Interactions between land use and soil type drive soil functions, highlighting water recharge potential, in the Cantareira System, Southeast of Brazil.

Most of the soil quality assessment protocols are focused on crop production and conservation management, while studies on vital soil functions, such as water recharge potential, should be incorporated into the monitoring of impacts on environmental quality. Our objective was to evaluate, through the Nexus approach, how dynamic (land use and management) and inherent (soil type) factors impact soil physical properties and processes that drive water recharge potential, biomass production, and water erosion in the Cantareira System, Brazil. The assessment considered three soils (Typic Hapludult, Typic Dystrudept, and Typic Usthortent) and four land uses (native forest, rotational grazing, extensive grazing, and eucalyptus), which constitute the main soils and land uses in the Cantareira System region. Representative soil samples were collected at 0-5 and 30-35 cm depth and analyzed for several soil physical quality indicators, which were used to calculate a Soil Physical Quality Index based on soil functions. Converting the native forest to eucalyptus and pasture reduced the overall soil physical quality and water recharge potential. The groundwater recharge potential function in the topsoil has the highest score of 0.72 for Typic Dystrudept in native forest contrasting with 0.16 for extensive pasture. Typic Dystrudept obtained the highest value of the SPQI value (0-5 cm: 0.85; 30-35 cm: 0.90) for native forests when compared to Typic Hapludult (0-5 cm: 0.76; 30-35 cm: 0.57) and Typic Usthortent (0-5 cm: 0.75; 30-35 cm: 0.72). Our findings sustain that land use effects on soil functions depends on soil type. Inclusion of soil type into the Nexus approach increases the understanding of natural resources and derived benefits of water, energy and food in the Cantareira System.

Biodiversity Management and Research in Multifunctional Landscapes / Gestão e pesquisa da biodiversidade em paisagens multifuncionais

Abstract: Despite their negative environmental impacts, human-modified environments such as agricultural and urban landscapes can have a relevant role on biodiversity conservation as complements of protected areas. Such anthropized landscapes may have endangered, valuable, and nuisance species, although most of them do not fit in any of these categories. Therefore, in such environments we must deal with the same decision-making process concerning the same possible interventions proposed by Caughley (1994) to wildlife management, which are related to biological conservation, sustainable use, control/coexistence, and monitoring. Such decision-making process should be based on good science and good governance. On such context, the first step should be to implement multifunctional landscapes, which keep their primary mission of human use, but incorporate a second but fundamental mission of biological conservation. In this study we present a summary of the research carried out at the Biota Program of Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) in this field since the late 1990's and propose priorities for biodiversity research and governance in multifunctional landscapes for the near future.

Resumo Apesar de seus impactos ambientais negativos, ambientes modificados pelo homem, como paisagens agrícolas e urbanas, podem ter um papel relevante na conservação da biodiversidade como complementos de áreas protegidas. Tais paisagens antropizadas podem ter espécies ameaçadas, valiosas e incômodas, embora a maioria delas não se enquadre em nenhuma dessas categorias. Portanto, em tais ambientes devemos lidar com o mesmo processo de tomada de decisão sobre as mesmas possíveis intervenções propostas por Caughley (1994) para o manejo da vida selvagem, que estão relacionadas à conservação biológica, uso sustentável, controle/coexistência e monitoramento. Esse processo de tomada de decisão deve ser baseado em boa ciência e boa governança. Neste contexto, o primeiro passo deverá ser a implementação de paisagens multifuncionais, que mantenham a sua missão primordial de uso humano, mas que incorporem uma segunda, mas fundamental missão de conservação biológica. Neste estudo apresentamos um resumo das pesquisas realizadas no Programa Biota da Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) neste campo desde o final da década de 1990 e propomos prioridades para pesquisa e governança da biodiversidade em paisagens multifuncionais para o futuro próximo.

Publisher Correction: Distance to range edge determines sensitivity to deforestation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Distance to range edge determines sensitivity to deforestation.

It is generally assumed that deforestation affects a species consistently across space, however populations near their geographic range edge may exist at their niche limits and therefore be more sensitive to disturbance. We found that both within and across Atlantic Forest bird species, populations are more sensitive to deforestation when near their range edge. In fact, the negative effects of deforestation on bird occurrences switched to positive in the range core (>829 km), in line with Ellenberg's rule. We show that the proportion of populations at their range core and edge varies across Brazil, suggesting deforestation effects on communities, and hence the most appropriate conservation action, also vary geographically.

ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America.

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820-2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities.

ATLANTIC BIRDS: a data set of bird species from the Brazilian Atlantic Forest.

