Supporting Information

Marek and Bond 10.1073/pnas.0810408106 SI Text them in color analyses testing mimetic resemblance. We did not Sampling Strategy. Specimens were collected during mid to late estimate phylogeny, conduct NCA, or calculate ␪. Support peak activity periods for apheloriines: August 16–20, 2006; and indices for all species clades were greater than 0.96 probability September 26 to October 4, 2006. Collection effort, speed, and for Bayesian posterior probabilities (except for the species B. time spent sampling were constant across sites. Overall, we mendota, with 0.73 posterior clade probability). Aligned species collected 398 at 29 sites. At each 50-m2 site, 2 datasets lacked signatures of complex indel events and varied sampling strategies were implemented to ensure precise popu- lengthwise on average by 6 bp. lation sampling: leaf raking (with a rake) and boulder/ log turning (with a rock hammer). One strategy was assigned to NCA and Estimation of Demographic Processes. We conducted each collector for 30 min and then exchanged for another 30 min. phylogeographic analyses by using NCA to test for an association Collection effort and speed (raking and turning) were therefore between DNA haplotype variation and geographical variation. constant across sites. Live specimens captured during these Nested haplotype networks were analyzed by using a permuta- surveys were brought back to the laboratory for color measure- tion contingency test in the program GEODIS, version 2.5 (5), ment and DNA sequencing. Table S1 summarizes sites and their to calculate the statistics Dc (geographical range of a clade) and respective species, haplotypes, color morphs, and abundances Dn (geographical distribution of a clade relative to its closest (species and site totals). sister). We used the program ANeCA, version 1.0 (6), to automate nesting and statistical calculations and to confirm DNA Sequencing, Alignment, and Phylogeny Estimation. Left legs manual inferences drawn from the NCA key (version 11, No- (segments 8–19) were removed, immersed in RNAlater (Qia- vember 2005). Hierarchical pattern was congruent, and the gen), and archived in an ultracold freezer. Protocols and primers network root nodes (determined by using a frequency-based used to amplify a region of the mitochondrial genome spanning estimate) were consistent with the Bayesian trees. We used the ribosomal RNA genes are described in detail previously (1). Templeton, Crandall, Sing (TCS) statistical parsimony (7) and a Initial cycle sequencing reactions consisted of 1 primer (LR-J- 95% connection limit to estimate haplotype networks in the 12887dip2) to prescreen for redundant mitochondrial sequences, program TCS, version 1.21 (8). Species haplotype networks were and a subsequent reaction with a second primer (LR-J-APHE1, similar to their estimated phylogenies. The networks for the which sequences an overlapping fragment) to screen for the species A. clade A, B. cedra, and B. mendota have unconnected unique 16S rDNA mitochondrial sequences reported herein. See clades with 3, 2, and 5 separate haplotype groups, respectively. Marek and Bond (1) for details on multiple sequence alignment. By using GEODIS contingency tests, we observed a number of First, sequences were aligned and analyzed within the context significant inferences favoring restricted gene flow with isolation of the phylogeny of Apheloriini (2) to categorize sequences into by distance at a lower nesting level (between 1-step and 3-step species. We estimated the phylogeny by using maximum likeli- clades) and allopatric fragmentation at a higher nesting level hood and Bayesian inference with the programs GARLI version (between 4-step and higher clades). Detailed results of the 0.951 (3) and MrBayes version 3.1.2 (4) using the settings nested clade analyses among the 7 codistributed species are described in Marek and Bond (2). In the phylogenetic analysis, available upon request from the corresponding author. some species did not fit preexisting . Individuals iden- tified as Apheloria virginiensis corrugata, Apheloria montana, and Species Population Sizes, Estimation of ␪, and Abundance. We used an undescribed species did not occur as monophyletic lineages on the program LAMARC, version 2.1.2 (9), to estimate the the phylogeny. Overall, there were 2 Apheloria clades, designated population parameter ␪. LAMARC employs a Markov chain clades ‘‘A’’ and ‘‘B.’’ The species Brachoria dentata and B. Monte Carlo sampling method to first estimate genealogies, and mendota are paraphyletic with respect to 2 new species and then it generates a maximum-likelihood estimation of popula- Brachoria evides. However, in this study, B. dentata and B. tion parameters. We estimated ␪ only for those clades in the 7 mendota are treated as a separate species because nested lin- endemic species connected at 95% statistical parsimony (10) and eages are considerably disjunct geographically (species in B. with Ն8 haplotypes (11), subsequently treating them as popu- dentata occur on the other side of Cumberland Mountain in lations in the analysis. The parameter ␪ is not directly related to Kentucky, and B. evides in Jefferson County, Tennessee), have Nc because we must factor in mutation rate, breeding ratio, and extensively different male genitalia, and represent independent overlapping generations—items that may affect Ne (12). How- genetic lineages. ever, we expect the magnitude of the values to be strongly related Subsequently, each cluster of sequences that represents a because ␪ is predominately governed by Ne, mutation rate is species in the Apheloriini phylogeny was then realigned on its assumed constant, and breeding and generational strategies are own to construct population-level phylogenies by using MrBayes. equal. To test the relationship between ␪ and Nc, we used linear Fig. S1 shows the 7 codistributed species population phylogenies regression of census abundance as a predictor of ␪ by using the and their location in the apheloriine phylogeny. The sequences statistical package JMP, version 7 (SAS). We found a strong 2 are available for download from the National Center for Bio- positive linear correlation of ␪ with Nc (R ϭ 0.64, ln- technology Information (accession nos. FJ667003–186). By using transformed Nc; Fig. S2). Because Nc is an accurate predictor of random population sampling, we collected 5 additional species ␪, we expect Nc to reflect the ancestral frequency-dependent representing populations at the edge of their distributions in the conditions under which evolved, provided ␪ has not study area that were uncommon (Appalachioria species ‘‘n,’’ changed substantially since that time. Brachoria species ‘‘e,’’ B. hoffmani, and Rudiloria kleinpeteri; Table 1). Because we did not comprehensively survey these Color Measurement. We measured millipede color patterns by additional species throughout their known ranges (as we did with using a USB4000-VIS-NIR fiber optic spectrometer (blazed at the 7 endemic species: A. clade A, A. clade B, B. cedra, B. dentata, 500 nm) attached to an LS-1 tungsten halogen light source with B. insolita, B. mendota, and B. species ‘‘n’’), we only included a QR400-7-VIS-NIR bifurcated probe with an acceptance angle

