Across‐taxa incongruence in patterns of collecting bias

If biological collections tend to be taken near accessible areas, and the number of such areas is limited, then we should expect a similar spatial distribution of collecting effort across taxa. Alternatively, if researchers working on a given taxon pick collection localities based on idiosyncratic criteria, then there should be no spatial similarity in collecting effort. This study compares the spatial distribution of collecting effort for plants and birds in Amazonia. Collection localities were transformed into a Thiessen network where polygon size works as a surrogate for collecting effort. A correlation between botanical and ornithological datasets, with an adjustment for spatial autocorrelation, showed little congruence in the spatial distribution of collecting effort between the two taxa. This incongruence of the distribution of collection effort among taxa suggests that the identification of priority areas for research, and correction for Wallacean and Linnean shortfalls based on taxon‐specific studies, should not be generalized.     

Geographic distribution of tree species occurring in the region of Manaus, Brazil: implications for regional diversity and conservation

The alpha-diversity of trees found in the region of Manaus, Brazil is among the highest recorded for one-hectare plots in Amazonia or any tropical forest. Based on a survey of the distributions of 2541 Neotropical tree species, we analyzed the geographic distribution of 364 species of terra firme forest trees that occur in the region and that are not edaphic specialists. Fifteen distinct distribution patterns were recognized for trees occurring in Manaus. The great majority of species (84.9%) have continuous, somewhat restricted distributions, 35 (9.6%) show broad distributions and 20 species (5.5%) show disjunction between Amazonia and Eastern Brazil. A remarkable 150 (41.2%) of these species showed the region of Manaus as one of their distribution limits. Using the same pool of 2541 species distributions, the percentage of species with a distribution limit in Manaus was compared with that for other localities known to be centers of botanical collection. The null hypothesis that the difference in proportion of species with distribution limits among these localities and Manaus is insignificant was rejected. We conclude that the results are not an artifact of collecting density, that Manaus is indeed a crossroads of distinct phytogeographic regions, and that this explains part of the high species diversity of trees in the region of Manaus. A number of scenarios proposed for the Pleistocene in Amazonia postulate some degree of fragmentation of Amazonian forests or at least populations. As much as these theories may conflict with each other in some respects, they are compatible with the concept of Manaus as a region of re-convergence of isolated or disrupted floras and faunas. The significance of the vicinity of Manaus in the history of the Amazon flora and its current status as a repository for surprisingly high tree diversity highlights the need to make this region a conservation priority.     

Reassessing Neotropical angiosperm distribution patterns based on monographic data: a geometric interpolation approach

Monographic data rely on specimens deposited in herbaria and museums, which have been thoroughly revised by experts. However, monographic data have been rarely used to map species richness at large scale, mainly because of the difficulties caused by spatially heterogeneous sampling effort. In this paper we estimate patterns of species richness and narrow endemism, based on monographic data of 4,055 Neotropical angiosperm species. We propose a geometric interpolation method to derive species ranges at a 1° grid resolution. To this we apply an inverse distance-weighted summation scheme to derive maps of species richness and endemism. In the latter we also adjust for heterogeneous sampling effort. Finally, we test the robustness of the interpolated species ranges and derived species richness by applying the same method but using a leave-one-out-cross-validation (LOOCV). The derived map shows four distinct regions of elevated species richness: (1) Central America, (2) the Northern Andes, (3) Amazonia and (4) the Brazilian Atlantic coast (‘Mata Atlantica’). The region with the highest estimated species richness is Amazonia, with Central America following closely behind. Centers of narrow endemism are located over the entire Neotropics, several of them coinciding with regions of elevated species richness. Sampling effort has a minor influence on the interpolation of overall species richness, but it substantially influences the estimation of regions of narrow endemism. Thus, in order to improve maps of narrow endemism and resulting conservation efforts, more collection and identification activity is required.     

