Assembling microbial communities: a genomic analysis of a natural experiment in neotropical bamboo internodes.

Microbes participate in ecological communities, much like multicellular organisms. However, microbial communities lack the centuries of observation and theory describing and predicting ecological processes available for multicellular organisms. Here, we examine early bacterial community assembly in the water-filled internodes of Amazonian bamboos from the genus Guadua. Bamboo stands form distinct habitat patches within the lowland Amazonian rainforest and provide habitat for a suite of vertebrate and invertebrate species. Guadua bamboos develop sealed, water-filled internodes as they grow. Internodes are presumed sterile or near sterile while closed, but most are eventually opened to the environment by animals, after which they are colonized by microbes. We find that microbial community diversity increases sharply over the first few days of environmental exposure, and taxonomic identity of the microbes changes through this time period as is predicted for early community assembly in macroscopic communities. Microbial community taxonomic turnover is consistent at the bacteria phylum level, but at the level of Operational Taxonomic Units (OTUs), internode communities become increasingly differentiated through time. We argue that these tropical bamboos form an ideal study system for microbial community ecology due to their near-sterile condition prior to opening, relatively consistent environment after opening, and functionally limitless possibilities for replicates. Given the possible importance of opened internode habitats as locations of transmission for both pathogenic and beneficial microbes among animals, understanding the microbial dynamics of the internode habitat is a key conservation concern for the insect and amphibian species that use this microhabitat.

Applied science facilitates the large-scale expansion of protected areas in an Amazonian hot spot.

Meeting international commitments to protect 17% of terrestrial ecosystems worldwide will require >3 million square kilometers of new protected areas and strategies to create those areas in a way that respects local communities and land use. In 2000-2016, biological and social scientists worked to increase the protected proportion of Peru's largest department via 14 interdisciplinary inventories covering >9 million hectares of this megadiverse corner of the Amazon basin. In each landscape, the strategy was the same: convene diverse partners, identify biological and sociocultural assets, document residents' use of natural resources, and tailor the findings to the needs of decision-makers. Nine of the 14 landscapes have since been protected (5.7 million hectares of new protected areas), contributing to a quadrupling of conservation coverage in Loreto (from 6 to 23%). We outline the methods and enabling conditions most crucial for successfully applying similar campaigns elsewhere on Earth.

Phylogenetic relationships and systematics of the Amazonian poison frog genus Ameerega using ultraconserved genomic elements.

The Amazonian poison frog genus Ameerega is one of the largest yet most understudied of the brightly colored genera in the anuran family Dendrobatidae, with 30 described species ranging throughout tropical South America. Phylogenetic analyses of Ameerega are highly discordant, lacking consistency due to variation in data types and methods, and often with limited coverage of species diversity in the genus. Here, we present a comprehensive phylogenomic reconstruction of Ameerega, utilizing state-of-the-art sequence capture techniques and phylogenetic methods. We sequenced thousands of ultraconserved elements from over 100 tissue samples, representing almost every described Ameerega species, as well as undescribed cryptic diversity. We generated topologies using maximum likelihood and coalescent methods and compared the use of maximum likelihood and Bayesian methods for estimating divergence times. Our phylogenetic inference diverged strongly from those of previous studies, and we recommend steps to bring Ameerega taxonomy in line with the new phylogeny. We place several species in a phylogeny for the first time, as well as provide evidence for six potential candidate species. We estimate that Ameerega experienced a rapid radiation approximately 7-11 million years ago and that the ancestor of all Ameerega was likely an aposematic, montane species. This study underscores the utility of phylogenomic data in improving our understanding of the phylogeny of understudied clades and making novel inferences about their evolution.

Widespread chytrid infection across frogs in the Peruvian Amazon suggests critical role for low elevation in pathogen spread and persistence.

Outbreaks of emerging infectious diseases are becoming more frequent as climate changes wildlife communities at unprecedented rates, driving population declines and raising concerns for species conservation. One critical disease is the global pandemic of chytridiomycosis in frogs, which can be caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Although there is clear evidence for Bd-induced mortality across high-elevation frog communities, little attention is given to the role of lowlands in Bd's persistence and spread because low elevations are assumed to be too warm to harbor significant levels of Bd. Here, we report widespread Bd infection across 80 frog species from three sites in the lowland Peruvian Amazon, an area with no documented Bd-related amphibian declines. Despite observing no clinical signs of infection in the field, we found that 24-46% of individuals were infected per site (up to ≈105,000 zoospore equivalents per frog) by three Bd strains from the global pandemic lineage (Bd-GPL). We also found collection site and seasonal effects to be only weak predictors of Bd prevalence and load, with lower elevation and drier habitats marginally decreasing both prevalence and load. We found no further effect of host phylogeny, ecotype, or body size. Our results showing high and widespread prevalence across a lowland tropical ecosystem contradict the expectations based on the global pattern of pathogenicity of Bd that is largely restricted to higher elevations and colder temperatures. These findings imply that the lowlands may play a critical role in the spread and persistence of Bd over time and space.

