Using river color to predict Amazonian floodplain forest avifaunas in the world's largest blackwater river basin

Despite the importance of rivers in Amazonian biogeography, avian distribution patterns in river‐created habitats (i.e., floodplain forests) have been sparsely addressed. Here, we explore geographic variation in floodplain forest avifaunas, specifically regarding one of the most striking aspects of the Amazon: the diversity of river “colors” (i.e., types, based on the color of the water). We sampled the avifauna at 30 sites, located in 17 different rivers (nine black‐ and eight whitewater), in the Rio Negro basin, northwestern Brazil. Our sampling comprised ten 15‐min point‐counts per site, distributed every 500–1000 m along the river. We recorded a total of 352 bird species, many of which occurred in both river types. Although bird species richness was similar among rivers, we found significant differences in species composition. Nearly 14 percent of the species were significantly associated with one or the other river type. Most floodplain forest specialists occurred predominantly in whitewater rivers, whereas species that are typically associated with white‐sand habitats occurred in blackwater. Despite significant distinctions between river types, occurrence patterns and levels of habitat association differed among indicator species and may vary in the same species throughout its global distribution. There were also “intermediate” avifauna in some of our sites, suggesting that continuous parameters characterizing river types structure species turnover. The water color‐based classification of Amazonian rivers represents a simple and powerful predictor of the floodplain forest avifauna, offering a stimulating starting point for understanding patterns of floodplain bird distributions and for prioritizing conservation efforts in these overlooked habitats. Abstract in Portuguese is available with online material.     

Sampling Effort in Neotropical Primate Diet Studies: Collective Gains and Underlying Geographic and Taxonomic Biases

Primates are among the most observable and best studied mammalian orders, yet the distribution of sampling effort by primatologists has inevitably concentrated on a few genera and a limited number of study sites. We present the first systematic review of sampling effort and associated biases in wild primate field research, focusing on dietary studies across the Neotropics. Our literature review of all 24 neotropical primate ecospecies spans 42 years (1969–2011) and covers 290 dietary studies at 164 study sites across 17 countries. We use a standardized measure of sampling effort to assimilate data sets derived from multiple methodologies and attempt to understand the distribution of effort (total equivalent to 193,804 h) using geographic variables and primate species traits. Results indicate that there are both geographic and taxonomic biases, with sampling effort generally skewed towards large-bodied species occupying large geographic ranges, and concentrated at a select few primatology research hubs. We also note that full primate assemblages at any given study site are rarely investigated. Our assessment thus reveals severely undersampled primate taxa and geographic regions that must be considered in future research. Current biases could be ameliorated by deliberately targeting poorly studied genera anywhere in their geographic distribution, well-studied genera in poorly studied regions, and striving to study multiple sympatric taxa within a single site. Although continued inequalities in sampling effort are probably inevitable, this study shows that this need not inhibit successful compilations and meta-analyses, provided that adequate data on feeding records and sampling effort can be made available.     

Forecasting insect species richness scores in poorly surveyed territories: the case of the Portuguese dung beetles (Col. Scarabaeinae)

Large-scale biodiversity assessment of faunal distribution is needed in poorly sampled areas. In this paper, Scarabaeinae dung beetle species richness in Portugal is forecasted from a model built with a data set from areas identified as well sampled. Generalized linear models are used to relate the number of Scarabaeinae species in each Portuguese UTM 50 × 50 grid square with a set of 25 predictor variables (geographic, topographic, climatic and land cover) extracted from a geographic information system (GIS). Between-squares sampling effort unevenness, spatial autocorrelation of environmental data, non-linear relationships between variables and an assessment of the models' predictive power, the main shortcomings in geographic species richness modelling, are addressed. This methodological approach has proved to be reliable and accurate enough in estimating species richness distribution, thus providing a tool to identify areas as potential targets for conservation policies in poorly inventoried countries.     

Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion

For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.     

