Importance of estimating matrix quality for modeling species distribution in complex tropical landscapes: a test with Atlantic forest small mammals

Information to guide decision making is especially urgent in human dominated landscapes in the tropics, where urban and agricultural frontiers are still expanding in an unplanned manner. Nevertheless, most studies that have investigated the influence of landscape structure on species distribution have not considered the heterogeneity of altered habitats of the matrix, which is usually high in human dominated landscapes. Using the distribution of small mammals in forest remnants and in the four main altered habitats in an Atlantic forest landscape, we investigated 1) how explanatory power of models describing species distribution in forest remnants varies between landscape structure variables that do or do not incorporate matrix quality and 2) the importance of spatial scale for analyzing the influence of landscape structure. We used standardized sampling in remnants and altered habitats to generate two indices of habitat quality, corresponding to the abundance and to the occurrence of small mammals. For each remnant, we calculated habitat quantity and connectivity in different spatial scales, considering or not the quality of surrounding habitats. The incorporation of matrix quality increased model explanatory power across all spatial scales for half the species that occurred in the matrix, but only when taking into account the distance between habitat patches (connectivity). These connectivity models were also less affected by spatial scale than habitat quantity models. The few consistent responses to the variation in spatial scales indicate that despite their small size, small mammals perceive landscape features at large spatial scales. Matrix quality index corresponding to species occurrence presented a better or similar performance compared to that of species abundance. Results indicate the importance of the matrix for the dynamics of fragmented landscapes and suggest that relatively simple indices can improve our understanding of species distribution, and could be applied in modeling, monitoring and managing complex tropical landscapes.

Comparative range use by three Atlantic Forest understorey bird species in relation to forest fragmentation

In this paper, we report on range use patterns of birds in relation to tropical forest fragmentation. Between 2003 and 2005, three understorey passerine species were radio-tracked in five locations of a fragmented and in two locations of a contiguous forest landscape on the Atlantic Plateau of Sao Paulo in south-eastern Brazil. Standardized ten-day home ranges of 55 individuals were used to determine influences of landscape pattern, season, species, sex and age. In addition, total observed home ranges of 76 individuals were reported as minimum measures of spatial requirements of the species. Further, seasonal home ranges of recaptured individuals were compared to examine site fidelity. Chiroxiphia caudata, but not Pyriglena leucoptera or Sclerurus scansor, used home ranges more than twice as large in the fragmented versus contiguous forest. Home range sizes of C. caudata differed in relation to sex, age, breeding status and season. Seasonal home ranges greatly overlapped in both C. caudata and in S. scansor. Our results suggest that one response by some forest bird species to habitat fragmentation entails enlarging their home ranges to include several habitat fragments, whereas more habitat-sensitive species remain restricted to larger forest patches.

Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil

(Relief influence on tree species richness in secondary forest fragments of Atlantic Forest, SE, Brazil). The aim of this work was to explore the relationship between tree species richness and morphological characteristics of relief at the Ibiuna Plateau (SE Brazil). We sampled 61 plots of 0.30 ha, systematically established in 20 fragments of secondary forest (2-274 ha) and in three areas within a continuous secondary forest site, Morro Grande Reserve (9,400 ha). At each plot, 100 trees with diameter at breast height > 5 cm were sampled by the point centered quarter method, and total richness and richness per dispersal and succession class were obtained. The relief was characterized by the mean and variance of slope, elevation, aspect and slope location. There was no significant relationship between relief heterogeneity and tree species richness. Relief parameters generally did not affect tree richness, but elevation was particularly important especially in the continuous forest. Despite the limited range of altitudinal variation (150 m), species richness increases with elevation. The highest areas were also those with the largest forest cover and the lowest disturbance degree, which should contribute to the greater richness of those sites. Our results suggest an indirect influence of relief, due to the fact that deforestation is less intense in higher regions, rather than a direct influence of abiotic factors related to the altitudinal gradient.

Successional stage and geographic features determine floristic similarity among Atlantic Forest remnants, Sao Paulo State, Brazil

Analysis of floristic similarity relationships between plant communities can detect patterns of species occurrence and also explain conditioning factors. Searching for such patterns, floristic similarity relationships among Atlantic Forest sites situated at Ibiuna Plateau, Sao Paulo state, Brazil, were analyzed by multivariate techniques. Twenty one forest fragments and six sites within a continuous Forest Reserve were included in the analyses. Floristic composition and structure of the tree community (minimum dbh 5 cm) were assessed using the point centered quarter method. Two methods were used for multivariate analysis: Detrended Correspondence Analysis (DCA) and Two-Way Indicator Species Analysis (TWINSPAN). Similarity relationships among the study areas were based on the successional stage of the community and also on spatial proximity. The more similar the successional stage of the communities, the higher the floristic similarity between them, especially if the communities are geographically close. A floristic gradient from north to south was observed, suggesting a transition between biomes, since northern indicator species are mostly heliophytes, occurring also in cerrado vegetation and seasonal semideciduous forest, while southern indicator species are mostly typical ombrophilous and climax species from typical dense evergreen Atlantic Forest.

