Supporting Information

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1 Supporting Information Rovito et al /pnas SI Text RT-PCR Batrachochytrium dendrobatidis Assay. This assay uses species-specific primers ITS1 3 Chytr and 5.8S Chytr and the probe ChytrMGB2 to amplify ITS-1 and 5.8S region (1). DNA was extracted by using the PrepMan Ultra protocol for DNA extraction (Applied Biosystems). DNA standards (provided by A. D. Hyatt, Commonwealth Scientific and Industrial Research Organisation, Geelong, Australia) were diluted to give 100, 10, and 1 genome equivalents for use in Taqman assay (1). Results from the assay are presented quantitatively as the number of genomic equivalents or zoospore equivalents recovered from tissue from each specimen. Analysis of Historical Field Note Data. The quantity and identification of the specimens were confirmed by checking the MVZ online database (mvzarctos.berkeley.edu) and, when necessary, by examining specimens in the collection. In cases where only a minimum number of salamanders found was given, this number was used to provide a conservative estimate of encounter rate. When only approximate search times were given, the following classification was used to quantify search time: brief stop 1h, a couple of hours 2 h, a few hours 3 h, morning or afternoon 3 h, most of a day 4 h, full day 6 h. In cases where the exact number of collectors was not recorded, the following numbers were assigned: several 5 collectors, many 10 collectors. These approximations were necessary because the original data were not collected for analysis in this framework. In most cases, only a portion of this time was actually spent actively searching, and fewer collectors were probably involved. The high estimates of search time and number of collectors were chosen to provide an extremely conservative estimate of salamander encounter rate, to avoid reporting an artifact as a decline in encounter rate. Mean encounter rate per species in the 1970s and from 2005 to 2007 was compared by using a t test (in cases of similar sample size) or a Wilcoxon test (in cases of unequal sample sizes) for the highest site on the gradient and at Buena Vista, where sample sizes from 2005 to 2007 were sufficiently large for statistical analyses. Collections from the Buena Vista site were made primarily by local collectors in the past who may have brought salamanders from both the upper and lower cloud forest zones. These collectors consistently worked in the same areas, however, justifying the inclusion of these collecting events in a single site. At this site, P. brunnata, P. goebeli, and P. sp. nov. San Marcos were only ever found in a very limited elevational range by MVZ researchers. For this reason, only collecting events between 2,350- and 2,400-m elevation were counted when calculating encounter rates for the three species of Pseudoeurycea. Although Bolitoglossa rostrata occurs at high elevations on the upper slopes of Volcan Tajumulco, many of the sites visited on this part of the transect in the past were above its upper elevational limit. For this reason, B. rostrata was analyzed only for the El Rincon site. Two seldom-encountered species from Finca Santa Julia, Oedipina stenopodia and Bolitolgossa salvinii, were excluded from the analysis because of a lack of data from the 1970s (19 O. stenopodia and 0 B. salvinii collected from ) and a lack of recent search effort. 1. Boyle DG, Boyle DB, Olsen V, Morgan JA, Hyatt AD (2004) Rapid quantitative detection of chytridiomycosis (Batrachochytrium dendrobatidis) in amphibian samples using real-time Taqman PCR assay. Dis Aquat Organ 60: of6

2 Fig. S1. Phylogeny of Neotropical plethodontid genera (redrawn from ref. 1], with branch lengths proportional to time. Genera containing species with reported declines in the literature (2,3) are shown in bold; numbers on branches indicate number of species shown to be declining in this study. At right, number of threatened species based on 2008 global amphibian assessment (IUCN categories CR, EN, VU)/total number of species in genus. Pseudoeurycea, shown to be paraphyletic in Wiens et al. (1), is shown as a single lineage (including Lineatriton) for simplicity. 1. Wiens JJ, Parra-Olea G, García-París M, Wake DB (2007) Phylogenetic history underlies elevational diversity patterns in tropical salamanders. Proc R Soc London Ser B 274: Whitfield SM, et al. (2007) Amphibian and reptile declines over 35 years at La Selva, Costa Rica. Proc Natl Acad Sci USA 104: Lips KR, et al. (2006) Emerging infectious disease and the loss of biodiversity in a Neotropical amphibian community. Proc Natl Acad Sci USA 103: of6