Insects associated with flowers of weeds of the Botanical Garden of Santiago de Cuba,with emphasis on Hymenoptera

The insect visitors of flowers in nine weeds species were studied in the Botanical Garden of Santiago de Cuba, Eastern Cuba, during 1993 (March-June, spring season) and 1994 (January-March, end of winter and beginning of spring season). About 50 hours of collecting efforts were made at three times (0900-0930 hr in 1993; 0900-0930 hr, 1200-1230 hr and 1500-1530 hr in 1994). More than 140 species of at least 37 families were found; Hymenoptera dominated (with more than a half of specimens), followed by Diptera, Coleoptera and Lepidoptera. Among Hymenoptera, bees (Apoidea) were the largest group, especially Apis mellifera L; followed by wasps (Vespidae, Pompilidae, Sphecidae) and ichneumon flies (Ichneumonidae); Microhymenopterans were not sampled. Hymenopterans of each weed were compared for diversity, similarity, dominant and subdominant species, visitation time, sampling efficiency, etc. Each plant species had a particular Hymenoptera complex, almost one third of which were natural enemies of agricultural pests, and most are believed to be potential pollinators. Closely related species showed similar patterns of daily activity, with a peak at 0900-0930 hr for all plant species. Second grade polynomial equations were the best fitted models to describe the relationships between number of species and number of specimens, and between total number of species and number of samples (R2 = 0.9734 and R2 = 0.9573, p < 0.01). The role of weeds in the biodiversity of the agroecosystems is analyzed; as well as the effectiveness of this collection method to study Hymenoptera.     

Efficient sampling of ground-dwelling arthropods using pitfall traps in arid steppes

Pitfall trapping is probably the most frequently used method for sampling ground-dwelling arthropods. While the capture of specimens in pitfall traps largely depends on the number of individuals in the sampled area, trap design and trapping effort for a given environment, can also affect sampling success. The aim of this study was to determine the best pitfall trapping design for collecting ground-dwelling arthropods in the wind-blown and cold arid steppe areas of Patagonia. We tested four designs of traps, six types of preservative and different times of activation as well as the quantity of traps. Both preservation attributes and sampling efficiency differed between different trap designs and fluids compared. We conclude that in order to obtain reliable data on the structure of a community of ground-dwelling arthropods in Patagonia, at least three pitfall traps per experimental unit are required. In addition, traps should be opened for a minimum of 10 days filled with 300 ml of 30% ethylene glycol. We also suggested the use of a simple trap design (i. e. without funnel or roof). We believe these findings will contribute to more appropriate sampling of the ground dwelling fauna of Patagonia as well as other arid areas, leading to more reliable diversity studies.     

Recent records of steppe species in Belarus,first indications of a steppe species invasion?

BELARUS IS SITUATED AT A CROSSROAD OF NATURAL BORDERS OF SPECIES DISTRIBUTIONS: the NE part is situated in a taiga zone, whereas the other part of terrain is in the European forest zone. The distance of Belarus to the steppe zone is about 330 kilometers. This geographical position and the extensive knowledge of its fauna can be used to monitor changes in the distribution of different species. An intensive study of open habitat ground beetles was carried out from 1975-2008 in Belarus, using pitfall traps, quadrate-sampling methods, hand collecting, netting and light traps. In total, more than 130 000 specimens of ground beetles belonging to 169 species were collected from 62 fields and 11 meadows of different types. 217 specimens of Calosoma investigator (Illiger 1798), 2 specimens of Calosoma denticolle (Gebler 1833), and one specimen of Harpalus subcylindricus (Dejean, 1829), Harpalus honestus (Duftschmid 1812) and Zabrus tenebrioides (Goeze 1777) were present in this material. All specimens were macropterous and exclusively caught at fields and waste grounds on sandy soil. Nowadays Belarus is the northernmost location for these species in Eastern Europe. Steppe species most probably migrated to SE Belarus from NE Ukraine, using Dnieper and its river valleys. The shift in the geographic distribution of steppe species during the last thirty years in Belarus have been attributed to a higher frequency of warmer and wetter summers in the last few decades.     