South America holds 30% of the world's avifauna, with the Atlantic Forest representing one of the richest regions of the Neotropics. Here we have compiled a data set on Brazilian Atlantic Forest bird occurrence (150,423) and abundance samples (N = 832 bird species; 33,119 bird individuals) using multiple methods, including qualitative surveys, mist nets, point counts, and line transects). We used four main sources of data: museum collections, on-line databases, literature sources, and unpublished reports. The data set comprises 4,122 localities and data from 1815 to 2017. Most studies were conducted in the Florestas de Interior (1,510 localities) and Serra do Mar (1,280 localities) biogeographic sub-regions. Considering the three main quantitative methods (mist net, point count, and line transect), we compiled abundance data for 745 species in 576 communities. In the data set, the most frequent species were Basileuterus culicivorus, Cyclaris gujanensis, and Conophaga lineata. There were 71 singletons, such as Lipaugus conditus and Calyptura cristata. We suggest that this small number of records reinforces the critical situation of these taxa in the Atlantic Forest. The information provided in this data set can be used for macroecological studies and to foster conservation strategies in this biodiversity hotspot. No copyright restrictions are associated with the data set. Please cite this Data Paper if data are used in publications and teaching events.

Implications of Fine-Grained Habitat Fragmentation and Road Mortality for Jaguar Conservation in the Atlantic Forest, Brazil.

Jaguar (Panthera onca) populations in the Upper Paraná River, in the Brazilian Atlantic Forest region, live in a landscape that includes highly fragmented areas as well as relatively intact ones. We developed a model of jaguar habitat suitability in this region, and based on this habitat model, we developed a spatially structured metapopulation model of the jaguar populations in this area to analyze their viability, the potential impact of road mortality on the populations' persistence, and the interaction between road mortality and habitat fragmentation. In more highly fragmented populations, density of jaguars per unit area is lower and density of roads per jaguar is higher. The populations with the most fragmented habitat were predicted to have much lower persistence in the next 100 years when the model included no dispersal, indicating that the persistence of these populations are dependent to a large extent on dispersal from other populations. This, in turn, indicates that the interaction between road mortality and habitat fragmentation may lead to source-sink dynamics, whereby populations with highly fragmented habitat are maintained only by dispersal from populations with less fragmented habitat. This study demonstrates the utility of linking habitat and demographic models in assessing impacts on species living in fragmented landscapes.

Time-Lag in Responses of Birds to Atlantic Forest Fragmentation: Restoration Opportunity and Urgency.

There are few opportunities to evaluate the relative importance of landscape structure and dynamics upon biodiversity, especially in highly fragmented tropical landscapes. Conservation strategies and species risk evaluations often rely exclusively on current aspects of landscape structure, although such limited assumptions are known to be misleading when time-lag responses occur. By relating bird functional-group richness to forest patch size and isolation in ten-year intervals (1956, 1965, 1978, 1984, 1993 and 2003), we revealed that birds with different sensitivity to fragmentation display contrasting responses to landscape dynamics in the Brazilian Atlantic Forest. For non-sensitive groups, there was no time-lag in response: the recent degree of isolation best explains their variation in richness, which likely relates to these species' flexibility to adapt to changes in landscape structure. However, for sensitive bird groups, the 1978 patch area was the best explanatory variable, providing evidence for a 25-year time-lag in response to habitat reduction. Time-lag was more likely in landscapes that encompass large patches, which can support temporarily the presence of some sensitive species, even when habitat cover is relatively low. These landscapes potentially support the most threatened populations and should be priorities for restoration efforts to avoid further species loss. Although time-lags provide an opportunity to counteract the negative consequences of fragmentation, it also reinforces the urgency of restoration actions. Fragmented landscapes will be depleted of biodiversity if landscape structure is only maintained, and not improved. The urgency of restoration action may be even higher in landscapes where habitat loss and fragmentation history is older and where no large fragment remained to act temporarily as a refuge.

Patterns of Vertebrate Diversity and Protection in Brazil.