Modelling the known and unknown plant biodiversity of the Amazon Basin

Aims The overall aim of this study is to provide the data needed for Amazonian conservation and the sustainable management of the region. To this end I model the hypothetical distribution of plant species richness across the Amazon Basin, the distribution of the proportion of this species richness that can be accounted for by described species, and hence the distribution of the biodiversity which remains unknown. Location Amazonia, Neotropics. Methods Species richness across the Amazon Basin is estimated by comparing the occurrences of 1584 species of Magnoliophyta whose taxonomy and geographical distributions are relatively well known. These data are used to collate checklists for squares of 1° latitude by 1° longitude. Comparison of the checklists allows estimation of the relative expected diversity in the vicinity of each degree square. Summing the distributions of the hypothetical real ranges gives the proportion of the biodiversity that can be accounted for by described species. Subtraction of the second distribution from the first gives a distribution of the contribution to the overall biodiversity that the model predicts, potentially, results from as yet undescribed species. Results Collections documented in recent botanical monographs show an extremely biased distribution with the best knowledge being found in a very few relatively well‐collected areas. At the degree square level, this model predicts that gamma biodiversity in the Amazon Basin is uniformly high across most of the basin. The model predicts that four large areas of the basin are particularly poorly known, and that they should contain large numbers of uncollected species. Main conclusions The model presented here highlights the difficulties of quantifying Amazonian plant diversity and its distribution. The low density of collections, and especially their extremely clumped distribution, undermines confidence in theories that seek to explain the apparent distribution of biodiversity. The model's prediction is substantially different from published predictions of the distribution of alpha diversity. Testing of this model in the areas identified as lacunae would require collecting programmes designed to collect fertile material of rare species. If the model's predictions are approximately accurate, the plant biodiversity of the Amazon Basin is considerably underestimated.     

Finding needles in the haystack: where to look for rare species in the American tropics

Tropical America (the Neotropics) harbours more plant species than any other region on Earth. The contribution of rare species to this diversity has been recently recognised, but their spatial distribution remains poorly understood. Here, we use all collection records of angiosperms from the Global Biodiversity Information Facility to delineate Neotropical bioregions, and to identify putatively rare species within the Neotropics and the Amazonian rainforest. We analyse the spatial distribution of these species and validate the results on a largely independent dataset based on vegetation plots from the Amazon Tree Diversity Network. We find that rare species are homogeneously distributed through most parts of the lowland Neotropics and Amazonia, but more concentrated in highlands. The second collection of any rare species is most often found in the close vicinity of the first, but in 20% of cases they are more than 580 km apart. We also find cross‐taxonomic patterns of disjunct distributions within the Andes, the Atlantic forest in eastern Brazil, and between Amazonia and the Atlantic forest, but no clear disjunction patterns within lowland areas. These results suggest that a considerable proportion of rare plant species have surprisingly large distribution ranges, and that collections of rare species across most of the lowland Neotropics, and in particular in Amazonia, show no clear directionality. The second record of many rare species may be found virtually anywhere, urging the need for intensifying and broadening biological sampling.     

What spatial data do we need to develop global mammal conservation strategies?

Spatial data on species distributions are available in two main forms, point locations and distribution maps (polygon ranges and grids). The first are often temporally and spatially biased, and too discontinuous, to be useful (untransformed) in spatial analyses. A variety of modelling approaches are used to transform point locations into maps. We discuss the attributes that point location data and distribution maps must satisfy in order to be useful in conservation planning. We recommend that before point location data are used to produce and/or evaluate distribution models, the dataset should be assessed under a set of criteria, including sample size, age of data, environmental/geographical coverage, independence, accuracy, time relevance and (often forgotten) representation of areas of permanent and natural presence of the species. Distribution maps must satisfy additional attributes if used for conservation analyses and strategies, including minimizing commission and omission errors, credibility of the source/assessors and availability for public screening. We review currently available databases for mammals globally and show that they are highly variable in complying with these attributes. The heterogeneity and weakness of spatial data seriously constrain their utility to global and also sub-global scale conservation analyses.     

Database records as a surrogate for sampling effort provide higher species richness estimations

The compilation of all the available taxonomic and distributional information on the species present in a territory frequently generates a biased picture of the distribution of biodiversity due to the uneven distribution of the sampling effort performed. Thus, quality protocol assessments such as those proposed by Hortal et al. (Conservation Biology 21:853–863, 2007) must be done before using this kind of information for basic and applied purposes. The discrimination of localities that can be considered relatively well-surveyed from those not surveyed enough is a key first step in this protocol and can be attained by the previous definition of a sampling effort surrogate and the calculation of survey completeness using different estimators. Recently it has been suggested that records from exhaustive databases can be used as a sampling-effort surrogate to recognize probable well-surveyed localities. In this paper, we use an Iberian dung beetle database to identify the 50 × 50 km UTM cells that appear to be reliably inventoried, using both data derived from standardized sampling protocols and database records as a surrogate for sampling effort. Observed and predicted species richness values in the shared cells defined as well-surveyed by both methods suggest that the use of database records provides higher species richness values, which are proportionally greater in the richest localities by the inclusion of rare species.     

