075 [-0.291, 0.104]

Bird3 3SLC39 49 1.500 0.158 0.179 0.048 [-0.353, 0.470] 77 3.000 0.422 0.423 -0.051 [-0.283, 0.147]

Bird4 3SLC45 23 5.000 0.562 0.587 -0.011 [-0.180, 0.141] 61 4.250 0.569 0.626 0.036 [-0.142, 0.173]

Bird5 3SLC38 11 3.000 0.354 0.467 0.188 [-0.095, 0.408] 32 4.500 0.475 0.619 0.183 [0.029, 0.295]

Bird6 3SLC54 24 5.000 0.519 0.537 -0.020 [-0.186, 0.114] 47 5.250 0.604 0.672 0.049 [-0.113, 0.182]

Bird7 3SLC65 39 3.875 0.532 0.570 0.011 [-0.227, 0.250] 74 3.875 0.425 0.492 0.085 [-0.178, 0.332]

Bird8 3SLC53 14 1.750 0.425 0.273 -0.593 [-0.810, -0.396] 38 4.375 0.713 0.653 -0.142 [-0.305, -0.003]

Bird9 3SLC66 10 1.875 0.222 0.230 -0.023 [-0.249, 0.148] 94 3.750 0.550 0.538 -0.077 [-0.257, 0.063]

Bird10 3SLC4315 12 4.375 0.390 0.493 0.154 [-0.022, 0.303] 32 4.000 0.550 0.576 -0.008 [-0.175, 0.170]

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Table S4. Indices of genetic diversity for pigeon flocks. The mean number of alleles observed (NA), observed heterozygosity (HO), expected heterozygosity (HS), and the inbreeding coefficient (FIS) with lower and upper 95% CIs in brackets are reported.

Sampling Site NA HO HS

FIS

Flock 1 9.94 0.550 0.540 -0.008 [-0.145, 0.101] Flock 2 10 0.590 0.560 -0.059 [-0.152, 0.004] Flock 3 9.59 0.550 0.540 -0.016 [-0.158, 0.083]

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Table S5. Pairwise FST estimates for body lice (Campanulotes compar) populations estimated from 8 microsatellite markers. Population comparisons that are statistically significant after correcting for false discovery rates are shaded in gray.

Floc

k 1

Floc

k 2

Floc

k 3

Body Lice B

ird1

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Bird

1

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Bird

1

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Flock 1 Bird1 0.00

Bird2 0.07 0.00

Bird3 0.04 0.07 0.00

Bird4 0.23 0.18 0.19 0.00

Bird5 0.14 0.10 0.09 0.22 0.00

Bird6 0.08 0.11 0.08 0.20 0.12 0.00

Bird7 0.05 0.10 0.07 0.24 0.15 0.05 0.00

Bird8 0.14 0.11 0.04 0.24 0.10 0.12 0.16 0.00

Bird9 0.08 0.08 0.07 0.20 0.10 0.09 0.14 0.10 0.00

Bird10 0.12 0.09 0.03 0.16 0.09 0.05 0.07 0.11 0.08 0.00

Flock 2 Bird1 0.11 0.00 0.04 0.10 0.07 0.02 0.01 0.12 0.02 0.03 0.00

Bird2 0.34 0.27 0.28 0.44 0.34 0.31 0.30 0.28 0.36 0.37 0.36 0.00

Bird3 0.00 0.05 0.05 0.19 0.08 0.05 0.04 0.10 0.06 0.02 -0.02 0.29 0.00

Bird4 0.06 0.11 0.10 0.24 0.16 0.15 0.12 0.18 0.12 0.12 0.05 0.35 0.09 0.00

Bird5 0.04 0.10 0.04 0.24 0.13 0.10 0.08 0.12 0.10 0.09 0.05 0.31 0.04 0.09 0.00

Bird6 0.04 0.07 0.03 0.18 0.07 0.05 0.07 0.09 0.07 0.04 0.00 0.28 0.04 0.08 0.04 0.00

Bird7 0.11 0.13 0.11 0.21 0.13 0.10 0.12 0.15 0.11 0.05 0.05 0.32 0.08 0.18 0.13 0.09 0.00

Bird8 0.35 0.26 0.30 0.46 0.32 0.30 0.28 0.37 0.33 0.38 0.32 0.42 0.26 0.38 0.30 0.29 0.31 0.00

Bird9 0.26 0.20 0.25 0.41 0.26 0.25 0.23 0.33 0.28 0.32 0.25 0.39 0.21 0.32 0.25 0.22 0.25 0.00 0.00