Most conservation decisions take place at national or finer spatial scales. Providing useful information at such decision-making scales is essential for guiding the practice of conservation. Brazil is one of the world's megadiverse countries, and consequently decisions about conservation in the country have a disproportionate impact on the survival of global biodiversity. For three groups of terrestrial vertebrates (birds, mammals, and amphibians), we examined geographic patterns of diversity and protection in Brazil, including that of endemic, small-ranged, and threatened species. To understand potential limitations of the data, we also explored how spatial bias in collection localities may influence the perceived patterns of diversity. The highest overall species richness is in the Amazon and Atlantic Forests, while the Atlantic Forest dominates in terms of country endemics and small-ranged species. Globally threatened species do not present a consistent pattern. Patterns for birds were similar to overall species richness, with higher concentrations of threatened species in the Atlantic Forest, while mammals show a more generalized pattern across the country and a high concentration in the Amazon. Few amphibians are listed as threatened, mostly in the Atlantic Forest. Data deficient mammals occur across the country, concentrating in the Amazon and southeast Atlantic Forest, and there are no data deficient birds in Brazil. In contrast, nearly a third of amphibians are data deficient, widespread across the country, but with a high concentration in the far southeast. Spatial biases in species locality data, however, possibly influence the perceived patterns of biodiversity. Regions with low sampling density need more biological studies, as do the many data deficient species. All biomes except the Amazon have less than 3% of their area under full protection. Reassuringly though, rates of protection do correlate with higher biodiversity, including higher levels of threatened and small-ranged species. Our results indicate a need for expanded formal protection in Brazil, especially in the Atlantic forest, and with an emphasis on fully protected areas.

Effect of forest fragmentation on tick infestations of birds and tick infection rates by rickettsia in the Atlantic forest of Brazil.

Habitat loss and modifications affect biodiversity, potentially contributing to outbreaks of infectious diseases. We evaluated if the patch sizeinfragmented areas of Atlantic Forest in southeastern Brazil influences the diversity of forest birds and consequently the prevalence of ticks on birds and the rickettsial infection of these ticks. During 2 years, we collected ticks from birds in 12 sites: four small forest patches (80-140 ha), four large ones (480-1,850 ha), and four forest control areas within the much larger Morro do Diabo State Park (approximately 36,000 ha). A total of 1,725 birds were captured (81 species, 24 families), from which 223 birds were infested by 2,339 ticks of the genus Amblyomma, mostly by the species A. nodosum. Bird diversity and richness were higher in larger than smaller forest fragments. The prevalence of ticks on birds was inversely correlated with bird diversity and richness. Among 174 A. nodosum tested for rickettsial infection by polymerase chain reaction, 51 were found to be infected by Rickettsia bellii or Rickettsia parkeri. However, tick infection rates by Rickettsia spp. were not statistically different between forest patch sizes. The higher prevalence of ticks on birds in degraded patches might be caused by a dominance of a few generalist bird species in small patches, allowing an easier transmission of parasites among individuals. It could also be related to more favorable microclimatic conditions for the free-living stages of A. nodosum in smaller forest fragments.The higher burden of ticks on birds in smaller forest fragments is an important secondary effect of habitat fragmentation, possibly increasing the likelihood of Rickettsia contagion.

Checklist das aves do Estado de São Paulo, Brasil / Checklist of birds from São Paulo State, Brazil

As listas de espécies são fundamentais para entender os padrões de distribuição espaciais e temporais dos táxons. A partir das bases de dados compiladas pelo CEO - Centro de Estudos Ornitológicos, do levantamento de Willis & Oniki (2003) e de buscas feitas em mais de 50 teses e dissertações, além de monografias e trabalhos técnicos, foram listadas todas as aves já registradas no Estado de São Paulo. Esses registros são compostos por peles ou outros materiais coletados e depositados em coleções, além de fotografias ou gravações. No total, foram registradas 793 espécies, distribuídas em 25 ordens e 85 famílias, correspondendo a cerca de 45% da avifauna brasileira. Um dos principais motivos para essa alta diversidade é a diversidade de ambientes encontrados no Estado, influenciados pelo gradiente altitudinal e geográfico, as diferentes fitofisionomias, a presença da região costeira, e o contato entre áreas florestais e Cerrados. O projeto Biota contribuiu principalmente no entendimento de como esse grupo responde às mudanças antrópicas do ambiente, como a fragmentação do habitat. Os principais grupos de pesquisa em ornitologia ainda estão alocados nas universidades e nos museus. As principais lacunas do conhecimento sobre as aves estão relacionadas à falta de padronização das metodologias para se inventariar este grupo, aos espaços geográficos sem amostragens, à falta de monitoramento em longo prazo das espécies ameaçadas de extinção, ao conhecimento limitado da capacidade das espécies em usarem as matrizes do entorno e ao pouco refinamento das delimitações das unidades evolutivas, que podem ser usadas na reintrodução das espécies em áreas em que estas não mais ocorrem.

