Systematics and biogeography of the Atlantic Forest endemic genus Juliomys (Rodentia: Cricetidae): a test of diversification hypothesis using mitochondrial data

The Atlantic Forest harbors a large species richness and high levels of endemism, but the processes that shaped its biodiversity are poorly studied, especially for mammals. Among them are the endemic mice Juliomys, which comprise forest dwellers distributed in southeastern and southern Brazil, northeastern Argentina, and eastern Paraguay. In this study, we investigate the phylogenetic relationships among species and perform phylogeographic analyses to evaluate the population structure and demographic scenarios through mitochondrial gene cytochrome b sequences. We investigate three hypotheses of diversification (forest refuges, montane isolate, and geomorphological events) to understand the evolution of the Juliomys species. Phylogenetic analyses recovered five clades/lineages, four of which are congruent with species currently recognized. The fifth lineage expands the range of the genus 659 km to the north and may represent a new species. The observed demographic and geographic structure of genetic diversity does not match the forest refuge hypothesis as mechanism to explain the diversification in Juliomys. Our results recovered J. rimofrons and J. ximenezi as sister species, supporting predictions of montane isolate hypothesis. We also detected a shallow genetic structure in J. pictipes and J. ossitenuis. Both phylogeographic breaks were congruent with limits of the São Paulo Basin, an area that has undergone Neogene reactivations of tectonic faults. It is suggested that geomorphological events led to a deformed landscape that influenced the dynamics of sedimentary basins and promoted an incipient population structure in J. pictipes and J. ossitenuis. Our findings demonstrate that the divergences whithin Juliomys species occurred during the Quaternary, too recently to have produced strong geographic structure.

Systematics and biogeography of the atlantic forest endemic genus Juliomys (Rodentia: Cricetidae): A test of diversification hypothesis using mitochondrial data

The Atlantic Forest harbors a large species richness and high levels of endemism, but the processes that shaped its biodiversity are poorly studied, especially for mammals. Among them are the endemic mice Juliomys, which comprise forest dwellers distributed in southeastern and southern Brazil, northeastern Argentina, and eastern Paraguay. In this study, we investigate the phylogenetic relationships among species and perform phylogeographic analyses to evaluate the population structure and demographic scenarios through mitochondrial gene cytochrome b sequences. We investigate three hypotheses of diversification (forest refuges, montane isolate, and geomorphological events) to understand the evolution of the Juliomys species. Phylogenetic analyses recovered five clades/lineages, four of which are congruent with species currently recognized. The fifth lineage expands the range of the genus 659 km to the north and may represent a new species. The observed demographic and geographic structure of genetic diversity does not match the forest refuge hypothesis as mechanism to explain the diversification in Juliomys. Our results recovered J. rimofrons and J. ximenezi as sister species, supporting predictions of montane isolate hypothesis. We also detected a shallow genetic structure in J. pictipes and J. ossitenuis. Both phylogeographic breaks were congruent with limits of the São Paulo Basin, an area that has undergone Neogene reactivations of tectonic faults. It is suggested that geomorphological events led to a deformed landscape that influenced the dynamics of sedimentary basins and promoted an incipient population structure in J. pictipes and J. ossitenuis. Our findings demonstrate that the divergences whithin Juliomys species occurred during the Quaternary, too recently to have produced strong geographic structure.

Molecular Detection of Rickettsia parkeri Strain Atlantic Rainforest in Ticks Parasitizing Small Mammals in Northeastern Brazil.

PURPOSE: Small mammals are important reservoirs of ticks and their pathogens in nature. However, studies reporting these associations are still rare in Brazil. In the present study, we investigated the presence of Rickettsia DNA in ticks parasitizing rodents and marsupials captured in different areas throughout the Atlantic rainforest biome, Bahia, Northeastern (NE), Brazil. METHODS: The study was conducted in five municipalities within of the Atlantic Forest biome, Bahia state, in NE Brazil. Two campaigns were done in each municipality. For host captures Sherman and Tomahawk traps were used, and pitfall traps. After being captured, the hosts were anesthetized and their entire body examined for ticks. When ticks were detected, they were manually removed and stored in eppendorf tubes (1.5 ml) containing absolute PA ethanol for future laboratory analysis (identification of ticks and detection of Rickettsia spp.). RESULTS: A total of 609 mammals were captured. Overall, 208 ticks of the genus Amblyomma and Ixodes were collected: A. ovale, I. loricatus and A. varium. Rickettsia DNA was detected in A. ovale and it was 99-100% of identity to the sequence deposited in GenBank as Rickettsia parkeri strain Atlantica rainforest. CONCLUSION: These results suggest that R. parkeri strain Atlantic rainforest occurs in the region, and A. ovale is likely the vector.

Helminths of sigmodontine rodents in an agroforestry mosaic in the Brazilian Atlantic Forest: Patterns and processes of the metacommunity structure.

