Typha

Annotation of the sequenced genomes was performed using DOGMA [55] (link), coupled with manual selections for start and stop codons and for intron/exon boundaries. We calculated the average cp genome size of subfamilies in Poaceae on the basis of the species listed in Table 3. We estimated the monocot mean cp genome size based on Acorus calamus (AJ879453) [56] (link), Dioscorea elephantipes (EF380353) [57] (link), Lemna minor (DQ400350) [58] (link), Oncidium Gower Ramsey (GQ324949) [59] (link), Phalaenopsis aphrodite (AY916449) [60] (link), Phoenix dactylifera (GU811709), and Typha latifolia (GU195652) [61] (link). The rpoC2 sequences from the grass family were aligned to the rpoC2 sequences of tobacco by MEGA 4.0 to determine the insertion size in the gene. We downloaded B. oldhamii and D. latiflorus cp genomes sequences from GenBank, and multiple alignments of eight bamboos cp genomes were made using MAFFT version 5 [62] (link). Full alignments with annotations were visualized using the VISTA viewer. The genetic divergence represented by p-distance was calculated by MEGA 4.0 with species of Arundinarieae as one group and those of Bambuseae as another.
We determined the three types of repeats, dispersed, tandem and palindromic, by first applying the program REPuter and then manually filtering the redundant output of REPuter. Gap size between palindromic repeats was restricted to a maximal length of 3 kb. Overlapping repeats were merged into one repeat motif whenever possible. A given region in the genome was designated as only one repeat type, and tandem repeat was prior to dispersed repeat if one repeat motif could be identified as both tandem and dispersed repeats. For coding, each repeat present in a given genome was ‘1’ and those absent were labeled as ‘0’. We performed MP analyses of this matrix using PAUP*4.0b10 [63] to implement exhaustive tree searches. Non-parametric bootstrap analysis was conducted under 1,000 replicates with TBR branch swapping.

To demonstrate the use of the ARBIMON-acoustic application we created species-specific models for amphibians, birds, mammals, and insects based on recordings from a site in Puerto Rico and a site in Costa Rica. The species were selected to cover a range of taxa with different types of vocalizations. Vocalizations of frogs and birds were confidently identified based on our experience and comparisons with different sources of animal calls. Unfortunately, the two insect species, most likely cicadas, could not be captured and identified, but we carefully documented the call characteristics to assure that we modeled a specific species in each site.
The site in Puerto Rico, Sabana Seca (SS), is a small (180 ha) wetland near the Caribbean Primate Research Center (CPRC) in Toa Baja, Puerto Rico (18°25′56.01″ N and 66°11′45.62″ W). Typha dominguensis (cattail) is the dominant species in the wetland. This site is the only known locality of Eleutherodactylus juanariveroi (coqui llanero), an endangered frog species that was recently discovered (Rios-Lopez & Thomas, 2007 ). The major motivation for establishing a permanent recording station in Sabana Seca was to improve the information on the calling activity and population dynamics of E. juanariveroi. The station was established in March 2008, and for this study we present the results of species-specific identification models of the endemic frog species, E. juanariveroi, an exotic frog species Rana gryllo (pig frog), and an unidentified insect (insect #1).
The other study site was La Selva Biological Station (LSBS) in Costa Rica (10°25′ N, 84°01′ W). This reserve encompasses approximately 1,510 ha of which 64% is primary tropical forest, and contains a high diversity of flora and fauna (Clark & Gentry, 1991 ). The objective of this project was to conduct broad acoustic monitoring within mature forest for all species that contribute to the acoustic community. For this site, we created species-specific identification models for six species: Tinamus major (great tinamou), Ramphastos swainsonii (chestnut-mandibled toucan), Oophaga pumilio (strawberry poison-dart frog), Diasporus diastema (tink frog), Alouatta palliata (mantled howler monkey), and an unidentified insect (insect #2).
In addition to the recordings from the two permanent stations described in this manuscript, other recordings have been added to the ARBIMON database from other permanent stations in Puerto Rico, Hawaii, and Arizona, and from portable recording systems in Puerto Rico, Costa Rica, Argentina, and Brazil. As of May 7, 2013, the system has >1.3 million 1-min recordings, which can be freely accessed through the project web page (arbimon.net).