Primate population densities in three nutrient-poor amazonian terra firme forests of south-eastern Colombia

We censused primate populations at three non-hunted 'terra firme' forests of south-eastern Colombian Amazonia. The aggregate biomass densities of diurnal primates at all sites were amongst the lowest recorded for any non-hunted forest in western Amazonia and elsewhere in the Neotropics. Densities of red howler monkeys were low, as is typical in Amazonian terra firme forests far removed from white-water rivers, and densities of woolly monkeys were 1.5-3.5 times lower than those estimated for this species in central-western Brazilian Amazonia. Densities of small to mid-sized primates except for brown capuchins (Cebus apella) and white-faced capuchins (Cebus albifrons) were similar to those of other oligotrophic Amazonian forest sites. Our results are in agreement with other studies showing that terra firme forests of lowland Amazonia typically sustain a low biomass density of primates and other mid-sized to large vertebrates. Large reserves are therefore required to assure the viability of primate populations in oligotrophic systems. Given the escalating negative impacts of human habitat disturbance and hunting in Colombian Amazonia, we urge that a baseline sampling protocol to quantify the abundance and distribution of the harvest-sensitive vertebrate fauna be established within protected areas and the large indigenous reserves so that conservation efforts can be defined and implemented.     

Lauraceae: A promising family for the advance of neotropical dendrochronology

The botanical family Lauraceae is ecologically and physiognomically very important in neotropical forests. It is one of the most frequent and distributed family both in number of individuals and species. Despite of this, we have noticed that a very few Lauraceae species have been considered in dendrochronological investigations. In order to analyze the potential of Lauraceae species in dendrochronology and to facilitate future studies we: (1) reviewed the literature on wood anatomy, cambial activity, tree growth and dendrochronology and compiled a list of species’ tree-ring features throughout the Neotropics; (2) Investigated wood anatomy, growth synchronism and climate-growth relationship using dendrochronological standard techniques in 14 species from subtropical forests of southern Brazil. Our review pointed out that the majority of Lauraceae forms distinct tree-rings in several biomes and climates in the Neotropics. Seasonal growth pattern related to water stress and to seasonal air temperature were identified in Amazonia and in subtropical high elevation sites, respectively. Time series of tree-ring width of Lauraceae species were successfully cross-dated and were already used in reconstruction of fire and vegetation dynamics. Our own dendrochronological investigations brought to light that all the 14 studied species form distinct tree-rings in seasonal or even rainforests. By analyzing time series of tree-ring width we found the same growth tendency within trees of Cinnamomum amoenum and Ocotea pulchella. Moreover, year-to-year variation in the growth time-series was linked to climate variations of temperature and precipitation, showing growth decreases when summer water stress occur. We evinced Lauraceae has distinct, synchronic and climate-sensitive tree-rings. Therefore, since Lauraceae has wide distribution and high frequency in the Neotropics and since many species become centenary, we strongly encourage the use of Lauraceae’s tree-rings in autoecology, climatology and on the reconstruction of vegetation and disturbance dynamics.     

Correspondence between Scientific and Traditional Ecological Knowledge: Rain Forest Classification by the Non-Indigenous Ribereños in Peruvian Amazonia

Traditional ecological knowledge (TEK) is a potential source of ecological information. Typically TEK has been documented at the species level, but habitat data would be equally valuable for conservation applications. We compared the TEK forest type classification of ribereños, the non-indigenous rural peasantry of Peruvian Amazonia, to a floristic classification produced using systematically collected botanical data. Indicator species analysis of pteridophytes in 300 plots detected two forest types on non-flooded tierra firme, each associated with distinct soil texture and fertility, and one forest type in areas subject to flooding. Nine TEK forest types were represented in the same set of plots. Each TEK forest type was consistently (>82%) associated with one of the three floristic classes and there were also clear parallels in the ecological characterizations of the forest types. Ribereños demonstrated clear preferences for certain forest types when selecting sites for slash-and-burn agriculture and hunting. Our results indicate that the non-tribal inhabitants of Amazonia possess valuable TEK that could be used in biodiversity inventories and wildlife management and conservation for characterizing primary rain forest habitats in Amazonia.     