Bird10 0.09 0.11 0.10 0.28 0.12 0.10 0.09 0.18 0.13 0.14 0.07 0.32 0.07 0.09 0.08 0.07 0.11 0.23 0.14 0.00

Flock 3 Bird1 0.09 -0.01 -0.02 0.15 0.05 0.04 0.00 0.07 0.04 0.02 0.04 0.30 -0.03 0.06 0.00 0.00 0.08 0.31 0.26 0.09 0.00

Bird2 0.11 0.14 0.11 0.22 0.15 0.08 0.13 0.15 0.14 0.10 0.06 0.36 0.09 0.19 0.14 0.09 0.12 0.38 0.32 0.15 0.07 0.00

Bird3 0.46 0.55 0.47 0.61 0.56 0.52 0.50 0.52 0.51 0.58 0.50 0.66 0.49 0.53 0.51 0.52 0.55 0.71 0.68 0.59 0.51 0.56 0.00

Bird4 0.02 0.03 0.04 0.15 0.07 0.08 0.07 0.10 0.05 0.03 -0.05 0.32 0.03 0.09 0.05 0.05 0.09 0.28 0.22 0.07 -0.08 0.10 0.52 0.00

Bird5 0.09 0.24 0.21 0.35 0.25 0.21 0.27 0.25 0.22 0.19 0.11 0.45 0.17 0.23 0.21 0.21 0.24 0.48 0.42 0.28 0.14 0.22 0.54 0.19 0.00

Bird6 0.04 0.08 0.06 0.21 0.11 0.07 0.09 0.14 0.07 0.09 0.00 0.33 0.04 0.10 0.05 0.07 0.07 0.29 0.22 0.03 0.02 0.06 0.53 0.01 0.18 0.00

Bird7 0.12 0.11 0.12 0.23 0.13 0.12 0.18 0.12 0.15 0.11 0.07 0.31 0.09 0.21 0.17 0.12 0.16 0.33 0.30 0.23 0.06 0.14 0.51 0.11 0.16 0.15 0.00

Bird8 0.32 0.38 0.34 0.42 0.44 0.39 0.35 0.40 0.42 0.39 0.38 0.53 0.35 0.39 0.34 0.39 0.41 0.55 0.52 0.42 0.32 0.45 0.71 0.33 0.46 0.38 0.41 0.00

Bird9 0.36 0.35 0.32 0.48 0.40 0.34 0.31 0.41 0.36 0.41 0.33 0.51 0.31 0.36 0.34 0.33 0.34 0.50 0.43 0.27 0.34 0.34 0.73 0.30 0.47 0.22 0.44 0.62 0.00

Bird10 0.11 0.10 0.08 0.23 0.10 0.06 0.10 0.12 0.09 0.10 0.03 0.34 0.07 0.14 0.10 0.06 0.07 0.31 0.25 0.08 0.05 0.05 0.59 0.05 0.22 0.02 0.15 0.43 0.28 0.00

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Table S6. Pairwise FST estimates for wing lice (Columbicola columbae) populations estimated from 8 microsatellite markers. Population comparisons that are statistically significant after correcting for false discovery rates are shaded in gray.

Floc

k 1

Floc

k 2

Floc

k 3

Wing Lice B

ird1

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Bird

1

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Bird

1

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Flock 1 Bird1 0.00

Bird2 0.07 0.00

Bird3 0.02 0.03 0.00

Bird4 0.16 0.07 0.13 0.00

Bird5 -0.02 0.01 0.04 0.12 0.00

Bird6 0.04 0.01 0.01 0.09 0.00 0.00

Bird7 0.05 0.06 0.02 0.16 0.02 -0.02 0.00

Bird8 0.05 0.02 0.00 0.08 0.07 0.00 0.05 0.00

Bird9 0.01 0.03 0.02 0.11 0.03 0.03 0.07 0.03 0.00

Bird10 0.05 -0.01 0.04 0.07 0.02 0.01 0.05 0.00 0.03 0.00

Flock 2 Bird1 0.09 -0.01 0.02 0.05 0.06 0.01 0.07 0.03 0.04 0.00 0.00

Bird2 0.11 0.02 0.06 0.13 0.07 0.10 0.13 0.07 0.06 0.04 0.04 0.00

Bird3 0.06 0.00 0.01 0.11 0.01 0.01 0.04 0.03 0.03 0.01 0.00 0.04 0.00

Bird4 0.11 0.04 0.10 0.10 0.11 0.07 0.14 0.05 0.05 0.02 0.05 0.10 0.05 0.00

Bird5 0.03 0.04 -0.01 0.09 0.01 0.03 0.05 0.00 0.02 0.03 0.02 0.07 0.03 0.06 0.00