Maximizing plant species inventory efficiency by means of remotely sensed spectral distances

Aim Inventorying plant species in an area based on randomly placed quadrats can be quite inefficient. The aim of this paper is to test whether plant species richness can be inventoried more efficiently by means of a spectrally‐based ordering of sites to be sampled. Location The study area was a complex wetland ecosystem, the Lake Montepulciano Nature Reserve, central Italy. This is one of the most important wetland areas of central Italy because of the diverse plant communities and the seasonal avifauna. Methods Field sampling, based on a random stratified sampling design, was performed in June 2002. Plant species composition was recorded within sampling units of 100 m² (plots) and 1 ha (macroplots). A QuickBird multispectral image of the same date was acquired and corrected both geometrically and radiometrically. Species accumulation curves based on spectral information were obtained by ordering sites to be sampled according to a maximum spectral distance criterion (i.e. by ordering sampling units based on the maximum distances among them in a four‐dimensional spectral space derived from the remotely sensed data). Different distance measures based on mean and maximum spectral distances among sampling units were tested. The performance of the species accumulation curve derived by the spectrally‐based ordering of sampling units was tested against a rarefaction curve obtained from the mean of 10,000 accumulation curves based on randomly ordered sampling units. Results The spectrally‐derived curve based on the maximum spectral distance among sampling units showed the most rapid accumulation of species, well above the rarefaction curve, at both the plot and the macroplot scales. Other ordering criteria of sampling units captured less richness over most of the species accumulation curves at both the spatial scales. The accumulation curves based on other measurements of distance were much closer to the random curve and did not show differences with respect to the species rarefaction curve based on random ordering of sampling units. Main conclusions The present investigation demonstrated that spectral‐based ordering of sites to be sampled can lead to the maximization of the efficiency of plant species inventories, an activity usually driven by the ‘botanist's internal algorithm’ (intuition), without any formalized rule to drive field sampling. The proposed approach can reduce costs of plant species inventorying through a more efficient allotment of time and sampling.     

Genetic differentiation of wild relatives of rice as assessed by RFLP analysis

To study genetic diversity and relationships of wild relatives of rice, 58 accessions of Oryza rufipogon, Oryza nivara, Oryza sativa f. spontanea and the cultivated Oryza sativa, representing a wide range of their distribution, were analyzed using the restriction fragment length polymorphism (RFLP) technique. All 30-used RFLP probes detected polymorphisms among the Oryza accessions, with an average of 3.8 polymorphic fragments per probe. Considerable genetic diversity was scored among the Oryza accessions with a similarity coefficient ranging from 0.28 to 0.93; but the cluster analysis of the accessions did not show an apparent grouping based on the species classification, instead they were scattered randomly in different groups. Noticeably, the Oryza accessions from the same geographic region, or near-by geographic regions, tended to be clustered in the same groups. The indica rice varieties showed relatively high genetic diversity and were scattered in different groups of their wild relatives, but the japonica varieties showed a relatively low variation and formed an independent group. It is concluded from the molecular analytical result that: (1) the four Oryza taxa have a remarkably close relationship and their independent species status need to be carefully reviewed; (2) geographic isolation has played a significant role in the differentiation of the Oryza accessions; therefore, a wide geographic range needs to be covered in collecting wild rice germplasm for ex situ conservation; and (3) the conventional conclusion of indica rice being directly domesticated from its ancestral wild species, and japonica rice being derived from indica, gains support from our data.     