Diet and food selection by small mammals in an old-growth Atlantic forest of south-eastern Brazil

Here we describe the stomach contents of nine small mammal species (seven rodents and two didelphid marsupials) co-occurring in an old-growth Atlantic forest area. For four terrestrial rodents, we also compared the importance of arthropods in the diet and the selection of arthropod groups by comparing consumption with availability. Small mammals and arthropods were sampled in a 36-ha grid containing 25 sampling stations spaced every 150 m, and 47 stomach contents were analysed. While plant matter was the predominant item in the stomach contents of two rodents (Oligoryzomys nigripes and Rhipidomys mastacalis), four species presented arthropods as the main food item (the rodents Brucepattersonius soricinus and Oxymycterus dasytrichus, and the marsupials Monodelphis n. sp. and Marmosops incanus) and three consumed more plant matter than arthropods, but had significant amounts of both items (the rodents Delomys sublineatus, Euryoryzomys russatus and Thaptomys nigrita). Our results suggest that differences in diet, coupled with differences in habit and microhabitat preferences, are important factors allowing resource partition among species of the diverse group of co-occurring terrestrial small mammals in Atlantic forest areas. Moreover, arthropods were not preyed opportunistically by any of the four terrestrial rodents, since consumption was not proportional to availability. Rather, selection or rejection of arthropod groups seems to be determined by aspects other than availability, such as nutritional value, easiness of capture and handling or palatability.

Variety matters: adaptive genetic diversity and parasite load in two mouse opossums from the Brazilian Atlantic forest

The adaptive potential of a species to a changing environment and in disease defence is primarily based on genetic variation. Immune genes, such as genes of the major histocompatibility complex (MHC), may thereby be of particular importance. In marsupials, however, there is very little knowledge about natural levels and functional importance of MHC polymorphism, despite their key role in the mammalian evolution. In a previous study, we discovered remarkable differences in the MHC class II diversity between two species of mouse opossums (Gracilinanus microtarsus, Marmosops incanus) from the Brazilian Atlantic forest, which is one of the most endangered hotspots for biodiversity conservation. Since the main forces in generating MHC diversity are assumed to be pathogens, we investigated in this study gastrointestinal parasite burden and functional associations between the individual MHC constitution and parasite load. We tested two contrasting scenarios, which might explain differences in MHC diversity between species. We predicted that a species with low MHC diversity would either be under relaxed selection pressure by low parasite diversity (`Evolutionary equilibrium` scenario), or there was a recent loss in MHC diversity leading to a lack of resistance alleles and increased parasite burden (`Unbalanced situation` scenario). In both species it became apparent that the MHC class II is functionally important in defence against gastrointestinal helminths, which was shown here for the first time in marsupials. On the population level, parasite diversity did not markedly differ between the two host species. However, we did observe considerable differences in the individual parasite load (parasite prevalence and infection intensity): while M. incanus revealed low MHC DAB diversity and high parasite load, G. microtarsus showed a tenfold higher population wide MHC DAB diversity and lower parasite burden. These results support the second scenario of an unbalanced situation.

SEASONAL MICROHABITAT SELECTION BY TERRESTRIAL RODENTS IN AN OLD-GROWTH ATLANTIC FOREST

We tested the hypothesis that microhabitat variables, abundance of terrestrial rodents, and microhabitat selection patterns of terrestrial rodents vary between the cool-dry and warm-wet season in the Atlantic forest of Brazil. We selected variables associated with ecological factors potentially important to terrestrial rodents (physical structure of litter and woody debris, and arthropod availability) and established 25 small, independent sampling units covering 36 ha of a homogenous, mature Atlantic forest patch. Litter humidity and height, amount of small woody debris, arthropod availability, and terrestrial rodent abundance increased, whereas the quantity of large woody debris decreased in the warm-wet season. Greater spatial segregation among terrestrial rodents also was observed in this season, especially between morphologically similar species. The distribution of 3 of the 4 most common terrestrial rodents was influenced by microhabitat variables in at least I of the seasons, and these species also differed in their pattern of microhabitat selection between seasons. In general, the amount of small woody debris and litter humidity were more important for the microscale distribution of terrestrial rodents in the cool-dry season, whereas in the mild warm-wet season species distributions were associated with food availability or were not clearly influenced by the measured variables. The patterns of microhabitat selection by 3 common terrestrial rodents, which were associated with features that characterize old-growth forest, may be responsible for their vulnerability to forest fragmentation.