3 Table S1. Total collection numbers for B. rostrata, B. morio, P. rex at localities in western Guatemala and Chiapas, Site Department/State Visits B. rostrata B. morio P. rex Search time in person hours Sierra de los Cuchumatanes Huehuetenango 2 (Oct. 2005, Aug. 2007) 56, 20 ** 1, , 23 Rancho de Tejo Totonicapan 1 (Nov. 2005) 39 ** ** 3.75 High point on Panamerican Highway Totonicapan/Solola 2 (Nov. 2005, Aug. 2007) 0, 0 0, 5 0, , 10 Cerro Tecpan Chimaltenango 2 (Oct. 2005, Aug. 2006) 0, 0 1, 0 0, 0 10, 5.4 Cerro Tzontehuitz Chiapas 1 (Aug. 2006) 2 ** ** 4 Cerro Mozotal Chiapas 1 (Aug. 2006) ** ** 0 8 Double asterisk indicates that site is outside the range of a species. Sierra de los Cuchumatanes totals do not include sites below lower elevational limit of P. rex. 3of6

4 Table S2. Collection totals for Thorius at Puerto del Aire, Veracruz/Puebla, Mexico Month Total Thorius collected Museum April, MVZ September, LACM September, LACM January, MVZ January, MVZ January, MVZ January, MVZ January, MVZ April, LACM July, LACM July, LACM September, NMNH February, MVZ February, MVZ February, MVZ July, NMNH July, MVZ July, MVZ July, MVZ July, MVZ July, MVZ July, MVZ January, MVZ October, MVZ April, MVZ August, MVZ January, MVZ September, MVZ January, MVZ MVZ, Museum of Vertebrate Zoology; LACM, Natural History Museum of Los Angeles County; NMNH, Smithsonian Institution National Museum of Natural History. 4of6

5 Table S3. Results of RT-PCR assay for Batrachochytrium dendrobatidis from salamanders on the San Marcos transect and other sites in western Guatemala and Chiapas Site No. tested Positives Species testing positive Zoospore equivalent San Marcos: Tajumulco 6 0 San Marcos: El Rincon 35 1 D. bromeliacius 20.5 San Marcos: Buena Vista 5 1 B. lincolni San Marcos: South transect 8 1 B. franklini lincolni hybrid Lowland sites ( 1,500 m elevation) 8 4 B. occidentalis 0.74, 2.1, 83.2, San Marcos Total 62 7 Sierra de los Cuchumatanes 17 0 High point on Panamerican Highway 6 0 San Cristobal de las Casas area 2 0 Volcan Chicabal 2 0 Western Guatemala and Chiapas Total of6

6 Table S4. Species present within each elevational zone on the San Marcos transect, elevation ranges of these zones, and survey sites Elevational zone Species present Elevational range, m Survey sites High-elevation grassland and woodland Upper cloud forest Lower cloud forest Lower wet forest Pseudoeurycea rex, Bolitoglosssa rostrata 2,800-4,200 Upper slopes of Volcán Tajumulco ( 3,000 m) Pseudoeurycea goebeli, Pseudoeurycea brunnata, 2,400 2,800 El Rincon (2,700 m), Buena Vista Pseudoeurycea sp. nov. San Marcos, (2,400 m) Bolitoglossa rostrata, Bolitoglossa lincolni, Bolitoglossa morio, Dendrotriton bromeliacius Bolitoglossa engelhardti, Bolitoglossa franklini, 1,600 2,400 Finca Insula (2,200 m) Bolitoglossa flavimembris, Dendrotriton bromeliacius Bolitoglossa occidentalis, Bolitoglossa flaviventris, Bolitoglossa salvinii, Oedipina stenopodia 0 1,600 Finca Santa Julia (1,100 m) 6of6