Marek and Bond www.pnas.org/cgi/content/short/0810408106 1of35 of 24.8° (Ocean Optics). No color changes occurred between color patches were analyzed by using the segment classification measurements taken in the field versus the lab, based on a method (SCM) (14) without calculating differences between time-series color analysis using Munsell color chips (13). Seven segments of the spectrum to estimate opponency. This method surface regions were measured on intact living millipedes (on the examines the unprocessed physical properties of color spectra eighth metatergite—1: right paranotal spot; 2: median metater- and does not base a comparison on a receiver model, because gal spot; and 3: metatergal background; and on the 11th metater- apheloriine predators have not been identified. The SCM is gite—4: left paranotal spot; 5: median metatergal spot; 6: appropriate because it preserves the general features of metatergal background; and 7: on the legs, apheloriines curl in visual processing in which spectra are divided into regions that a defensive ball with legs tightly appressed). Supplementary have a variable probability of exciting different photoreceptor measurements were made, when needed, to sample proportion- classes. In the SCM, brightness and color are decoupled for ally to additional color spots if present (on the eighth proter- separate analysis, as in the case for animal visual modalities that gite—8: median protergal spot; on the 11th protergite—9: process intensity, or brightness, separately from hue. We divided median protergal spot). Ambient habitat light, or irradiance, was radiance spectra from millipede body patches into 4 equally measured at 2 old-growth mixed mesophytic Appalachian forests spaced segments (B: 400–475 nm; G: 475–550 nm; Y: 550–625 near the area (Joyce Kilmer Memorial Forest, Swain County, nm; and R: 625–700 nm) and calculated each segment’s total North Carolina, and Blanton Woods, Harlan County, Kentucky; intensity by integrating between segmental limits; in practice, by forest shade canopies, mostly closed but with a few small gaps) summation of radiant photon flux across discrete wavelength during the same time of day (12:01 PM) and under similar intervals because the spectral formula is unknown. We divided weather conditions (no clouds). Irradiance was measured by segment intensities (QB, QG, QY, QR) by the total spectrum using a radiometrically calibrated spectrometer and a QP600-2- intensity (QT) to get the composition quadruple: b, g, y, and r; UV-VIS irradiance probe connected to a CC-3 cosine-corrected i.e., intensity-standardized and adding up to one. The LAD- filter to collect light at an 180° solid angle aligned with the MRPP test is equivalent to a multivariate nonparametric nested millipede’s visual background according to Endler (14). Irradi- analysis of variance and yields a test statistic, ␦, and its proba- ance spectra I(␭) were consistent with published results for bility under the null hypothesis (that all samples have been drawn closed canopy, forest shade light habitats (15). For both, a large from the same distribution). It also gives an effect size statistic, contribution of irradiant photon flux (peak at 550 nm) comes K, which increases with larger aggregate differences between sets from sunlight’s transmission, fluorescence, and reflectance from of color patches; i.e., among species compared. We used the the canopy leaves. The total light intensity (between 400 and 700 LAD-MRPP at each site to test the null hypothesis of no color nm) is 3.288 in Joyce Kilmer and 2.560 ␮mol mϪ2 sϪ1 in Blanton differences (expected with a single monomorphic species) and to Woods. Irradiance spectra [I(␭), (␮mol mϪ2 sϪ1 nmϪ1)] from the quantify the color difference, measured by K, between hypoth- 2 forests were averaged and multiplied by reflectance probabil- esized mimics. We tested composite color differences for 18 ity, R(␭) (Pr) to calculate radiance [Q(␭), (␮mol mϪ2 sϪ1 srϪ1 instances at 26 sites. We conducted the test between species, nmϪ1)]. Reflectance and irradiance data files are available upon typically Apheloria and Brachoria species. At sites with only one request from the corresponding author. species present, we conducted the analysis between morphs. In some cases, we conducted analyses multiple times per site (e.g., Color Analyses. We used a statistical nonparametric permutation if some species were hypothesized mimics and others were not). method, LAD-MRPP (16), designed to test for aggregate color Sites containing too few individuals, and thereby violating pattern differences between groups—in our case, hypothetical sample size requirements of the LAD-MRPP, were excluded mimics (Table S1). It is based on a nonparametric multivariate from the analyses (sites 3a, 7b, 8, 11, 14, 18, 19, 23, 25, and 27). technique involving a combination of least absolute difference Three comparisons (at sites 20, 26, and 28) violated within-group regression analysis and a multirange permutation procedure homogeneity prerequisite (P Ͻ 0.01). In these instances, strong (16). When the receiver of color signals is known precisely, color and pattern outliers (usually a single individual; e.g., 1 red spectra are appropriately studied by using the chromaticity millipede out of a group of yellow) were removed and the method, where radiant photon flux Q(␭) is analyzed as a function analysis rerun, upon which homogeneity was accepted. At 4 sites, of its probability of stimulating ocular photoreceptors unique to we failed to reject the null hypothesis that samples were drawn a certain receiver species (16). Radiance spectra from millipede from the same distribution (P Ͼ 0.05: sites 3b, 10, 22, and 29).