Species lists are essential to understand both temporal and distributional patterns of taxa. Based on data compiled by CEO (Centro de Estudos Ornitológicos), Willis and Oniki (2003), and from a search of more than 50 theses, dissertations, monographs and technical works, we listed all bird species recorded in the State of São Paulo. These records are composed of skins and other evidence collected and deposited in collections, and on photographs and voice samples. A total of 793 species were registered, distributed in 25 orders and 85 families, and corresponding to 45% of the Brazilian avifauna. Reasons for this high diversity are related to the environmental diversity found in the state, influenced by altitudinal and geographical ranges, different phytophysiognomies, presence of a coastal region, and areas of contact between forest ecosystems and Cerrado. Results of the Biota project contributed to a better understanding of how birds respond to anthropogenic alterations of the environment, such as habitat fragmentation. The main ornithological research groups are still based in universities and museums. Deficiencies of knowledge concerning bird studies in São Paulo are related to the lack of standardization of survey methodologies; paucity in the monitoring of threatened species in the long term; restricted knowledge about species capacity to use matrix; and lack of refinement in the delimitation of evolutionary units and their distribution, which is essential for species reintroduction in regions where they have gone extinct.

Ticks (Acari: Ixodidae) infesting wild birds in the Atlantic Forest in northeastern Brazil, with notes on rickettsial infection in ticks.

A total of 232 individuals representing 46 species of birds were mist-netted and screened for ticks in a region of the Atlantic Forest, State of Bahia, Brazil. Thirty-eight (16.4%) of these birds representing 17 species were found infested by immature stages of Amblyomma ticks, namely, Amblyomma longirostre (Koch, 1844) (15 larvae and seven nymphs), Amblyomma nodosum (Neumann, 1899) (nine nymphs), Amblyomma calcaratum (Neumann, 1899) (five nymphs), Amblyomma cajennense (Fabricius, 1787) (seven larvae), and Amblyomma parkeri (Fonseca and Aragão, 1952) (four larvae). Overall, 21 larvae and five nymphs collected from birds could not be identified to species and were morphologically identified as Amblyomma spp. Among 13 A. longirostre larvae and two A. parkeri larvae, two individuals of A. longirostre (15.4%) were found infected by Rickettsia amblyommii. This study provides some bird species found infested by A. longirostre, A. parkeri, A. calcaratum, A. nodosum, or A. cajennense for the first time and expands the distribution of R. amblyommii-infected A. longirostre ticks.

Concordant phylogeographies of 2 malaria vectors attest to common spatial and demographic histories.

The phylogeography of South American lineages is a topic of heated debate. Although a single process is unlikely to describe entire ecosystems, related species, which incur similar habitat limitations, can inform the history for a subsection of assemblages. We compared the phylogeographic patterns of the cytochrome oxidase I marker from Anopheles triannulatus (N = 72) and previous results for A. darlingi (N = 126) in a broad portion of their South American distributions. Both species share similar population subdivisions, with aggregations northeast of the Amazon River, in southern coastal Brazil and 2 regions in central Brazil. The average capital EF, Cyrillic(ST) between these groups was 0.39 for A. triannulatus. Populations northeast of the Amazon and in southeastern Brazil are generally reciprocally monophyletic to the remaining groups. Based on these initial analyses, we constructed the a priori hypothesis that the Amazon and regions of high declivity pose geographic barriers to dispersal in these taxa. Mantel tests confirmed that these areas block gene flow for more than 1000 km for both species. The efficacy of these impediments was tested using landscape genetics, which could not reject our a priori hypothesis but did reject simpler scenarios. Results form summary statistics and phylogenetics suggest that both lineages originated in central Amazonia (south of the Amazon River) during the late Pleistocene (579 000 years ago) and that they followed the same paths of expansion into their contemporary distributions. These results may have implications for other species sharing similar ecological limitations but probably are not applicable as a general paradigm of Neotropical biogeography.

Ticks (Acari: Ixodidae) infesting wild birds in the eastern Amazon, northern Brazil, with notes on rickettsial infection in ticks.

The aim of the study was to report tick infestations on wild birds in a region of the eastern Brazilian Amazon and evaluate the rickettsial infection of these ticks. Wild birds captured by mist nets were examined for the presence of ticks, which were collected and identified to species by morphology or molecular methods. In addition, part of these ticks was individually tested by polymerase chain reaction targeting portions of the rickettsial genes gltA and ompA. Among 331 captured birds, representing 56 species, 133 individuals (40.2%) from 34 species were found infested by 443 ticks, being Amblyomma longirostre (Koch) the most common (103 larvae, 12 nymphs), followed by Amblyomma humerale Koch (15 larvae, 3 nymphs), Amblyomma geayi Neumann (seven larvae, one nymph), Amblyomma calcaratum Neumann (one larva, four nymphs), Amblyomma coelebs Neumann (two larvae), and Haemaphysalis juxtakochi Cooley (one larva, two nymphs). Other 285 larvae and 7 nymphs collected from birds could not be identified to species and were morphologically identified as Amblyomma spp. The species A. humerale and A. geayi are recorded for first time parasitizing birds in the Neotropical region. Among 67 A. longirostre and 7 A. geayi, 38 (56.7%) and 4 (57.1%), respectively, were found infected by Rickettsia amblyommii. In spite of R. amblyommii being not currently recognized as human or animal pathogen, there has been serological evidence for human and canine infection by this agent in the USA and in the Brazilian western Amazon.