Thermal physiological traits in tropical lowland amphibians: Vulnerability to climate warming and cooling.

Climate change is affecting biodiversity and ecosystem function worldwide, and the lowland tropics are of special concern because organisms living in this region experience temperatures that are close to their upper thermal limits. However, it remains unclear how and whether tropical lowland species will be able to cope with the predicted pace of climate warming. Additionally, there is growing interest in examining how quickly thermal physiological traits have evolved across taxa, and whether thermal physiological traits are evolutionarily conserved or labile. We measured critical thermal maximum (CTmax) and minimum (CTmin) in 56 species of lowland Amazonian frogs to determine the extent of phylogenetic conservatism in tolerance to heat and cold, and to predict species' vulnerability to climate change. The species we studied live in sympatry and represent ~65% of the known alpha diversity at our study site. Given that critical thermal limits may have evolved differently in response to different temperature constraints, we tested whether CTmax and CTmin exhibit different rates of evolutionary change. Measuring both critical thermal traits allowed us to estimate species' thermal breadth and infer their potential to respond to abrupt changes in temperature (warming and cooling). Additionally, we assessed the contribution of life history traits and found that both critical thermal traits were correlated with species' body size and microhabitat use. Specifically, small direct-developing frogs in the Strabomantidae family appear to be at highest risk of thermal stress while tree frogs (Hylidae) and narrow mouthed frogs (Microhylidae) tolerate higher temperatures. While CTmax and CTmin had considerable variation within and among families, both critical thermal traits exhibited similar rates of evolutionary change. Our results suggest that 4% of lowland rainforest frogs assessed will experience temperatures exceeding their CTmax, 25% might be moderately affected and 70% are unlikely to experience pronounced heat stress under a hypothetical 3°C temperature increase.

Systematics of the Ameerega rubriventris complex (Anura: Dendrobatidae) with descriptions of two new cryptic species from the East-Andean versant of Peru.

We describe two new species of poison frog from central and southern Peru that have been referred to as Ameerega picta, A. hahneli, or A. altamazonica throughout the past thirty years. Our phylogenies generated with genomic data provide strong support that the two new species are successive sisters to two described taxa, A. rubriventris and A. altamazonica, and collectively comprise the Ameerega rubriventris complex. The first new taxon, Ameerega panguana sp. nov., can be distinguished from all other Ameerega by its combination of a unique white venter and an advertisement call of 1-2 notes per second. The second new taxon, Ameerega imasmari sp. nov., is the only cryptically colored Ameerega species that is disttributed across the Fitzcarrald Arch in Southern Peru which possesses a 'peep' advertisement call consisting of 3-4 notes per second and a dominant frequency of 4.3-4.5 kHz. Within the Ameerega rubriventris complex, we observed differences between species in their ventral coloration, tympanum diameter, and call, which suggest that these taxa are reproductively isolated from each other.

Beetles in bamboo forests: community structure in a heterogeneous landscape of southwestern Amazonia.

Amazonian bamboo forests dominated by large woody bamboo plants in the genus Guadua cover approximately 180,000 km2 and represent a key resource for many organisms. In southwestern Amazonia, native bamboo forests differ in structure, biodiversity, and growth dynamics from other forest types in the region. However, with the exception of a few species in which habitat specialization or a strong habitat association has been demonstrated, little is known about how bamboo forests influence animal community structure. In an effort to understand more about the animal assemblages associated with Amazonian bamboo forests, we characterized the structure of ground-dwelling beetle assemblages living in bamboo forests and adjacent terra firme forests in a lowland rainforest site in Peru. We conducted intensive pitfall trap surveys in 13 bamboo habitat patches and 13 adjacent terra firme habitat patches to determine if there were differences in the abundance and richness of beetle species in these two habitat types. Additionally, given that southwestern Amazonia experiences distinct dry and wet seasons, we conducted our study during the dry and wet season of one year to account for differences in seasonality. We found a distinct beetle assemblage associated with each forest type, and identified a set of dominant species that significantly contributed to the distinctness in beetle community structure between bamboo and terra firme forest. The terra firme forest had a greater number of rare species than the bamboo forest. Several beetle species exhibited a strong association with the bamboo forest, including a large species of Scarabaeidae that appears to be specializing on bamboo. We also found marked differences in beetle assemblages between dry and wet seasons. Our results support the prediction that beetle community structure in bamboo forest differs from that of terra firme in terms of species richness, abundance, and composition. Bamboo-associated animal communities require more exploration and study, and must be included in regional conservation plans seeking to protect entire animal communities in southwestern Amazonia.