Bird6 0.11 0.03 0.08 0.04 0.06 0.05 0.10 0.02 0.06 0.02 0.02 0.08 0.07 0.02 0.06 0.00

Bird7 0.13 0.09 0.10 0.09 0.10 0.08 0.13 0.03 0.11 0.08 0.09 0.14 0.14 0.11 0.09 0.01 0.00

Bird8 0.06 0.03 0.03 0.05 0.04 0.05 0.10 0.01 0.03 0.02 0.01 0.06 0.05 0.04 0.04 0.01 0.03 0.00

Bird9 0.09 0.06 0.04 0.13 0.06 0.05 0.06 0.02 0.11 0.06 0.08 0.12 0.09 0.15 0.06 0.09 0.05 0.08 0.00

Bird10 0.04 0.03 0.05 0.06 -0.01 0.07 0.10 0.07 0.02 0.03 0.04 0.06 0.04 0.08 0.02 0.06 0.13 0.06 0.10 0.00

Flock 3 Bird1 0.09 0.10 0.09 0.16 0.05 0.11 0.15 0.12 0.11 0.11 0.10 0.11 0.14 0.14 0.09 0.07 0.10 0.09 0.12 0.10 0.00

Bird2 0.06 0.02 0.01 0.08 0.01 0.01 0.00 0.00 0.05 0.00 0.03 0.07 0.03 0.07 0.02 0.05 0.07 0.04 0.04 0.06 0.11 0.00

Bird3 0.21 0.16 0.19 0.15 0.17 0.22 0.26 0.21 0.16 0.19 0.15 0.11 0.20 0.24 0.13 0.13 0.19 0.14 0.23 0.10 0.17 0.20 0.00

Bird4 0.06 0.01 0.01 0.09 0.03 0.03 0.04 0.02 0.03 0.01 0.00 0.02 0.02 0.07 0.03 0.04 0.09 0.02 0.07 0.06 0.08 0.01 0.12 0.00

Bird5 0.08 -0.01 0.02 0.03 0.03 0.02 0.05 0.00 0.05 0.00 -0.01 0.04 0.03 0.06 0.02 0.00 0.05 0.02 0.05 0.04 0.07 0.00 0.12 0.00 0.00

Bird6 0.04 0.03 0.02 0.07 0.02 0.00 0.02 0.01 0.02 0.01 0.02 0.09 0.04 0.05 0.02 0.02 0.06 0.02 0.08 0.06 0.09 0.00 0.19 0.02 0.00 0.00

Bird7 0.15 0.12 0.14 0.11 0.15 0.18 0.24 0.14 0.12 0.14 0.11 0.09 0.16 0.18 0.10 0.13 0.16 0.09 0.18 0.10 0.15 0.16 0.04 0.10 0.11 0.17 0.00

Bird8 0.06 0.01 0.02 0.05 0.02 0.03 0.06 0.02 0.02 0.02 0.00 0.05 0.03 0.06 0.02 0.02 0.07 0.03 0.09 0.03 0.09 0.01 0.12 0.02 -0.01 0.00 0.11 0.00

Bird9 0.09 0.10 0.04 0.20 0.09 0.06 0.09 0.09 0.10 0.09 0.07 0.17 0.08 0.12 0.06 0.12 0.18 0.11 0.15 0.13 0.10 0.07 0.28 0.08 0.06 0.05 0.24 0.07 0.00

Bird10 0.08 0.09 0.09 0.15 0.04 0.12 0.17 0.10 0.09 0.08 0.09 0.10 0.11 0.09 0.03 0.09 0.12 0.09 0.12 0.05 0.03 0.11 0.16 0.11 0.09 0.10 0.13 0.09 0.14 0.00

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Table S7. (a) Global estimates of FST values with lower and upper 95% CIs in brackets for body and wing lice. (b) Global estimates of G”ST values with lower and upper 95% CIs in brackets for body and wing lice.

a

FST Body Lice Wing Lice All sites 0.226 [0.210, 0.244] 0.069 [0.053, 0.087] Site 1 0.130 [0.103, 0.162] 0.043 [0.017, 0.075] Site 2 0.204 [0.173, 0.237] 0.061 [0.036, 0.091] Site 3 0.316 [0.289, 0.345] 0.090 [0.062, 0.123]

b

G”ST Body Lice Wing Lice All sites 0.444 [0.421, 0.468] 0.181 [0.150, 0.214] Site 1 0.295 [0.248, 0.347] 0.130 [0.071, 0.198] Site 2 0.376 [0.331, 0.423] 0.161 [0.110, 0.216] Site 3 0.576 [0.546, 0.607] 0.220 [0.169, 0.274]

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Table S8. The optimal number of genetic clusters chosen from body lice genotypes. Cluster membership and host identity of individual lice are indicated in the table.