Ticks (Acari: Ixodidae) infesting birds in an Atlantic rain forest region of Brazil.

Brazil has the third richest bird diversity of the world; however, there are few data concerning ticks (Acari: Ixodidae) parazitizing birds. The aim of the study was to report tick infestations on wild birds from an Atlantic rain forest region of Brazil. During 2 yr, ticks were collected from birds and from the environment in 12 forest sites. A total of 1,725 birds were captured representing 80 species from 24 families. In total, 223 (13%) birds were found infested by immature stages of Amblyomma ticks: 1,800 larvae and 539 nymphs. The prevalence of ticks was higher among birds from the families Thamnophilidae, Conopophagidae, and Momotidae. The most common tick parasitizing birds was Amblyomma nodosum Koch. Other tick species, Amblyomma coelebs Neumann, Amblyomma cajennense (F.), Amblyomma ovale Koch, Amblyomma longirostre (Koch), Amblyomma calcaratum Neumann, and Amblyomma naponense (Packard), were found sporadically. Among free-living ticks collected in the environment, A. cajennense was the most common, followed by A. coelebs, A. naponense, Amblyomma brasilense Aragão, and Hemaphysalis juxtakochi Cooley.

Ticks (Acari: Ixodidae) infesting wild birds in an Atlantic forest area in the state of São Paulo, Brazil, with isolation of rickettsia from the tick Amblyomma longirostre.

During field work in Nazaré Paulista, state of São Paulo, Brazil, we found 13 (56.5%) of 23 birds (mostly Passeriformes) to be infested by 28 larvae and 1 nymph of Amblyomma spp. Two larvae were reared to the adult stage, being taxonomically identified as Amblyomma parkeri Fonseca and Aragio, whereas five larvae and one nymph were identified as Amblyomma longirostre Koch. All six A. longirostre specimens were shown to be infected by rickettsia, as demonstrated by polymerase chain reaction (PCR) targeting two rickettsial genes (gltA and ompA) or isolation of rickettsia in cell culture from one of the ticks. This isolate was designated as strain AL, which was established in Vero cell culture and was molecularly characterized by DNA sequencing fragments of the rickettsial genes gltA, htrA, ompA, and ompB. Phylogenetic analyses inferred from ompA and ompB partial sequences showed a high degree of similarity of strain AL with Rickettsia sp. strain ARANHA, previously detected by PCR in A. longirostre ticks from Rondônia, northern Brazil. We conclude that strain AL is a new rickettsia genotype belonging to the same species of strain ARANHA, which are closely related to Candidatus 'R. amblyommii'. Further studies should elucidate if strains AL and ARANHA are different strains of Candidatus 'R. amblyommii' or are a new species.

[Ticks (Acari: Ixodidae) collected in the Natural Reserve of the Vale do Rio Doce, Linhares, State of Espírito Santo]. / Carrapatos (Acari: Ixodidae) capturados na Reserva Natural da Vale do Rio Doce, Linhares, Espírito Santo.

We confirm, after decades without new registers, the occurrence of the ticks Amblyomma obolongoguttatum Koch, 1844, A. brasiliense Aragão, 1908, and A. humerale Koch, 1844 in the State of Espírito Santo, Brazil, besides the first record of A. naponense (Packard, 1869) in this state.

Carrapatos (Acari: Ixodidae) capturados na Reserva Natural da Vale do Rio Doce, Linhares, Espírito Santo / Ticks (Acari: Ixodidae) collected in the Natural Reserve of the Vale do Rio Doce, Linhares, State of Espírito Santo

O presente trabalho confirma, após décadas sem novos relatos, a ocorrência dos carrapatos Amblyomma obolongoguttatum Koch, 1844, A. brasiliense Aragão, 1908, e A. humerale Koch, 1844 no Estado do Espírito Santo, Brasil, além do primeiro relato de A. naponense (Packard,1869) para este estado.

We confirm, after decades without new registers, the occurrence of the ticks Amblyomma obolongoguttatum Koch, 1844, A. brasiliense Aragão, 1908, and A. humerale Koch, 1844 in the State of Espírito Santo, Brazil, besides the first record of A. naponense (Packard, 1869) in this state.