Evolutionary radiation of earless frogs in the Andes: molecular phylogenetics and habitat shifts in high-elevation terrestrial breeding frogs.

The loss of hearing structures and loss of advertisement calls in many terrestrial breeding frogs (Strabomantidae) living at high elevations in South America are common and intriguing phenomena. The Andean frog genus Phrynopus Peters, 1873 has undergone an evolutionary radiation in which most species lack the tympanic membrane and tympanic annulus, yet the phylogenetic relationships among species in this group remain largely unknown. Here, we present an expanded molecular phylogeny of Phrynopus that includes 24 nominal species. Our phylogeny includes Phrynopus peruanus, the type species of the genus, and 10 other species for which genetic data were previously unavailable. We found strong support for monophyly of Phrynopus, and that two nominal species-Phrynopus curator and Phrynopus nicoleae-are junior synonyms of Phrynopus tribulosus. Using X-ray computed tomography (CT) imaging, we demonstrate that the absence of external hearing structures is associated with complete loss of the auditory skeletal elements (columella) in at least one member of the genus. We mapped the tympanum condition on to a species tree to infer whether the loss of hearing structures took place once or multiple times. We also assessed whether tympanum condition, body size, and body shape are associated with the elevational distribution and habitat use. We identified a single evolutionary transition that involved the loss of both the tympanic membrane and tympanic annulus, which in turn is correlated with the absence of advertisement calls. We also identified several species pairs where one species inhabits the Andean grassland and the other montane forest. When accounting for phylogenetic relatedness among species, we detected a significant pattern of increasing body size with increasing elevation. Additionally, species at higher elevations tend to develop shorter limbs, shorter head, and shorter snout than species living at lower elevations. Our findings strongly suggest a link between ecological divergence and morphological diversity of terrestrial breeding frogs living in montane gradients.

A new species of Phrynopus (Amphibia, Anura, Craugastoridae) from upper montane forests and high Andean grasslands of the Pui Pui Protected Forest in central Peru.

We describe a new species of Phrynopus from the upper montane forests and high Andean grasslands (puna) of the Pui Pui Protected Forest and its close surroundings (Región Junín, central Peru) and compare it morphologically and genetically with other species of Phrynopus. Phrynopus intisp. n. is known from four localities outside and two localities inside the Pui Pui Protected Forest between 3350 and 3890 m a.s.l. Studied specimens of the new species are characterized by a snout-vent length of 27.2-35.2 mm in males (n = 6), and 40.4 mm in a single female, by having the skin on dorsum and flanks smooth with scattered tubercles, venter smooth, by lacking a tympanum, and males without vocal slits and nuptial pads. In life, the dorsum is pale grayish brown with or without dark brown blotches, or dorsum blackish brown with small yellow flecks, throat, chest and venter are pale grayish brown with salmon mottling, groin is pale grayish brown with salmon colored flecks, and the iris is golden orange with fine dark brown reticulations. The new species is morphologically most similar to Phrynopus kauneorum and P. juninensis. For the latter we describe the coloration in life for a specimen obtained at the type locality. A molecular phylogenetic analysis based on mitochondrial and nuclear DNA sequences inferred that the new species is most closely related to Phrynopus kauneorum, P. miroslawae, P. tautzorum, and an undescribed species distributed at high elevation in Región Pasco, central Peru.