1. Marek PE, Bond JE (2006) Phylogenetic systematics of the colorful, cyanide-producing 8. Clement M, Posada D, Crandall KA (2000) TCS: A computer program to estimate gene millipedes of Appalachia (, , Apheloriini) using a total genealogies. Mol Ecol 9:1657–1659. evidence Bayesian approach. Mol Phylogenet Evol 41:704–729. 9. Kuhner MK (2006) LAMARC 2.0: Maximum likelihood and Bayesian estimation of 2. Marek PE, Bond JE (2007) A reassessment of apheloriine millipede phylogeny: Addi- population parameters. Bioinformatics 22:768–770. tional taxa, Bayesian inference, and direct optimization (Polydesmida: Xystodesmi- 10. Chatzimanolis S, Caterino MS (2007) Toward a better understanding of the ‘‘Transverse dae). Zootaxa 1610:27–39. Range Break’’: Lineage diversification in southern California. Evolution 61:2127–2141. 3. Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large 11. Felsenstein J (2006) Accuracy of coalescent likelihood estimates: Do we need more sites, biological sequence datasets under the maximum likelihood criterion. Ph.D. disserta- more sequences, or more loci? Mol Biol Evol 23:691–700. tion (Univ of Texas, Austin, TX). 12. Felsenstein J (1971) Inbreeding and variance effective numbers in populations with 4. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. overlapping generations. Genetics 68:581–597. Bioinformatics 17:754–755. 13. Munsell Color Services (2000) The Munsell Book of Color (Gretag Macbeth, New 5. Posada D, Crandall KA, Templeton AR (2000) GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487–488. Windsor, NY), p 40. 6. Panchal M, Beaumont MA (2007) The automation and evaluation of nested clade 14. Endler JA (1990) On the measurement and classification of color in studies of animal phylogeographic analysis. Evolution 61:1466–1480. color patterns. Biol J Linn Soc 41:315–352. 7. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associa- 15. Endler JA (1993) The color of light in forests and its implications. Ecol Monogr 63:1–27. tions with haplotypes inferred from restriction endonuclease mapping and DNA 16. Endler JA, Mielke PW (2005) Comparing entire colour patterns as birds see them. Biol sequence data. III. Cladogram estimation. Genetics 132:619–633. J Linn Soc 86:405–431.

