*2.1. Study Site*

Research was performed at Los Amigos Biological Station (LABS; 12◦34-07--S, 70◦05-57--W, 250 m elev; also known as CICRA in previous literature), located in Manu province, Madre de Dios region, southeast Peru. In addition, we carried out field surveys at Centro de Monitoreo 1 (CM1; 12◦34-17-- S, 70◦04-29-- W), located ca. 3.5 km east from LABS, and Centro de Monitoreo 2 (CM2; 12◦26-57-- S, 70◦15-06-- W, 260 m), located ca. 25 km northwest from LABS. The annual rainfall recorded at LABS ranges between 2700 and 3000 mm [22]. The dry season (June–September) has markedly lower rainfall and is slightly cooler than the wet season. The mean annual temperature ranges between 21 ◦C and 26 ◦C (N. Pitman, pers. comm.). Most of our surveys took place in four forest types: mature floodplain forest (hereafter referred to as floodplain forest), terra firme forest, bamboo forest dominated by two native woody bamboo species (*Guadua sarcocarpa* and *G. weberbaueri*), and palm swamp dominated by a native palm (*Mauritia flexuosa*). We also surveyed other terrestrial habitats including secondary forest, riparian forest, clearings, and river banks; and various types of aquatic habitats including oxbow lakes, streams, permanent ponds (e.g., "Pozo Don Pedro"), seasonal ponds, and other wetlands (e.g., small swamps dominated by other palm species). Further details regarding primary forest types and aquatic habitats is available in earlier references [20,21,23–25].

## *2.2. Data Collection*

From 2001 to 2018, we surveyed reptile and amphibian communities at LABS using a variety of sampling techniques. Survey methodologies included (1) leaf-litter plot surveys, (2) nocturnal visual encounter surveys, (3) passive trapping using pitfall traps and funnel traps, and (4) a variety of active and targeted search strategies to increase encounter probabilities for specific taxa and/or within particular microhabitats. Leaf-litter sampling protocols used at this location have been described previously [20] and involved exhaustive search through randomly-selected 100 m<sup>2</sup> or 25 m<sup>2</sup> square plots by teams of trained observers at night. Nocturnal visual encounter surveys were performed by actively search for reptiles and amphibians along the official LABS trail network (trail surveys), and by searching along 50 m or 100 m transects (transect surveys) that we established away from major trails [20]. Both trail and transect surveys typically involved groups of 2–3 researchers, but survey procedures differed, with trail surveys conducted at a more rapid walking pace (mean pace: 0.36 km/hr) relative to transect surveys (mean pace: 0.10 km/hr). Use of vertebrate animals was approved by the Animal Care and Use Committee of the University of Michigan (protocol PRO00008306).

In general, fieldwork from 2001–2015 emphasized transect surveys and leaf-litter plot surveys, and work from 2016–2018 was focused primarily on trail surveys and passive trapping. However, pitfall trapping and trail surveys occurred prior to 2016, and some transect/leaf-litter sampling occurred between 2016–2018. From 2016–2018, we conducted approximately 340 km and 14,500 min of nocturnal trail surveys. We also performed at least 32.5 km and 20,500 min of transect surveys (~650 transects), along with approximately 375 leaf-litter plot surveys.

Preliminary surveys with drift fences and pitfall traps took place in the dry seasons of 2005 and 2006. In four forest types (floodplain forest, terra firme forest, bamboo forest, and palm swamp), we set up three arrays of drift fences and pitfall traps. Each array had three fences of 5 m each in length. We used plastic sheets for making the fences and we buried each fence 10 cm in the ground, leaving at least 50 cm of fence above ground. We used four 19 L plastic buckets as pitfall traps, following a lineal construction design. The opening of each bucket was flush with the ground surface. The arrays remained in the same location up to four weeks, and were checked at least once per day.

From 2016–2018, we established a regular grid of pitfall and funnel traps in multiple habitats; sites were surveyed in March–April 2016, November–December 2016, November–December 2017, and November–December 2018. Each trapline involved either three pitfall traps or four funnel traps. Funnel trap [26] dimensions were 18 cm × 18 cm × 79 cm, and were purchased from Terrestrial Ecosystems (Mt Claremont, Australia). Traps were connected by 12 m of plastic drift fencing. All traps were checked at least once per day. From 2016–2018, we conducted a total of 9181 trap-days of funnel trap sampling, and 6670 trap-days of pitfall sampling. Many records were also obtained through opportunistic sampling, particularly medium-to-large diurnal snakes that were most commonly encountered on trails while researchers checked traps or performed other activities.