ResumenDescribimos una nueva especie de Phrynopus de los bosques montanos altos y los pajonales altoandinos (Puna) del Bosque de Protección Pui Pui y sus áreas cercanas (Región de Junín, Perú central) y la comparamos morfológica y genéticamente con otras especies de Phrynopus. Phrynopus intisp. n. es conocido de cuatro localidades fuera y dos localidades dentro del Bosque de Protección Pui Pui entre 3350 y 3890 m s.n.m. La nueva especie se caracteriza por tener una longitud hocico-cloaca de 27.2­35.2 mm en machos (n = 6) y 40.4 mm en una hembra, por tener la piel dorsal y los flancos lisos con tubérculos dispersos, el vientre liso, por carecer de un tímpano, y los machos carecer de hendiduras vocales y almohadillas nupciales. En vida, el dorso es marrón grisáceo pálido con o sin manchas marrón oscuro o el dorso es marrón oscuro con pequeñas manchas amarillas; la garganta, pecho y vientre son marrón grisáceo pálido con motas de color salmón, la ingle es marrón grisácea con manchas de color salmón y el iris es dorado naranja con finas reticulaciones marrón oscuro. La nueva especie es morfológicamente muy similar a Phrynopus kauneorum y P. juninensis. Para este último, describimos la coloración en vida de un espécimen obtenido en la localidad tipo. Un análisis filogenético molecular basado en secuencias de ADN mitocondrial y nuclear infirió que la nueva especie está más estrechamente relacionada con Phrynopus kauneorum, P. miroslawae, P. tautzorum, y una especie no descrita distribuida en zonas altoandinas de la Región Pasco, Perú central.

A new species of terrestrial-breeding frog (Amphibia, Craugastoridae, Pristimantis) from high elevations of the Pui Pui Protected Forest in central Peru.

We describe a new species of Pristimantis from upper montane forests and high Andean grasslands of the Pui Pui Protected Forest and its close surroundings, Región Junín, central Peru. The description of the new species is based on 34 specimens found at elevations between 3400 and 3936 m a.s.l. Pristimantis attenboroughisp. n. is characterized by a snout-vent length of 14.6-19.2 mm in adult males (n = 21), 19.2-23.0 mm in adult females (n = 10), and is compared morphologically and genetically with other taxonomically and biogeographically relevant species of Pristimantis. The new species is characterized by having narrow digits that lack circumferential grooves, irregularly shaped, discontinuous dorsolateral folds, and absence of both tympanic membrane and tympanic annulus. The high similarity in morphology between P. attenboroughisp. n. and members of the Andean genera Phrynopus and Bryophryne provides an example for convergent evolution, and highlights the importance of using molecular data to justify generic assignment. Pristimantis attenboroughisp. n. is most similar to Phrynopus chaparroi from the Región Junín, suggesting that the generic placement of this species needs to be revised. Phylogenetically the new species belongs to the Pristimantis danae species Group, a clade that includes several Pristimantis species distributed in the montane forests of central Peru, including P. albertus, P. aniptopalmatus, P. ornatus, and P. stictogaster.

Divergence of thermal physiological traits in terrestrial breeding frogs along a tropical elevational gradient.

Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae) distributed along a tropical elevational gradient. We measured the critical thermal maximum (CT max; n = 22 species) and critical thermal minimum (CT min; n = 14 species) of frogs captured between the Amazon floodplain (250 m asl) and the high Andes (3,800 m asl). After inferring a multilocus species tree, we conducted a phylogenetically informed test of whether body size, body mass, and elevation contributed to the observed variation in CT max and CT min along the gradient. We also tested whether CT max and CT min exhibit different rates of change given that critical thermal limits (and their plasticity) may have evolved differently in response to different temperature constraints along the gradient. Variation of critical thermal traits was significantly correlated with species' elevational midpoint, their maximum and minimum elevations, as well as the maximum air temperature and the maximum operative temperature as measured across this gradient. Both thermal limits showed substantial variation, but CT min exhibited relatively faster rates of change than CT max, as observed in other taxa. Nonetheless, our findings call for caution in assuming inflexibility of upper thermal limits and underscore the value of collecting additional empirical data on species' thermal physiology across elevational gradients.

A new species of Pristimantis (Amphibia, Anura, Craugastoridae) from the foothills of the Andes in Manu National Park, southeastern Peru.

We describe a new species of Pristimantis from the humid sub-montane forest of the Región Cusco in Peru. Pristimantis pluvialis sp. n. was collected in the Kosñipata and Entoro valleys at elevations from 740 to 1110 m a.s.l., near the borders of Manu National Park and within the Huachiperi Haramba Queros Conservation Concession. The new species can be distinguished from other members of the genus Pristimantis by its rostral tubercle, smooth dorsal skin, and by its advertisement call. Pristimantis lacrimosus and Pristimantis waoranii superficially most resemble the new species, but Pristimantis pluvialis sp. n. differs from both species by having a rostral tubercle (absent in Pristimantis waoranii and variable in Pristimantis lacrimosus) and larger size, from Pristimantis lacrimosus by its call emitted at a lower frequency, and from Pristimantis waoranii for its dorsal coloration with dark markings. Two other species have partially overlapping distributions and resemble the new species, Pristimantis mendax and Pristimantis olivaceus, but they produce advertisement calls with much higher dominant frequencies than the advertisement call of the new species. Furthermore, Pristimantis mendax differs from the new species by lacking a rostral tubercle and by having a sigmoid inner tarsal fold, whereas Pristimantis olivaceus differs by being smaller and by having dorsal skin shagreen with scattered tubercles. The new species has snout-vent length of 21.8-26.9 mm in males (n = 12) and 28.8 mm in a single female.