Marek and Bond www.pnas.org/cgi/content/short/0810408106 2of35 Fig. S1. Population phylogenies for each of the 7 species and phylogenetic locations in the Apheloriini tree. Species population phylogenies and their location (indicated by dashed lines) in the phylogeny of Apheloriini [Marek PE, Bond JE (2007) Zootaxa 1610:27–39], central circular tree. Colored circles indicate color morphs. Legend (bottom left) depicts the millipede’s ninth segment for each morph. Color morphs for each haplotype were mapped onto the phylogeny by using parsimony in the program Mesquite [Maddison WP, Maddison DR (2007) Mesquite: A modular system for evolutionary analysis, 2.01. Available at http:// mesquiteproject.org, accessed 12/10/07]. Bottom right table shows results from the test of evolutionary relatedness to evaluate the null hypothesis—putative mimic species are closely related, and shared coloration is likely a result of recent common ancestry. Blue rectangles indicate that the null hypothesis was rejected for the species compared (P Ͻ 0.05). Green branches denote Brachoria species; red, Apheloria; blue, Appalachioria; purple, Dixioria; tan, Rudiloria; orange, Deltotaria; pink, Sigmoria; light blue, Furcillaria; light green, Dynoria; light red, Croatania; brown, Brevigonus; gray, Cleptoria; dark orange, Falloria; and yellow, Prionogonus.

Marek and Bond www.pnas.org/cgi/content/short/0810408106 3of35 2 2 Fig. S2. Linear regression of population genetic parameter ␪ and species census number Nc (R ϭ 0.60, R ϭ 0.64 ln-transformed Nc). Species ␪ (y axis) over species population abundance Nc (x axis). Seven endemic species are colored by taxa.

Marek and Bond www.pnas.org/cgi/content/short/0810408106 4of35 Fig. S3. Images of millipedes from sites 1–5. Species names and specimen codes (in parentheses) are below specimen images. Page 5, site 1; page 6, site 2; page 7, site 3; page 8, site 4; page 9, site 5.

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Marek and Bond www.pnas.org/cgi/content/short/0810408106 9of35 Fig. S4. Images of millipedes from sites 6–10. Species names and specimen codes (in parentheses) are below specimen images. Page 10, site 6; page 11, site 7; page 12, site 8; page 13, site 9; page 14, site 10.

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Marek and Bond www.pnas.org/cgi/content/short/0810408106 14 of 35 Fig. S5. Images of millipedes from sites 11–15. Species names and specimen codes (in parentheses) are below specimen images. Page 15, site 11; page 16, site 12; page 17, site 13; page 18, site 14; page 19, site 15.

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Marek and Bond www.pnas.org/cgi/content/short/0810408106 19 of 35 Fig. S6. Images of millipedes from sites 16–20. Species names and specimen codes (in parentheses) are below specimen images. Page 20, site 16; page 21, site 17; page 22, site 18; page 23, site 19; page 24, site 20.

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Marek and Bond www.pnas.org/cgi/content/short/0810408106 24 of 35 Fig. S7. Images of millipedes from sites 21–25. Species names and specimen codes (in parentheses) are below specimen images. Page 25, site 21; page 26, site 22; page 27, site 23; page 28, site 24; page 29, site 25.

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Marek and Bond www.pnas.org/cgi/content/short/0810408106 33 of 35 Movie S1. Video of mimicry community from site 1, Stone Mountain, Virginia. Species shown: Apheloria clade A, Brachoria cedra, B. dentata, B. insolita, and B. hoffmani.

Movie S1 (MOV)

Marek and Bond www.pnas.org/cgi/content/short/0810408106 34 of 35 Table S1. Summary of the 29 study sites Site No. Species