Cluster # Sampling

Site Host Bird Host

Field ID 1 2 3 4 5 6 7 8 9 10 11 12 13 14

Flock 1 Bird1 1SLC4235 4 1 3 2 Bird2 1SLC42 1 2 3 2 2 Bird3 1SLC67 2 2 1 3 2 Bird4 1SLC72 10 Bird5 1SLC50 5 5 Bird6 1SLC78 3 2 4 1 Bird7 1SLC82 1 7 1 1 Bird8 1SLC56 3 1 3 3 Bird9 1SLC77 1 2 6 1 Bird10 1SLC4229 1 2 2 1 1

Flock 2 Bird1 2SLC4290 5 2 1 1 1 Bird2 2SLC50 10 Bird3 2SLC51 1 3 1 3 1 1 Bird4 2SLC56 4 6 Bird5 2SLC69 1 2 1 1 5 Bird6 2SLC68 1 2 5 2 Bird7 2SLC63 6 1 1 1 1 Bird8 2SLC53 10 Bird9 2SLC57 9 1 Bird10 2SLC54 3 1 4 2

Flock 3 Bird1 3SLC4316 3 2 1 2 1 1 Bird2 3SLC46 1 1 2 4 2 Bird3 3SLC39 10 Bird4 3SLC45 1 3 2 1 1 2 Bird5 3SLC38 9 1 Bird6 3SLC54 1 3 1 3 1 1 Bird7 3SLC65 1 2 4 Bird8 3SLC53 10 3

Bird9 3SLC66 1 9 Bird10 3SLC4315 3 1 3 2 1

Total # of lice 24 10 10 39 16 27 27 15 31 15 11 31 10 31 Total # of hosts in cluster 5 1 1 16 6 15 13 5 13 4 2 13 2 15

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Table S9. The optimal number of genetic clusters chosen from wing lice genotypes. Cluster membership and host identity of individual lice are indicated in the table.

Cluster # Sampling

Site Host Bird Host

Field ID 1 2 3 4 5 6 7 8 9 10

Flock 1 Bird1 1SLC4235 1 1 4 2 2 Bird2 1SLC42 3 1 1 2 3 Bird3 1SLC67 1 1 4 1 3 Bird4 1SLC72 1 2 1 6 Bird5 1SLC50 1 1 2 1 1 2 1 1 1 Bird6 1SLC78 1 2 3 1 3 Bird7 1SLC82 2 2 3 1 2 Bird8 1SLC56 1 3 2 1 2 2 Bird9 1SLC77 4 1 1 1 1 2 Bird10 1SLC4229 2 1 1 1 3 2

Flock 2 Bird1 2SLC4290 2 3 1 1 3 Bird2 2SLC50 5 1 1 2 Bird3 2SLC51 2 2 1 1 3 1 Bird4 2SLC56 6 1 2 Bird5 2SLC69 2 5 1 1 1 Bird6 2SLC68 1 3 1 2 3 Bird7 2SLC63 1 7 1 1 Bird8 2SLC53 3 2 2 1 1 1 Bird9 2SLC57 3 3 2 1 1 Bird10 2SLC54 5 2 1 2

Flock 3 Bird1 3SLC4316 2 5 2 1 Bird2 3SLC46 2 1 1 1 4 1 1 Bird3 3SLC39 2 7 Bird4 3SLC45 2 1 1 1 2 1 1 1 Bird5 3SLC38 1 1 1 2 1 4 Bird6 3SLC54 1 1 1 4 2 1 Bird7 3SLC65 1 1 6 1 1 Bird8 3SLC53 2 1 1 4 2

Bird9 3SLC66 1 2 6 1 Bird10 3SLC4315 1 7 1 1

Total # of lice 29 27 27 37 25 26 33 36 25 35 Total # of hosts in cluster 15 12 11 20 11 16 19 17 14 16

11

Figures

Figure S1. Map of sampling sites in Salt Lake City, Utah. Pigeon flocks were sampled at each of the three sites (Flock 1 = Site 1, Flock 2 = Site 2, Flock 3 = Flock 3).