Distribution and habitat preferences of species within the genus Elaphoidella Chappuis, 1929 (Crustacea: Copepoda: Harpacticoida) in Slovenia

Twelve species of the harpacticoid genus Elaphoidella, most of them exclusively groundwater species, have been recorded in Slovenia (SE Europe). Their distribution and ecology are reviewed with the aim of evaluating distribution patterns, species preferences for groundwater habitats, ecological preferences and interactions with other copepod species at regional scale. Data on Elaphoidella species were obtained partly from the existing literature and partly from the author's (AB) own sampling campaigns carried out together with his co-workers. During the rich history of collecting copepods in Slovenia (from the 1920s to present), Elaphoidella species were recorded at 78 sampling sites altogether. The majority of collecting was conducted in the southern (Dinaric region) and north-western (Alpine region) Slovenia. The most intensively sampled habitats were porous aquifers of alluvial plains, springs in the karstic unsaturated zone and percolation water in caves. The highest species richness of Elaphoidella was recorded in the southern Slovenia, where 10 species were found. The strictly “Dinaric” species are E. charon, E. franci, E. karstica, E. stammeri, E. sp. 1 and E. sp. 2, while E. phreatica and E. bidens were found exclusively in the north-western Slovenia. From the latest data on the copepod distributions (2002–2004), where the environmental characteristics of sampling sites were also measured, the relationship between selected environmental characteristics of the habitats and the presence of Elaphoidella species was analysed. The distribution of Elaphoidella species in Slovenia was found to be related with the region, habitat type, altitude, conductivity and pH of the water.     

Elasmobranchs from the upper Paleocene of Togo

Bulk sampling and surface collecting of two glauconitic horizons located in Southern Togo yielded a diverse elasmobranch fauna described here. This fauna includes 30 species dominated by carcharhiniforms (eleven species), myliobatiforms (nine species) and lamniforms (five species); it also comprises three orectolobiforms, whereas the squatiniforms and rhinopristiforms are represented by one species each. Although the poor preservation of the specimens hampered numerous species-level identifications, the vast majority of taxa identified were formerly reported from the Paleocene–Ypresian interval, four of which being exclusively known from the upper Paleocene. This, along with the six associated benthic foraminifera species, indicates a late Thanetian age for the sampled horizons and provide age constraints on a geographically widespread benchmark horizon in Western Africa. The composition of the elasmobranch assemblage shows strong resemblances with upper Paleocene faunas from Morocco and differs markedly from known assemblages from geographically closer localities in Niger and Nigeria, which suggests strong palaeoenvironmental control on the distribution of Thanetian elasmobranch diversity.     

Spatial patterns of plant diversity and communities in Alpine ecosystems of the Hengduan Mountains,Northwest Yunnan,China

Aims Conduct a quantitative, but rapid, regional-level assessment of the alpine flora across northwest Yunnan (NWY) to provide a broad-based understanding of local and regional patterns of the composition, diversity and health of alpine ecosystems across NWY.Methods A stratified random sampling design was employed to select sites across the different mountain ranges of NWY. Vegetation was sampled by stratifying each site by the three major alpine vegetation community types: meadow, dwarf shrub and scree. Two 50-m transects were randomly located within each community type at each sampling site with 10 1-m 2 subplots systematically placed along each transect. Environmental variables were recorded at each transect. Multivariate analyses were used to classify the major plant community assemblages and link community patterns to environmental and habitat variables.Important findings Forb species richness varied from 19 to 105 species per site (21 sites total) with an average of 59 species per site (60 m 2 sampled per site). Most species were patchily distributed with narrow distributions and/or small population sizes; over half the species occurred at only one or two sites. Distinct species assemblages were identified in the meadow vegetation that was strongly aggregated by geographic location suggesting the presence of distinct phytogeographic zones of the meadow alpine flora. Elevation and geographic location were the dominant environmental gradients underlying the variations in species composition. Jaccard's coefficient of similarity averaged only 10% among sites indicating there was little similarity in the alpine flora across the region. The alpine vegetation is highly heterogeneous across the complex landscape of the Hengduan Mountains of NWY. Conservation strategies need to take into account the large geographic differences in the flora to maximize protection of biodiversity.     