We were interested in assessing the relationship between the presence of schistosome-competent snails and infection burden in nearby humans. Both B. globosus and B. truncatus were of interest as intermediate hosts of S. hematobium (55 (link), 56 (link)), causative agent of human urogenital schistosomiasis (SI Appendix, Text S3). Patchiness in snail distributions could arise from snails’ strong association with ephemeral environmental features like vegetation (SI Appendix, Text S3). Because we wanted to quantify snails as accurately as possible, we made independent measures of their density in open-water/mud-bottom habitat, nonemergent vegetation (e.g., Ceratophyllum spp., Ludwigia spp., and Potamogeton spp.), and emergent vegetation (e.g., Typha spp., Phragmites spp.) within each site.
We adopted an area-specific technique for snail surveys, which allowed us to explore the spatial and temporal scale of heterogeneity in snail density (details in SI Appendix, Text S3). To randomly select snail-sampling locations within each of the sites, we used Google Earth to delineate a boundary around each site (Fig. 1D). Fifteen random points were stratified across the 3 microhabitat types (emergent vegetation, nonemergent vegetation, and open water/mud bottom) in proportion to the area of those microhabitats within the boundary of the site. We exhaustively sampled each quadrat (76.2-cm length × 48.26-cm width × 48.26-cm height; area, 0.3677 m²), placed all snails found into labeled vials, and returned them to the laboratory, where they were counted, identified to species, measured (shell height to the nearest 0.01 mm), and screened for parasite infection by shedding and dissection. All trematode infections of fork-tailed cercariae (57 (link)) were placed individually on WhatmanFTA cards (GE Healthcare Life Sciences) for molecular identification (58 (link)) and sequenced, and only snails infected with S. hematobium or S. hematobium–bovis hybrids were considered to be infected (since these are the only species occurring in B. truncatus/globosus that are capable of infecting humans; refs. 59 (link) and 60 (link)). Cercariae on FTA cards and snail tissue vouchers were accessioned into the Schistosomiasis Collection at the Natural History Museum (SCAN) (61 (link)). Schistosome-competent snails can be sensitive to water conditions, so at each site, we also measured water flow rate, water temperature, salinity, turbidity, pH, and nitrate, nitrite, and phosphate (SI Appendix, Text S3).

We conducted our research at the RNUP in Toronto, Ontario, Canada (43.8188° N, 79.1728° W). The RNUP is the first urban national park in Canada and is part of a pilot project carried out by Parks Canada to conserve urban biodiversity, Indigenous cultural landscapes, and agricultural heritage of the area [27 ]. It is an ecologically protected zone established in 2015 under the Rouge National Urban Park Act [28 ] that encompasses 80 km² of forests, meadows, rivers, wetlands, and fragments of rare habitats such as oak savannah and Carolinian woodlands [27 ]. Situated at the center of the Canada’s largest metropolitan area (Fig 1), the park is surrounded by major highways, freight and passenger railways, residential, commercial, and industrial developments, and agricultural lands [27 ].
Our study site is situated in the southern portion of the RNUP. In the early 1990s, the area was restored to a wetland complex of vernal pools, and more permanent ponds of various sizes with littoral vegetation including alders (Alnus spp.), cattails (Typha spp.), sedges (Carex spp.), and willows (Salix spp.) [21 ]. More recently, invasive species, such as European common reed (Phragmites australis), garlic mustard (Alliaria petiolate), purple loosestrife (Lythrum salicaria), and reed canary grass (Phalaris arundinacea) have become ubiquitous. Once restoration efforts were completed, the Toronto Zoo’s Adopt-A-Pond Wetland Conservation Program began wetland surveys to evaluate species occurrence in the area. The surveys found three at-risk turtle species: Painted Turtle (Chrysemys picta), Snapping Turtle (Chelydra serpentina), and the globally endangered [33 ] Blanding’s Turtle. In Canada, Painted and Snapping turtles are designated as ‘Special Concern’ by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) [34 , 35 ], and Blanding’s Turtle is designated as ‘Endangered’ [36 ].
In 2005, the Blanding’s Turtle population within the park boundary was known to be comprised of three adult turtles (two males and one female) and a juvenile. Two additional adult turtles (one male and one female) were discovered in 2006 in an adjacent creek approximately 4 km from the RNUP (Toronto Zoo [Unpublished]). Given that the Blanding’s Turtle population in the RNUP was presumed functionally extinct, the Toronto Zoo initiated a headstarting program in 2012 to supplement the wild population [21 ]. A preliminary population viability analysis (PVA) showed that 40 headstarted turtles with 1:1.5 male:female sex ratio would need to be released each year for 20 years to reach a self-sustaining population of 150 adult Blanding’s Turtles (Toronto Zoo [Unpublished]). The first release occurred in 2014 with 10 juveniles, followed by 21 in 2015, 36 in 2016, 49 in 2017, 49 in 2018, 48 in 2019, 57 in 2020 for a total of 270 headstarted turtles released to date (Toronto Zoo [Unpublished]). An additional 184 hatchlings were released without headstarting because the number of eggs that hatched exceeded the capacity of the Toronto Zoo rearing facility.