1ϩ 43 B. insolita (18 i and 6 h): 14 road, 4 checkers; Apheloria clade A (11 i and 9 h): 9 caution, 2 yellowjacket; B. cedra (9 i and 2 h): 9 road; B. dentata (4 i and 3 h): 4 road; B. hoffmani (1 i and 1 h): 1 road. 2ϩ 31 Apheloria clade A (24 i and 8 h): 12 striped, 7 yellowjacket, 4 caution, 1 road; B. cedra (4 i and 2 h): 4 road; B. insolita (2 i and 1 h): 1 road, 1 checkers; B. hoffmani (1 i and 1 h): 1 road. 3ϩ 28 Apheloria clade B (16 i and 4 h): 16 striped; Apheloria clade A (9 i and 3 h): 9 striped; B. dentata (1 i and 1 h): 1 road. (3a ϭ striped and road morphs; 3b ϭ striped morph.) 4ϩ 9 Apheloria clade A (6 i and 5 h): 6 caution; B. mendota (3 i and 3 h): 2 caution, 1 road. 5ϩ 16 Apheloria clade A (11 i and 8 h): 11 road; B. mendota (5 i and 2 h): 5 road. 6Ϫ 11 Apheloria clade B (8 i and 6 h): 8 chess; B. mendota (3 i and 2 h): 3 taillight. 7ϩ 13 B. mendota (10 i and 5 h): 10 taillight; Apheloria clade A (1 i and 1 h): 1 chess; Apheloria clade B (1 i and 1 h): 1 chess; Appalachioria species ЉnЉ (1 i and 1 h):1 chess. (7a ϭ taillight and chess morphs; 7b ϭ chess morph.) 8Ϫ 9 B. mendota (8 i and 4 h): 8 taillight; Appalachioria species ЉnЉ (1 i and 1 h): 1 chess. 9Ϫ 5 Apheloria clade B (4 i and 3 h): 4 chess; B. mendota (1 i and 1 h): 1 taillight. 10Ϫ 9 Apheloria clade B (9 i and 5 h): 9 chess. 11Ϫ 3 Apheloria clade B (2 i and 2 h): 2 chess; Rudiloria kleinpeteri (1 i and 1 h): 1 taillight. 12Ϫ 1 B. mendota (1 i and 1 h): 1 taillight. 13Ϫ 21 B. mendota (21 i and 11 h): 18 taillight, 2 headlight, 1 checkers. 14ϩ 3 Apheloria clade A (2 i and 2 h): 2 caution; B. dentata (1 i and 1 h): 1 road. 15ϩ 12 B. cedra (7 i and 2 h): 7 road; B. mendota (3 i and 1 h): 3 road; Apheloria clade A (2 i and 1 h): 2 caution. 16ϩ 11 Apheloria clade A (6 i and 4 h): 6 caution; B. mendota (4 i and 2 h): 4 road; B. dentata (1 i and 1 h): 1 road. 17Ϫ 1 Apheloria clade A (1 i and 1 h): 1 caution. 18ϩ 11 B. dentata (10 i and 7 h): 6 caution, 4 road; Apheloria clade A (1 i and 1 h): 1 caution. 19ϩ 11 Apheloria clade A (10 i and 6 h): 10 caution; B. cedra (1 i and 1 h): 1 road. 20ϩ 20 Apheloria clade A (14 i and 8 h): 3 road, 11 headlight; B. species ЉnЉ (6 i and 5 h): 1 road, 4 headlight, 1 checkers. 21ϩ 18 B. cedra (9 i and 1 h): 8 road, 1 headlight; B. dentata (7 i and 4 h): 7 caution; B. species ЉnЉ (2 i and 1 h): 2 caution. 22ϩ 18 Apheloria clade A (16 i and 6 h): 9 caution, 5 headlight, 2 road; B. dentata (2 i and 2 h): 2 road. 23ϩ 3 Apheloria clade A (2 i and 2 h): 2 headlight; B. species ЉnЉ (1 i and 1 h): 1 headlight. 24Ϫ 24 B. hoffmani (24 i and 9 h): 8 striped, 16 road. 25Ϫ 5 Apheloria clade A (5 i and 5 h): 5 caution. 26ϩ 16 Apheloria clade A (8 i and 3 h): 8 headlight; B. dentata (8 i and 3 h): 8 headlight. 27ϩ 15 B. species ЉeЉ (14 i and 5 h): 14 road; Aph. clade A (1 i and 1 h): 1 road. 28ϩ 10 Apheloria clade A (5 i and 4 h): 5 chess; B. dentata (3 i and 2 h): 2 chess, 1 checkers; B. mendota (2 i and 1 h): 1 road, 1 headlight. 29Ϫ 21 Apheloria clade A (21 i and 7 h): 21 chess.

In the site column, a plus sign indicates mimicry present; and a minus sign mimicry absent. No. column shows the total sum of individuals at a site. In the species column, i indicates the number of individuals, or abundance; h, the number of unique mtDNA haplotypes. Color morphs (see Fig. S1) and frequencies follow species names.

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