Evaluating sample allocation and effort in detecting population differentiation for discrete and continuously distributed individuals

One of the most pressing issues in spatial genetics concerns sampling. Traditionally, substructure and gene flow are estimated for individuals sampled within discrete populations. Because many species may be continuously distributed across a landscape without discrete boundaries, understanding sampling issues becomes paramount. Given large-scale, geographically broad conservation efforts, researchers are looking for guidance as to the trade-offs between sampling more individuals within a population versus few individuals scattered across more populations. Here, we conducted simulations that address these issues. We first established two archetypical patterns of dispersion: (1) individuals within discrete populations, and (2) continuously distributed individuals with limited dispersal. We used genotypes generated from a spatially-explicit, individual-based program and simulated genetic structure in individuals from nine different population sizes across a landscape that either had barriers to movement (defining discrete populations) or isolation-by-distance patterns (defining continuously distributed individuals). Then, given each pattern of dispersion, we allocated samples across four different sampling strategies for each of the nine population sizes in various configurations for sampling more individuals within a population versus fewer individuals scattered across more populations. We assessed the population genetic substructure with both the population-based metric, F _ST, and an individual-based metric, D _PS regardless of the true pattern of dispersion to allow us to better understand the effect of incorrectly matching the metric and the distribution (e.g., F _ST with continuously distributed individuals, and vice versa). We show that sampling many subpopulations (or sampling areas), thus sampling fewer individuals per subpopulation, overestimates measures of population subdivision with the population-based metric for both patterns of dispersion. In contrast, using the individual-based metric gives the opposite results: sampling too few subpopulations, and many individuals per subpopulation, produces an underestimate of the strength of isolation-by-distance. By comparing all results, we were able to suggest a strong predictive model of a chosen genetic structure metric for elucidating the sampling design trade-offs given each pattern of dispersion and configuration on the landscape.     

Anthropogenic noise reduces bird species richness and diversity in urban parks

Anthropogenic noise is becoming more prevalent in the world and has been shown to affect many animal species, including birds. The impact of such noise was measured in Neotropical urban parks to assess how the noise affects avifauna diversity and species richness. We sampled bird species, and concurrently measured sound pressure (noise) levels (L_eq, equivalent noise levels) in eight urban green areas or parks located in a large city (Belo Horizonte) in south‐eastern Brazil over a 1‐year period. The diversity of sampled points was measured by means of total species richness, Fisher's alpha and Shannon–Wiener diversity indices. Noise levels within all parks were greater than those in natural areas. We found that an increase in noise levels and the area of open habitats surrounding sampling points were negatively related to species richness. Social factors reflecting increased urbanization, such as higher incomes, were also negatively correlated with bird species richness. However, noise was the factor that explained most of the variance. These results suggest that anthropogenic noise can have a significant negative impact on the conservation value of urban parks for bird species.     

Mapping patterns of ferns species richness through the use of herbarium data

This paper aims to analyse the spatial patterns of sampling effort and species richness of pteridophyte in a well-investigated region as Tuscany, Italy, by using data stored from a geodatabase storing information on the specimens preserved in the main herbaria of the region. A total of 6,905 records about pteridophyte specimens were extracted from the geodatabase, and 5,638 of such specimens were studied through the use of spatial statistical techniques. The data about the sampling effort and species richness were analysed in relation to topographical variables to assess any significant relationship. Specimen-based rarefaction techniques were used to compare areas with different number of detected species. The analysis of the sampling effort data showed a nonhomogeneous distribution of herbarium data, with some areas being intensively sampled and others being almost unsampled. Thus, the geographical distribution of specimens was extremely clustered. The comparison across geographical areas through specimen-based rarefaction curves showed great differences in species richness and sampling completeness. The analysis of the residuals of species–area relationships evidenced that the distance to water bodies was the only significant topographical variable in controlling species diversity.     

Geographic sampling bias in the South African Frog Atlas Project: implications for conservation planning

Quality conservation planning requires quality input data. However, the broad scale sampling strategies typically employed to obtain primary species distribution data are prone to geographic bias in the form of errors of omission. This study provides a quantitative measure of sampling bias to inform accuracy assessment of conservation plans based on the South African Frog Atlas Project. Significantly higher sampling intensity near to cities and roads is likely to result in overstated conservation priority and heightened conservation conflicts in urban areas. Particularly well sampled protected areas will also erroneously appear to contribute highly to amphibian biodiversity targets. Conversely, targeted sampling in the arid northwest and along mountain ranges is needed to ensure that these under-sampled regions are not excluded from conservation plans. The South African Frog Atlas Project offers a reasonably accurate picture of the broad scale west-to-east increase in amphibian richness and abundance, but geographic bias may limit its applicability for fine scale conservation planning. The Global Amphibian Assessment species distribution data offered a less biased alternative, but only at the cost of inflated commission error.     