The PPR (41.7° to 54.7°N latitude, 92.5° to 114.5°W longitude) covers ~820,000 km² of the Great Plains in the United States and Canada and is home to millions of depressional wetlands (16 ). These depressions were formed during the Wisconsin glaciation, approximately 12,000 years ago (17 ). The underlying glacial till has low permeability, allowing depressions to fill and hold water and to ultimately develop into palustrine and lacustrine ecosystems made up of wetlands, ponds, and shallow lakes. We collectively refer to these depressional waterbodies as “wetlands” because the majority of them are less than 1 ha (0.01 km²) in size, less than 1 m deep, and seasonally (nonpermanent) ponded, meeting the definition of a wetland (sensu the Cowardin classification system) (61 ). In the PPR, larger wetlands often are shallow (<2 m) and have similar biogeochemical processes as smaller wetlands (62 ). Wetlands contain methanogenic microbial communities that are adapted to anoxic saturated soils, where they decompose organic material and produce CH₄ (9 (link)). PPR wetlands range from fresh to hypersaline (up to three times more saline than the ocean) (17 ). This salinity is attributable to groundwater transport of dissolved sulfate through the ion-rich glacial till. PPR wetlands with higher sulfate concentrations have suppressed CH₄ emissions (23 ), albeit high dissolved organic carbon concentrations in some PPR wetlands can support CH₄ production in the presence of sulfate (24 (link)). Larger wetlands in topographically lower landscape positions tend to accumulate groundwater-derived solutes, while smaller, shallower wetlands are filled with rainwater and snowmelt (45 ). Vegetation characteristics of PPR wetlands are influenced by water depth and chemistry, typically with concentric zones with open water with submerged aquatic vegetation toward their centers and marshes and meadows with floating and emergent macrophytes such as Typha toward their edges (37 , 44 ).
The climate of the PPR is continental with a north to south temperature gradient ranging from ~2° to 8°C mean annual temperature and a northwest to southeast precipitation gradient ranging from ~400 to 900 mm year⁻¹ (63 , 64 (link)). The PPR is centered on the confluence of tropical Pacific Ocean (El Niño–Southern Oscillation), eastern Pacific Ocean (Pacific Decadal Oscillation), and North Atlantic (Atlantic Multidecadal Oscillation) oscillations (65 ). Synergistic effects from synchronization of these oscillations lead to decadal periods of drought and deluge that influence groundwater levels. Wetland surface water is also extremely sensitive to variability in seasonal and annual precipitation (66 ). Thus, the size and hydroperiod of PPR wetlands are the result of complex interactions between long-term climate and short-term weather. An extreme multiyear drought from 1988 to 1992 led to the drying of many wetlands, with 1991 having the lowest wetland extent (45 ). Following the extreme drought, much of the PPR experienced a shift to a wetter climate. Annual precipitation in 2011 was one of the highest on record, and 2011 had some of the highest numbers of wetlands with ponded water (45 ). Therefore, we use 1991 and 2011 as extreme dry and wet years, respectively, in our modeling.
The PPR is intensively used for agricultural crop and biofuels production, which has led to extensive wetland drainage and upland conversion from prairie grassland to cropland (16 ). Drainage reduces CH₄ emissions and soil organic carbon stocks but increases CO₂ and nitrous oxide (N₂O) emissions (22 (link), 67 ). Upland conversion from grassland to cropland can affect CH₄ emissions indirectly through increased nutrient loading, resulting in increased CH₄ emissions (38 (link)). However, wetlands nested in croplands are also subject to tillage and aeration of soils, thereby lowering CH₄ emissions (22 (link)). Wetland drainage often results in consolidation of water from multiple smaller wetlands into one larger wetland. These larger wetlands are deeper with fewer fluctuations in water levels, as well as greater coverage of invasive emergent hybrid cattail, all of which favors CH₄ production and emissions (37 ). Consolidation of wetlands also targets the smallest wetlands changing the distribution of wetland size classes, albeit the vast majority of wetlands are still <1 ha.

LLNWP (123°41′~123°48′ E, 42°15′~42°18′ N) is an urban wetland park that is located in the south of Northeast China, close to Shenyang City. This is a location that is well-known in China for its old industrial base, located at the junction of the Liao River, Fan River, and Chai River. The study area was 776.74 hm² (Figure 2). The climate is a temperate continental monsoon climate, with an average annual temperature of 6.3 °C, average annual precipitation of 700 mm, an annual sunshine duration of 2801 h, and a frost-free period of 127–165 days. The wetland is located on the alluvial plain of the Liao River and the first terrace of the Chai River, with flat terrain and an altitude of 50.5 m~61.8 m. The topography is composed of alluvial plains–floodplains–flat depressions in the low terraces, and the soil consists of meadow soil and paddy soil. Water resources are abundant, and most groundwater levels are between 1.0 m and 3.0 m. LLNWP is mainly comprised of natural wetlands combined with the restoration and reconstruction of artificial wetlands. The northeast and southern areas mainly consist of artificial wetlands, and the remaining areas are comprised of natural wetlands. The natural wetland types are mainly freshwater river wetlands and swamps, and the artificial wetlands are mainly paddy fields and reservoir ponds. The water flow is mainly horizontal, but there will be some vertical water flow changes due to miniature terrain drops. LLNWP has a total of 9.1 million aquatic plants of 26 species, including reeds, cattails, and water onions. The main vegetation in the natural wetland is reeds, lotus, wild rice stems, etc. In the northeast artificial wetland, the main vegetation types are reeds and rice; the southern right side mainly includes landscape plants, including calamus, cattails, etc., and the southern left side is dominated by rice plants. As the main function of the artificial wetland is to restore the original degraded natural wetland, LLNWP contains less porous materials of three main types: limestone, zeolite and crushed stone. This area possesses crucial value in providing animal and plant habitats and breeding grounds, maintaining species diversity, and ensuring urban ecological security.