Fig.1 Fig.2

Fig. 3

Fig. 4Fig. 5

Site 1 Body LiceSite 2 Body LiceSite 3 Body Lice

0.1

0.2

0.3

FST

body licewing lice

All Sites Site 1 Site 2 Site 3Site 2 40.65 ° N

-111.90 ° W

Site 1 40.71 ° N

-111.87 ° W

Site 3 40.74 ° N

-111.94 ° W

Site 1 Wing LiceSite 2 Wing LiceSite 3 Wing Lice

< 0.05 0.05 – 0.1 0.1 – 0.2 0.2 – 0.3 0.3 – 0.6 > 0.6

Bird 2 Bird 3 Bird 4 Bird 5 Bird 6 Bird 7 Bird 8 Bird 9 Bird 10


Bird 1

Bird 1


Bird 1

Floc

k 1

Floc

k 2

Floc

k 3




Bird 1

Bird 1

Bird 1

Floc

k 1

Floc

k 2

Floc

k 3

Bird

2

Bird

3

Bird

4

Bird

5

Bird

6

Bird

7

Bird

8

Bird

9

Bird

10

Bird

1

Flock 1

Bird

2

Bird

3

Bird

4

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< 0.05 0.05 – 0.1 0.1 – 0.2 0.2 – 0.3 0.3 – 0.6 > 0.6

12

Figure S2. Ordination plot showing the first two principal components of the DAPC for pigeons. Colors show the sites/flock from which birds were collected (Site 1: blue; Site 2: red; Site 3: gray). Dots represent individual pigeon genotypes. Circles represent confidence intervals of the DAPC.

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Fig. S1 Fig. S2 Fig. S3

Figure S1. Observed heterozygosity of louse infrapopulations in relation to infrapopulation size for (a) body lice and (b) wing lice.

Figure S2. Ordination plots showing the first two principal components of the DAPC for body lice (a) and wing lice (b). Colors indicate which flock of birds lice were collected from (Site 1 is blue, Site 2 is red, Site 3 is gray) and different shapes represent different louse infrapopulations.

Figure S3. Ordination plots showing the first two principal components of the DAPC for body lice (a) and wing lice (b) grouped by k means clustering. Different colors indicate different genetic clusters and different shapes represent different louse infrapopulations.

Fig. S4

Figure S4. Ordination plot showing the first two principal components of the DAPC for pigeons. Colors indicate which flock the bird belonged to (Site 1 is blue, Site 2 is red, Site 3 is gray) and dots represent individual pigeon genotypes.

13

Figure S3. Ordination plots showing the first two principal components of the DAPC for (a) body lice and (b) wing lice, grouped by bird. Colors show the sites from which lice were collected (Site 1: blue; Site 2: red; Site 3: gray). Different symbols represent different subpopulations of lice. Circles represent confidence intervals of the DAPC.

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Fig. S4


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Fig. S4


14

Figure S4. Ordination plots showing the first two principal components of the DAPC for (a) body lice and (b) wing lice grouped by k means clustering assignments. Different colors indicate different genetic clusters and different symbols represent different louse subpopulations. Circles represent confidence intervals of the DAPC. See Table S7 for individual body lice cluster assignments and Table S8 for individual wing lice cluster assignments.

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Fig. S4


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Fig. S4


15

Figure S5. Ordination plots showing the first two principal components of the DAPC for body lice. Figure S4a is shown here (a) for easy reference. Colors indicate the sites from which lice were collected (Site 1: blue; Site 2: red; Site 3: gray). Different symbols represent genotypes of individuals belonging to one subpopulations of lice. Circles represent confidence intervals of the DAPC. This plot shows a clear separation of three body louse supopulations (bird 4 - flock 1, bird 3 - flock 3, bird 8 - flock 3). (b) Ordination plot showing the same data as S5a but with the three most genetically distinct body louse subpopulations (those labeled in S5a) removed. In this plot, colors indicate different hosts from which lice were collected. Two body louse subpopulations have non-overlapping clusters indicating a high degree of genetic differentiation (bird 2 - flock 2, bird 9 - flock 3). (c) Ordination plot showing the same data as S4a but with the five most genetically distinct body louse subpopulations (those labeled in S5a and S5b) removed. In this plot, colors indicate the different hosts from which lice were collected. Although this plot shows a separation of three additional body louse subpopulations (bird 5 - flock 3, bird 7 - flock 3, bird 2 - flock 3), the clusters are fairly close together. Thus, even when the most unique body louse subpopulations are excluded from the analysis, body lice are more differentiated than wing lice (Fig. S3b).

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Fig. S4


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0 0 333SLC39_B103SLC39 B10

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a ca b c

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16

R code Data Fi les birdglm.csv and locglm.csv wil l be uploaded to Dryad

By Bird Host birdglm

phoretic dispersal influences parasite population genetic...

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