ResumenDescribimos una nueva especie de Pristimantis de los bosques sub-montanos de la Región Cusco, en Perú. Pristimantis pluvialissp. n. fue colectada en los valles de Kosñipata y Entoro a altitudes entre 740 y 1110 m.s.n.m., cerca del límite del Parque Nacional del Manu y dentro de la Concesión para Conservación Huachiperi Haramba Queros. La nueva especie se diferencia de otros miembros del género Pristimantis por su tubérculo rostral, piel dorsal lisa, y por su canto de anuncio. Superficialmente, Pristimantis lacrimosus y Pristimantis waoranii se asemejan a la nueva especie, pero Pristimantis pluvialissp. n. difiere de ambas por tener un tubérculo dorsal (ausente en Pristimantis waoranii y variable en Pristimantis lacrimosus) y mayor tamaño; además, se diferencia de Pristimantis lacrimosus por tener un canto de anuncio producido a frecuencias más bajas, y de Pristimantis waoranii por su coloración dorsal con manchas oscuras. Dos especies con distribución parcialmente simpátrica se asemejan morfológicamente a la nueva especie, Pristimantis mendax y Pristimantis olivaceus. Ambas especies producen cantos de anuncio a frecuencias mucho más altas que la nueva especie. Además, Pristimantis mendax se distingue de Pristimantis pluvialissp. n. por carecer de tubérculo rostral y por tener un pliegue tarsal interno sigmoideo, mientras que Pristimantis olivaceus se distingue por su menor tamaño, y por tener piel finamente granular con algunos tubérculos diseminados en la parte dorsal. La nueva especie tiene una longitud hocico-cloaca de 21.8­26.9 mm en machos (n = 12) y de 28.8 mm en una hembra.

A new species of Noblella (Amphibia, Anura, Craugastoridae) from the humid montane forests of Cusco, Peru.

A new species of Noblella is described from the humid montane forest of the Región Cusco in Peru. Specimens were collected at 2330-2370 m elevation in Madre Selva, near Santa Ana, in the province of La Convención. The new species is readily distinguished from all other species of Noblella by having a broad, irregularly shaped, white mark on black background on chest and belly. The new species further differs from known Peruvian species of Noblella by the combination of the following characters: tympanic membrane absent, small tubercles on the upper eyelid and on dorsum, tarsal tubercles or folds absent, tips of digits not expanded, no circumferential grooves on digits, dark brown facial mask and lateral band extending from the tip of the snout to the inguinal region. The new species has a snout-to-vent length of 15.6 mm in one adult male and 17.6 mm in one adult female. Like other recently described species in the genus, this new Noblella inhabits high-elevation forests in the Andes and likely has a restricted geographic distribution.

ResumenDescribimos una nueva especie de Noblella de bosques nublados de la Región Cusco en Perú. Los especímenes fueron colectados a una elevación de 2330­2370 m en Madre Selva, cerca de Santa Ana, en la provincia de La Convención. La nueva especie se diferencia fácilmente de todas las demás especies de Noblella por su coloración de fondo negra con una mancha irregular blanca en el pecho y vientre. Además la nueva especie se diferencia de las demás especies de Noblella conocidas de Perú por la combinación de las siguientes características: membrana timpánica ausente, pequeños tubérculos en los párpados y en la espalda, tubérculos o pliegues tarsales ausentes, puntas de los dedos no expandidas, surcos circunferenciales ausentes, y máscara facial y banda lateral marrón oscuras que se extienden desde la punta del rostro hasta la ingle. La nueva especie tiene una longitud hocico­cloaca (LHC) de 15.6 mm en un macho adulto y de 17.6 mm en una hembra adulta. Al igual que otras especies recientemente descritas en el género, esta nueva Noblella habita bosques altoandinos y es probable que tenga una distribución geográfica restringida.