In general, we collected multiple voucher specimens per species, to facilitate taxonomic work, to generate a permanent and curated record of squamate biodiversity for LABS and to enable us to create and curate community resources that can only be provided by physical specimens (e.g., samples of venom, Duvernoy's gland, glandular skin, and internal parasites). Multiple tissue types were taken from all vouchered animals and preserved in RNAlater. All vouchered specimens were deposited in the herpetological collections at the Museo de Historia Natural, Universidad Nacional Mayor de San Marcos (MUSM; Lima, Peru), or in the University of Michigan Museum of Zoology (UMMZ). Records for several species were obtained through opportunistic sampling by researchers or visitors to LABS who were unaffiliated with our research group. In these cases, we required that the records be accompanied by photographs and specific sublocality information.

## *2.3. Data Tabulation and Analysis*

We compiled three lists of squamate reptiles for LABS. First, we consider only the set of species documented explicitly by our group from the immediate vicinity of the LABS station. The area of this survey region is approximately 10 km2, and thus provides a useful "local scale" counterpart to other spatially explicit, localized surveys in Amazonia (e.g., surveys at Cusco Amazonica, Peru; Tiputini Biological Station, Ecuador; Reserva Ducke, Brazil). The second list includes all species documented from the Los Amigos conservation concession, including parts of the reserve or its buffer zone that were located across the Rio Los Amigos (CM1) or some distance upriver from LABS (CM2). Finally, we generated an expected list that included all species known from lowland Amazonian rainforest with documented occurrences in the broader Los Amigos / Madre de Dios region; this includes all species known from other lowland sites within roughly 150 km of LABS, and which we consider to have a high likelihood of detection with continued work at the site. Where possible, we used recent taxonomic works to update the identifications of many specimens in our dataset (e.g., *Erythrolamprus;* [27]).

We analyzed the tempo of species accumulation through time for our 2016–2018 fieldwork, where much of our efforts were focused on squamate sampling, and where we believe we had a reasonably consistent sampling effort from day-to-day. We used randomized sampling from the full set of survey days from 2016–2018 (112 days) to generate an expected species accumulation curve as a function of survey effort. Using nonlinear regression, we fitted a simple hyperbolic model for species accumulation through time (equation 2 in [28]), and used it to predict both the total richness of the LABS squamate fauna and to estimate the effort required to achieve a comprehensive inventory. In this model [28], the estimated species richness is given by *S*(*n*) = *Smax n*/(*B* + *n*), where *B* and *Smax* are fitted constants, and *n* is the number of samples. Here, a sample is equated to a "survey day", and *Smax* is the asymptotic richness as *n* becomes large.

For comparative purposes, we also compiled data on squamate richness from a number of previous studies. Where possible, we updated records from those previous lists to reflect recent taxonomic changes. However, we did not attempt to comprehensively address taxonomic changes to species lists, because most taxonomic changes involved updates to specific epithets, and thus had little impact on either the total or generic species richness at a given site. We also obtained estimates of species richness at the local-to-regional scale for a range of other taxa (e.g., trees, birds, lianas), focusing in particular on northern and southern lowland sites in the western Amazon basin. This generally involved comparing sites from the Rio Napo drainage (Yasuní, Tiputini) to those from southern Peru (Madre de Dios watershed). These and other locations discussed in text are shown in Figure 2.

**Figure 2.** Localities in the western and central Amazon basin discussed in this article. YA: Yasuní National Park and Tiputini Biodiversity Station; IQ: Iquitos (Loreto, Peru); PA: Panguana Biological Station; CC: Cocha Cashu Biological Station; LA: Los Amigos Biological Station (LABS); ML: Manu Learning Centre; EI: Explorer's Inn; CA: Cusco Amazónico; LP: Las Piedras Biological Station; SA: Samuel Hydroelectric Project (Rondônia, Brazil); MA: Manaus, Brazil. All localities are lowland rainforest sites that receive approximately 2200–3200 mm of precipitation annually, although southern sites are markedly more seasonal than those in the north.