Where are the survivors? Tracking relictual populations of endangered frogs in Costa Rica

Aim We used abiotic environmental variables and historical locality records to infer distributions of endangered anuran species of Costa Rica to promote efficient strategies for future amphibian surveys. Location Costa Rica. Methods We used a Maximum Entropy Algorithm (Maxent) to predict potential distribution maps for 17 species of endangered anurans and create a consensus map of species richness. We compared the environmental conditions from localities where relictual amphibian populations were recently rediscovered with the conditions across their historical range to evaluate the possibility that these relictual populations might occur in specific climatic conditions that could explain their persistence. We used a multicriteria analysis considering the following factors: the intersection zones between the consensus map, conservation areas, potential Batrachochytrium dendrobatidis (Bd) distribution, collecting effort and areas within the precipitation range at which reappearances had occurred to locate sites for future surveys. Results The resulting predictions suggest that suitable areas for the highest number of species occur between 1300 and 2500 m.a.s.l and are concentrated along the Pacific slopes of the Cordillera de Talamanca and Cordillera Volcánica Central. Around 45% of the high potential richness area is under protection. Relictual populations of declined species seem to persist mainly in highly humid localities (2500–3500 mm of mean annual precipitation). Around 240 km² has an ideal environment for the rediscovery of relictual populations. The multicriteria analysis showed that around 0.5% of the Costa Rican territory should be surveyed exhaustively for frogs. Main conclusions Many of the potential refugia we identified here have not been surveyed since 2000, the areas identified by the best model predictions correspond well with the localities of the relictual populations recently reported. We suggest future surveys of missing amphibian species should focus on these areas. The discovery of populations of endangered species can be used to propose conservation areas.     

Thiessen polygons as a model for animal territory estimation

Thiessen polygons are often used to model territory characteristics. However, information about the quality of Thiessen polygon‐based estimates is currently lacking. We used published data to investigate the match between Thiessen polygons and mapped bird territories regarding territory size, shape and neighbourhood. Although territory sizes and the number of neighbours were strongly correlated between these two methods, both parameters were overestimated by the Thiessen polygons. Therefore, caution is required when Thiessen polygons are used as a model for absolute values and when the assumptions of Thiessen polygons, such as formation of discrete territories and a contiguous study area, are not met.     

High local species richness of parasitic wasps (Hymenoptera: Ichneumonidae; Pimplinae and Rhyssinae) from the lowland rainforests of Peruvian Amazonia

Abstract.  1. The parasitic wasp family Ichneumonidae (Hymenoptera) is of great interest because it has been claimed that its species richness does not increase with decreasing latitude.
2. No extensive studies of the family have been conducted in South American localities.
3. Arthropods were sampled using 27 Malaise traps in the Allpahuayo–Mishana National Reserve (56 000 ha) in the north-eastern Peruvian Amazonian lowland rainforest. The total duration of the sampling programme was 185 Malaise trap months.
4. Altogether, 88 species were collected. This is one of the highest local pimpline and rhyssine species numbers ever recorded. A comparison with results from Mesoamerica revealed that at equal numbers of individuals sampled, the number of Pimplinae and Rhyssinae species in Peruvian Amazonia is at least twofold compared with lowland locations in Mesoamerica and somewhat higher than in the most species-rich Costa Rican higher altitude localities.
5. Non-parametric methods of estimating species richness were applied. These suggest that additional sampling would yield a considerable number of new Pimplinae and/or Rhyssinae species.     

Sampling bias and the use of ecological niche modeling in conservation planning: a field evaluation in a biodiversity hotspot

Ecological niche modeling (ENM) has become an important tool in conservation biology. Despite its recent success, several basic issues related to algorithm performance are still being debated. We assess the ability of two of the most popular algorithms, GARP and Maxent, to predict distributions when sampling is geographically biased. We use an extensive data set collected in the Brazilian Cerrado, a biodiversity hotspot in South America. We found that both algorithms give richness predictions that are very similar to other traditionally used richness estimators. Also, both algorithms correctly predicted the presence of most species collected during fieldwork, and failed to predict species collected only in very few cases (usually species with very few known localities, i.e., <5). We also found that Maxent tends to be more sensitive to sampling bias than GARP. However, Maxent performs better when sampling is poor (e.g., low number of data points). Our results indicates that ENM, even when provided with limited and geographically biased localities, is a very useful technique to estimate richness and composition of unsampled areas. We conclude that data generated by ENM maximize the utility of existing biodiversity data, providing a very useful first evaluation. However, for reliable conservation decisions ENM data must be followed by well-designed field inventories, especially for the detection of restricted range, rare species.     

