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Table S1. Information for voucher specimens added to collections of Lankester Botanic Garden, Costa Rica.

Table S2. Sampling locations for all study species.

Table S3. Details of AFLP method used for each study species.

Table S4. Scoring analysis details for AFLP datasets.

Table S5. GenBank accession numbers for newly generated matK sequences.

Table S6. Ecological characteristics of study clades.

Table S7. Branch circumference mean and variance for all study species.

Figure S1. Sampling locations for study species from the Masdevallia-Trisetella and Lepanthes-Lepanthopsis clade pairs.

Figure S2. Sampling locations for study species from the Platystele-Dryadella and Epidendrum-Brassavola clade pairs.

Figure S3. Sampling locations for study species from the Scaphyglottis-Jacquiniella clade pair.

Figure S4. The relationship between Φst and distance for all study species, for the reduced dataset.

Figure S5. Associations of overall neutral genetic differentiation and species range size with species phylogeny (data from the reduced dataset).

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