Time-lag in biological responses to landscape changes in a highly dynamic Atlantic forest region

Time-lagged responses of biological variables to landscape modifications are widely recognized, but rarely considered in ecological studies. In order to test for the existence of time-lags in the response of trees, small mammals, birds and frogs to changes in fragment area and connectivity, we studied a fragmented and highly dynamic landscape in the Atlantic forest region. We also investigated the biological correlates associated with differential responses among taxonomic groups. Species richness and abundance for four taxonomic groups were measured in 21 secondary forest fragments during the same period (2000-2002), following a standardized protocol. Data analyses were based on power regressions and model selection procedures. The model inputs included present (2000) and past (1962, 1981) fragment areas and connectivity, as well as observed changes in these parameters. Although past landscape structure was particularly relevant for trees, all taxonomic groups (except small mammals) were affected by landscape dynamics, exhibiting a time-lagged response. Furthermore, fragment area was more important for species groups with lower dispersal capacity, while species with higher dispersal ability had stronger responses to connectivity measures. Although these secondary forest fragments still maintain a large fraction of their original biodiversity, the delay in biological response combined with high rates of deforestation and fast forest regeneration imply in a reduction in the average age of the forest. This also indicates that future species losses are likely, especially those that are more strictly-forest dwellers. Conservation actions should be implemented to reduce species extinction, to maintain old-growth forests and to favour the regeneration process. Our results demonstrate that landscape history can strongly affect the present distribution pattern of species in fragmented landscapes, and should be considered in conservation planning. (C) 2009 Elsevier Ltd. All rights reserved.

The challenge of maintaining Atlantic forest biodiversity: A multi-taxa conservation assessment of specialist and generalist species in an agro-forestry mosaic in southern Bahia

Recent developments have highlighted the importance of forest amount at large spatial scales and of matrix quality for ecological processes in remnants. These developments, in turn, suggest the potential for reducing biodiversity loss through the maintenance of a high percentage of forest combined with sensitive management of anthropogenic areas. We conducted a multi-taxa survey to evaluate the potential for biodiversity maintenance in an Atlantic forest landscape that presented a favorable context from a theoretical perspective (high proportion of mature forest partly surrounded by structurally complex matrices). We sampled ferns, butterflies, frogs, lizards, bats, small mammals and birds in interiors and edges of large and small mature forest remnants and two matrices (second-growth forests and shade cacao plantations), as well as trees in interiors of small and large remnants. By considering richness, abundance and composition of forest specialists and generalists, we investigated the biodiversity value of matrix habitats (comparing them with interiors of large remnants for all groups except tree), and evaluated area (for all groups) and edge effects (for all groups except trees) in mature forest remnants. our results suggest that in landscapes comprising high amounts of mature forest and low contrasting matrices: (1) shade cacao plantations and second-growth forests harbor an appreciable number of forest specialists; (2) most forest specialist assemblages are not affected by area or edge effects, while most generalist assemblages proliferate at edges of small remnants. Nevertheless, differences in tree assemblages, especially among smaller trees, Suggest that observed patterns are unlikely to be stable over time. (C) 2009 Elsevier Ltd. All rights reserved.

STRUCTURE OF THE SHRUB-ARBOREAL COMPONENT OF AN ATLANTIC FOREST FRAGMENT ON A HILLOCK IN THE CENTRAL LOWLAND OF RIO DE JANEIRO, BRAZIL

The present study describes and evaluates the horizontal and vertical structures of a lowland forest fragment on a hillock in the municipality of Silva Jardim, Rio de Janeiro State, Brazil (22 degrees 31`56 `` S and 42 degrees 20`46 `` W). Twenty plots (10x2m) totaling 0.5ha were laid out following the slope grade using DBH >= 5cm as the inclusion criterion. A total of 734 individuals were encountered, yielding a total density of 1468 ind./ha and a total basal area of 10783m(2). The richness values (129 species/41 families), Shannon-Wiener diversity (4.22) and equitability (0.87) indices indicated an accentuated floristic heterogeneity and low ecological dominance. Lauraceae, Myrtaceae, Fabaceae and Euphorbiaceae showed the greatest species richness, corroborating other studies that indicated these species as the most representative of Atlantic Forest areas in southeastern Brazil. The species with the greatest importance values (VI) were Aparisthmium cordatum, Guapira opposita, Lacistema pubescens, Xylopia sericea, Tapirira guianensis and Piptocarpha macropoda. The high diversity observed was influenced by earlier anthropogenic actions and by the current successional stage. The forest fragment studied demonstrated closer floristic similarity to areas inventoried in a close-by biological reserve than to fragments dispersed throughout the coastal plain. Similarities in soil type, degree of soil saturation and use-history of forest resources all support these relationships. The fragmented physiognomy of the central lowland in this region and the use-history of the landscape make these small remnant forest areas important in terms of establishing strategies for landscape restoration and species conservation.