Toward an optimal sampling protocol for Hemiptera on understorey plants

There are no standardised sampling protocols for inventorying Hemiptera from understorey or canopy plants. This paper proposes an optimal protocol for the understorey, after evaluating the efficiency of seven methods to maximise the richness of Hemiptera collected from plants with minimal field and laboratory time. The methods evaluated were beating, chemical knockdown, sweeping, branch clipping, hand collecting, vacuum sampling and sticky trapping. These techniques were tested at two spatial scales: 1 ha sites and individual plants. In addition, because efficiency may differ with vegetation structure, sampling of sites was conducted in three disparate understorey habitats, and sampling of individual plants was conducted across 33 plant species. No single method sampled the majority of hemipteran species in the understorey. Chemical knockdown, vacuum sampling and beating yielded speciose samples (61, 61 and 30 species, respectively, representing 53, 53 and 26% of total species collected). The four remaining methods provided species-poor samples (<18 species or <16% of total species collected). These methods also had biases towards particular taxa (e.g., branch clipping and hand collecting targeted sessile Hemiptera, and sticky trapping were dominated by five species of Psyllidae). The most time-efficient methods were beating, sweeping and hand collecting (200 minutes of field and laboratory time yielded >7 species for each technique). By comparison, vacuum sampling, sticky trapping, branch clipping and chemical knockdown yielded <5 species for the same period. Chemical knockdown had further disadvantages; high financial cost and potential spray drift. The most effective methods for a standardised sampling protocol to inventory Hemiptera from the understorey are beating and vacuum sampling. If used in combination, these methods optimise the catch of understorey hemipteran species, as their samples have high complementarity.     

Effect of sampling pattern on estimation of species distributions along gradients

Computer simulation and statistical theory indicate that estimation of species distribution is difficult when species reach maximum abundance near one end of the sampled portion of a gradient or when they have wide ecological breadth. Relative to balanced sampling of the whole gradient, concentration of sampling effort near the ends increases accuracy in estimation of distributions of truncated species more than it decreases accuracy for other species. Hence, overall accuracy in the estimation of distributions for a collection of species with modes scattered about on a gradient is greatest when sampling is somewhat more intense near the extremes of the gradient.     

Patterns of Genetic Population Differentiation in Four Species of Amazonian Frogs: A Test of the Riverine Barrier Hypothesis1

Patterns and levels of allozyme variation among populations of Amazonian frogs were used to test the riverine barrier hypothesis of species differentiation. Two frog species were sampled from each of the two main forest habitats on both banks of the Juruá River in the southwestern Brazilian Amazon Basin at various points along its course to contrast different barrier strengths. Scarthyla ostinodactyla and Scinax rubra were sampled from flooded forest (varzea), and Physalaemus petersi and Epipedobates femoralis from non-flooded forest (terra firme). All species showed high levels of within-population genetic variation. Average Nei's (1978) and Rogers’ (1972) genetic distances between sampled sites for all species were high indicating substantial among-population differentiation. The observation of low gene flow between sampled sites within species was further substantiated with Slatkin's (1993) M? analyses. Randomization tests suggested that there was some population structure at a few assayed polymorphic loci that was consistent with the riverine barrier hypothesis. However, it was apparent from the raw allozyme frequency data that these results were largely driven by substantial differentiation at one or a few collecting localities rather than by basin-wide patterns of riverine differentiation. Phenograms using genetic distance matrices supported this interpretation. Patterns of geographic variation are probably more consistent with the idea of this region being a zone of secondary contact.