Bat flies on phyllostomid hosts in the Cerrado region: component community, prevalence and intensity of parasitism

Streblidae flies are specialised parasites of bat hosts, mainly phyllostomids. There is a high richness of streblids in the savannah-like Cerrado region; however, there is little quantitative data available in parasitological indices. Here, we describe the component community, prevalence and intensity of a streblid infestation on a phyllostomid bat assemblage in Serra da Bodoquena, a Cerrado region in Southwest Brazil. We conducted surveys by capturing and inspecting bat hosts during the seven-month period between October 2004-December 2005. All the ectoparasites found on the bats were collected in the field and then counted and identified in the laboratory. We captured 327 bats belonging to 13 species, of which eight species were parasitized by 17 species of streblids. Carollia perspicillata and Glossophaga soricina were infested with seven streblid species, whereas the other bat species were infested with four or fewer streblid species. Megistopoda proxima and Aspidoptera falcata flies were found on Sturnira lilium, and Trichobius joblingi was the most prevalent fly on C. perspicillata. Megistopoda aranea and Aspidoptera phyllostomatis were highly prevalent and had a high intensity of infestation on Artibeus planirostris. Overall comparisons of the available data suggest that the component communities of streblids vary more between the Cerrado and Atlantic Forest phytogeographical regions than between localities within the same phytogeographical region.     

Biogeographical relationships among tropical forests in north-eastern Brazil

Aim To use parsimony analysis of endemicity and cladistic analysis of distributions and endemism to evaluate two hypotheses addressing biogeographical relationships among Amazonia, the Caatinga forest enclaves, Pernambuco Centre and the southern Atlantic Forest. Location North‐eastern Brazil, South America. Methods To find the most parsimonious areagram we analysed a matrix composed of the presence (1) or absence (0) of 745 taxa (i.e. 293 genera and 452 species of woody plants) within 16 localities belonging to the four large regions addressed in this study. Results One most parsimonious areagram was found and it shows a basal separation between the southern Atlantic Forest and all other regions. This break is followed by a separation between all Caatinga forest enclaves (except Baturité) from a cluster composed of Baturité, the Pernambuco Centre and Amazonia. In this cluster, the most basal separation isolates Baturité from the cluster formed by localities from Amazonia and the Pernambuco Centre. The biogeographical relationships among sites could not be explained by either a random distribution of species among sites or by the geographical distance between sites. Main conclusions We found strong cladistic signal within the raw distribution and phylogenetic data used in our analysis, indicating structured species assemblages in the surveyed localities. They have resulted from the fragmentation of an ancestral biota that was once widely distributed in the region. Our results also support the hypothesis that Atlantic Forest is not a biogeographically natural area, because the Pernambuco Centre is more closely related to Amazonia than to the southern Atlantic Forest. Finally, our data do not support the notion that Caatinga forest enclaves comprise a single biogeographical region, because one Caatinga forest enclave (Baturité) is much more closely related to the cluster formed by Amazonia and the Pernambuco Centre than to other sites. These relationships suggest the occurrence of forest connections between Amazonia and the Atlantic Forests across Caatinga during several periods of the Tertiary and Quaternary. However, palaeoecological data currently available for the Caatinga region are still scarce and do not have either the spatial or temporal resolution required to reconstruct the history of connections among the forests in north‐eastern Brazil.     

Herbarium collections and field data-based plant diversity maps for Burkina Faso

A map of plant species diversity in Burkina Faso is presented based on field observations and specimen data from the Ouagadougou University Herbarium (OUA) and the Herbarium Senckenbergianum (FR). A map of collecting intensity and field observations illustrates centres of botanical research activities in Burkina Faso. To overcome problems associated with biased sampling intensity, distributions of species have been modelled and extrapolated to maps of vascular plant diversity, life forms and diversity of four selected families (Poaceae, Cyperaceae, Dioscoreaceae and Rubiaceae). The area of most intensive collection and observation is around Gorom‐Gorom and Fada N’Gourma. Modelled diversity generally increases towards the south, as does the proportion of phanerophytes, lianas and hemicryptophytes, while the opposite trend is observed for therophytes. Poaceae diversity is highly correlated with total vascular plant diversity, making the family especially suitable as an indicator for overall plant diversity. Cyperaceae are rather evenly distributed throughout the country, Dioscoreaceae are restricted to the Sudanian Zone. Rubiaceae have their highest diversities in the very south. Our approach can be transferred to areas with a similar database, certainly to other areas within West Africa. Future research should focus on distribution data for rare species, enabling our approach to evaluate the West African system of protected areas.     

Patterns,biases and prospects in the distribution and diversity of Neotropical snakes

Motivation

We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases.

Main types of variables contained

We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset.

Spatial location and grain

Neotropics, Behrmann projection equivalent to 1° × 1°.

Time period

Specimens housed in museums during the last 150 years.

Major taxa studied

Squamata: Serpentes.

Software format

Geographical information system (GIS).

Results

The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well‐sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed.

Main conclusions

The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high‐diversity areas and sampling efforts be directed towards Amazonia and poorly known species.