Phylogenetically or taxonomically related hosts may harbour similar parasite communities due to phylogenetic conservatism. In addition, host attributes may favour their exposure to parasites. This study aimed to characterize the helminth fauna of sigmodontine rodents in an Atlantic Forest area in northeastern Brazil and determine the pattern of the helminth metacommunity structure. The influence of host attributes and host taxonomy on the metacommunity structure was also investigated. The most abundant helminth species were Raillietina sp. and Hassalstrongylus lauroi. Euryoryzomys russatus was the most infected host species for helminth parasites, as approximately 81% (35/43) of the animals were infected by at least one helminth species. The helminth metacommunity structure was coherent at both the infracommunity and the component community scales, indicating that species responded to the same environmental gradient. A quasi-Clementsian pattern was observed for the infracommunities, indicating the occurrence of compartments of parasite species that were substituted along the environmental gradient, which was formed by host individuals. A quasi-Gleasonian pattern was found at the component community scale, showing random boundary clumping, which is consistent with the individualistic responses of parasite species to each host species. These patterns corroborated the high values of beta-diversity observed, indicating high species turnover among communities at both scales. Host taxonomic distance was the most important variable explaining the patterns of the helminth metacommunity structure.

Helminth communities of sigmonontine rodents in cocoa agroforestry systems in Brazil.

Agroforestry is an alternative kind of land use where the native vegetation is surrounded or intercalated by crops of economic interest. This system may maintain species richness by promoting the habitat heterogeneity or serving as ecological corridors. The aim of this study was to describe the gastrointestinal helminth fauna and to analyse the parasitological parameters of the helminth communities of six sigmodontine rodents in a cocoa agroforestry system in the municipality of Ilhéus, state of Bahia, Northeast Brazil. This is a novel study of helminth fauna in this kind of agroforestry. Rodents were captured in live-traps and euthanised for helminth recovery. Specimens were counted and identified to the species level whenever possible. Helminth abundance, intensity, and prevalence were calculated for each species and each host. The total abundance and prevalence of helminths were compared among localities and three attributes of the host: species, gender and age using generalised linear models. Considering all rodents, 52.14% of them were parasitised with at least one helminth species. Eight nematode species were identified and another seven morphospecies were identified to the genus level. The most abundant species were Hassalstrongylus epsilon, Stilestrongylus eta, Guerrerostrongylus zetta, and Syphacia alata. The opportunistic host species Oligoryzomys nigripes and Akodon cursor, besides the water rat Nectomys squamipes, were the most infected species for helminth parasites. Hylaeamys seuanezi was also an important host with the highest helminth species richness. This is the first report of the helminth fauna for this host. The locality most distant from the native vegetation and closest to the city had the highest helminth prevalence and mean species richness. The species richness in the helminth communities of Euryoryzomys russatus, N. squamipes and O. nigripes in these Cabruca agroforestries were within the range found in studies carried out in Atlantic Forest areas.

ATLANTIC MAMMAL TRAITS: a data set of morphological traits of mammals in the Atlantic Forest of South America.

Measures of traits are the basis of functional biological diversity. Numerous works consider mean species-level measures of traits while ignoring individual variance within species. However, there is a large amount of variation within species and it is increasingly apparent that it is important to consider trait variation not only between species, but also within species. Mammals are an interesting group for investigating trait-based approaches because they play diverse and important ecological functions (e.g., pollination, seed dispersal, predation, grazing) that are correlated with functional traits. Here we compile a data set comprising morphological and life history information of 279 mammal species from 39,850 individuals of 388 populations ranging from -5.83 to -29.75 decimal degrees of latitude and -34.82 to -56.73 decimal degrees of longitude in the Atlantic forest of South America. We present trait information from 16,840 individuals of 181 species of non-volant mammals (Rodentia, Didelphimorphia, Carnivora, Primates, Cingulata, Artiodactyla, Pilosa, Lagomorpha, Perissodactyla) and from 23,010 individuals of 98 species of volant mammals (Chiroptera). The traits reported include body mass, age, sex, reproductive stage, as well as the geographic coordinates of sampling for all taxa. Moreover, we gathered information on forearm length for bats and body length and tail length for rodents and marsupials. No copyright restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.

Abundance of small mammals in the Atlantic Forest (ASMAF): a data set for analyzing tropical community patterns.

Local abundance results from the interaction between populational and environmental processes. The abundance of the species in a community is also one of the most basic descriptors of its structure. Despite its importance, information about species abundances is fragmentary, creating a knowledge gap about species abundances known as the Prestonian Shortfall. Here we present a comprehensive data set of small mammal abundance in the Atlantic Forest. Data were extracted from 114 published sources and from unpublished data collected by our research groups spanning from 1943 to 2017. The data set includes 1,902 records of at least 111 species in 155 localities, totaling 42,617 individuals represented. We selected studies that (1) were conducted in forested habitats of the Atlantic Forest, (2) had a minimum sampling effort of at least 500 trap-nights, and (3) contained species abundance data in detail. For each study, we recorded (1) latitude and longitude, (2) name of the locality, (3) employed sampling effort, (4) type of traps used, (5) study year, (6) country, and (7) species name with (8) its respective abundances. For every locality, we also obtained information regarding its (9) ecoregion, (10) predominant vegetation type, and (11) biogeographic subdivision. Whenever necessary, we also (12) updated the species names as new species were described and some genera suffered taxonomic revision since the publication. The localities are spread across the Atlantic Forest and most of the small mammal species known to occur in Atlantic Forest are present in the data set, making it representative of communities of the entire biome. This data set can be used to address various patterns in community ecology and geographical ecology, as the relation between local abundance and environmental suitability, hypothesis regarding local and regional factors on community structuring, species abundance distributions (SAD), functional and phylogenetic mechanisms on community assembling.