Sex ratio and morphological characteristics of Rufous Gnateaters, Conopophaga lineata (Aves, Passeriformes) in Atlantic forest fragments

Unequal sex ratios lead to the loss of genetic variability, decreasing the viability of populations in the long term. Anthropogenic activities often disturb the natural habitats and can cause alterations in sex ratio and morphological characteristics of several species. Forest fragmentation is a major conservation concern, so that understanding its effects in natural populations is essential. In this study, we evaluated the sex ratio and the morphological characteristics of Rufous Gnateaters (Conopophaga lineata (Wied, 1831)) in small and large forest fragments in Minas Gerais, Brazil. Birds (n = 89) were sexed by plumage characteristics and molecular markers. The molecular analysis showed that plumage is not a totally reliable method for sexing Rufous Gnateaters. We observed that sex ratio did not differ between large and small forest fragments, but birds in small fragments had larger wings and tarsus. Wing and tarsus changes may affect the movement ability of individuals within and among forest fragments. In conclusion, Rufous Gnateaters have been able to survive in both small and large Atlantic rain forest fragments without altering their sex ratio, but morphological changes can be prejudicial to their long term survival.

The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.

Importance of interhabitat gaps and stepping-stones for lesser woodcreepers (Xiphorhynchus fuscus) in the Atlantic forest, Brazil

Translocation experiments showed that a woodcreeper bird species is able to move between isolated forest fragments, but this ability is limited by increasing interpatch distances. Larger distances (> 100 m) were overcome by using small stepping-stones (isolated trees), which enhance connectivity and are useful for the species conservation in fragmented landscapes.

Dynamics of Dissolved Forms of Carbon and Inorganic Nitrogen in Small Watersheds of the Coastal Atlantic Forest in Southeast Brazil

Based on the fact that streamwater quality reflects landscape conditions, the objectives of this study were: to investigate nitrogen (N), carbon (C), and major ion concentrations in six streams crossing minimally disturbed Atlantic Forest areas, with similar geomorphological characteristics; to determine N and C fluxes in one of these pristine streams (Indaia); and assess the impact of human activity on the biogeochemistry of two other streams in the same region, crossing urbanized areas. The distribution pattern of carbon and inorganic nitrogen dissolved forms, as well as the major ion and biogenic gas concentrations in the streamwater, was similar in pristine streams, indicating that the C and N dynamics were determined by influence of some factors, such as climate, atmospheric deposition, geology, soil type, and land covering, which were analogous in the forested watersheds. The urban streams were significantly different from the pristine streams, showing low dissolved oxygen concentrations, high respiration rates, and high concentrations of carbon dioxide, dissolved inorganic nitrogen, dissolved inorganic carbon, and major ion. These differences were attributed to anthropogenic impact on water quality, especially domestic sewage discharge. Additionally, in the Indaia stream, it was possible to observe the importance of rainfall over temporal dynamics of dissolved carbon forms, and also, the obtained specific flux of dissolved inorganic nitrogen was relatively elevated (approximately 11 kg ha(-1) year(-1)). These results reveal the influence of human activity over the biogeochemistry of coastal streams and also indicate the importance N export of Atlantic Forest to the ocean.

Natural History of the Lutz`s Frog Cycloramphus lutzorum Heyer, 1983 (Anura: Cycloramphidae) in the Brazilian Atlantic Forest: Description of the Advertisement Call, Tadpole, and Karyotype

We describe the advertisement call, tadpole, karyotype, and additional information on the natural history of Cycloramphus lutzorum from southern Brazil. Sonograms were generated from digitally recorded calls. Tadpoles were collected in the field for description in the lab, and an adult was collected for karyotyping. Data on seasonal activity were gathered monthly from November 2005 to November 2007. All tadpoles (N = 21), juveniles (N = 18), and adults (N = 52) were found exclusively in streams. Reproduction, as identified by calling frogs, occurred from July through November. Frogs call all day long, but mostly at dusk, from rock crevices inside the stream edges near the splash zone. The call is short and loud, with 11 pulsed notes, of 491-641 ms, with a dominant frequency of 0.98-1.39 kHz. We describe the exotrophic and semiterrestrial tadpoles, always found in constantly humid vertical rock walls in the stream. Tadpoles of C. lutzorum are recognized by differences in labial tooth row formula, eye diameter, body shape, position of nares, and development of tail. Like congeneric species, the karyotype of C. lutzorum comprises 26 metacentric and submetacentric chromosomes. Cycloramphus lutzorum is restricted to and adapted for living in fast flowing streams, many of which are threatened by deforestation, pollution, and habitat loss. Therefore, we recommend the status of C. lutzorum be changed from its current ""Data Deficient"" to ""Near Threatened (NT)"" in the IUCN species red list.