The patterns of vascular plant discoveries in China.

AIM: (1) To understand geographic patterns of species discovery by examining the effect of growth form, range size, and geographic distribution on discovery probability of vascular plant species in China; (2) to find out which taxa harbor the largest number of undiscovered species and where those species locate; and (3) to find out the determinants of province-level mean discovery time and inventory completeness. LOCATION: China. METHODS: We compiled the discovery time and province-level geographic distributions of ~31,000 vascular plant species described between 1753 and 2013 from Flora of China. We used a Cox proportional hazard model to determine the biological and geographic correlates of discovery probability. Accumulation curves of species discoveries were fitted by a logistic discovery model to estimate inventory completeness of different growth forms and of different provinces. We then used linear regression to identify the determinants of mean discovery time and beta regression to identify the determinants of inventory completeness. RESULTS: We found that species with larger range size and distributed in northeastern part of China have a higher discovery probability. Coastal species were discovered earlier than inland species. Trees and shrubs of seed plants have the highest discovery probability while ferns have the lowest discovery probability. Herbs have the largest number of undiscovered species in China. Most undiscovered species will be found in southwest China, where three global biodiversity hot spots locate. Spatial patterns of mean discovery time and inventory completeness are mainly driven by the total number of species, human population density in an area, and latitude and longitude of a province. MAIN CONCLUSIONS: Socioeconomic factors primarily determine the discovery patterns of vascular plants in China. Undiscovered species are most likely to be narrow-ranged, inconspicuous endemic species such as herbs and ferns, which are prone to extinctions and locate in biodiversity hot spots in southwestern China.

Syrphidae of Southern Illinois: Diversity, floral associations, and preliminary assessment of their efficacy as pollinators.

Syrphid flies (Diptera: Syrphidae) are a cosmopolitan group of flower-visiting insects, though their diversity and importance as pollinators is understudied and often unappreciated. Data on 1,477 Syrphid occurrences and floral associations from three years of pollinator collection (2017-2019) in the Southern Illinois region of Illinois, United States, are here compiled and analyzed. We collected 69 species in 36 genera off of the flowers of 157 plant species. While a richness of 69 species is greater than most other families of flower-visiting insects in our region, a species accumulation curve and regional species pool estimators suggest that at least 33 species are yet uncollected. In order to further the understanding of Syrphidae as pollinators in the Southern Illinois region, we produced a NMDS ordination of floral associations for the most common syrphid species. The NMDS did not sort syrphid species into discrete ecological guilds, and syrphid floral associations generally fit those predicted by traditional pollination syndromes. We also conducted a preliminary analysis of the pollen-carrying capacity of different syrphid taxa, which found several Eristalis species to carry pollen loads comparable to the European Honey Bee, Apis mellifera, and showed significant differences in the pollen-carrying capacity of various syrphid species. Notably, the extremely common genus Toxomerus and other small Syrphinae species carried very little pollen, while large and pilose Eristalinae species carried large pollen loads.

Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments.

For many types of high-throughput sequencing experiments, success in downstream analysis depends on attaining sufficient coverage for individual positions in the genome. For example, when identifying single-nucleotide variants de novo, the number of reads supporting a particular variant call determines our confidence in that variant call. If sequenced reads are distributed uniformly along the genome, the coverage of a nucleotide position is easily approximated by a Poisson distribution, with rate equal to average sequencing depth. Unfortunately, as has become well known, high-throughput sequencing data are never uniform. The numerous factors contributing to variation in coverage have resisted attempts at direct modeling and change along with minor adjustments in the underlying technology. We propose a new nonparametric method to predict the portion of a genome that will attain some specified minimum coverage, as a function of sequencing effort, using information from a shallow sequencing experiment from the same library. Simulations show our approach performs well under an array of distributional assumptions that deviate from uniformity. We applied this approach to estimate coverage at varying depths in single-cell whole-genome sequencing data from multiple protocols. These resulted in highly accurate predictions, demonstrating the effectiveness of our approach in analyzing complexity of sequencing libraries and optimizing design of sequencing experiments.

Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines.

The vertebrate fauna of the Philippines, known for its diversity and high proportion of endemic species, comprises mainly small- to medium-sized forms with a few large exceptions. As with other tropical ecosystems, the major threats to wildlife are habitat loss, hunting and invasive species, of which the feral cat (Felis catus) is considered the most damaging. Our camera-trapping study focused on a terrestrial vertebrate species inventory on Bohol Island and tempo-spatial co-occurrences of feral cats with their prey and competitors. The survey took place in the Rajah Sikatuna Protected Landscape, and we examined the primary rainforest, its border with agricultural land, and rural areas in the vicinity of villages. Altogether, over 2,885 trap days we captured 30 species of vertebrates-10 mammals (including Sus philippensis), 19 birds and one reptile, Varanus cumingi. We trapped 81.8% of expected vertebrates. Based on the number of events, the most frequent native species was the barred rail (Gallirallus torquatus). The highest overlap in diel activity between cats and potential prey was recorded with rodents in rural areas (Δ = 0.62); the lowest was in the same habitat with ground-dwelling birds (Δ = 0.40). Cat activity was not recorded inside the rainforest; in other habitats their diel activity pattern differed. The cats' activity declined in daylight in the proximity of humans, while it peaked at the transition zone between rainforest and fields. Both rodents and ground-dwelling birds exhibited a shift in activity levels between sites where cats were present or absent. Rodents tend to become active by day in cat-free habitats. No cats' temporal response to co-occurrences of civets (Paradoxurus hermaphroditus and Viverra tangalunga) was found but cats in diel activity avoided domestic dogs (Canis lupus familiaris). Our first insight into the ecology of this invasive predator in the Philippines revealed an avoidance of homogeneous primary rainforest and a tendency to forage close to human settlements in heterogeneous habitats. A detailed further investigation of the composition of the cat's diet, as well as ranging pattern, is still needed.

Applications of species accumulation curves in large-scale biological data analysis.

The species accumulation curve, or collector's curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45-63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.

Efeitos da distância entre iscas nas estimativas de abundância e riqueza de formigas em uma floresta de terra-firme na Amazônia Central / Effects of bait spacing on ant abundance and richness in one forest at Central Amazonia

Coletas com iscas são amplamente utilizadas para investigar a atividade de formigas de solo e vegetação e também podem ser empregadas para estimar o número de espécies e a abundância de formigas. Apesar de ser barata e fácil de implementar, a riqueza e abundância das formigas estimadas por iscas podem ser enviesadas por alguns fatores, como a distância entre iscas. Neste trabalho, avaliamos se a distância entre iscas altera as estimativas de abundância e riqueza de formigas e qual distância entre iscas resulta na melhor relação entre custo financeiro e número de espécies amostradas, objetivo da maioria dos relatórios de impacto ambiental. Amostramos 30 transectos de 100 m com distância entre iscas diferentes (2,5; 3,4; 5; 6,7; 10 e 20 m), distribuídos em uma área de 1 km² em uma floresta de terra-firme ao norte de Manaus. Independente da distância entre iscas, o número de espécies coletado a cada cinco iscas, foi aproximadamente 8, e a abundância média foi maior que 50 indivíduos. No entanto o número de espécies por isca foi maior em transectos com maior distância entre iscas. Transectos com distância entre iscas de 10 e 20 m, coletaram 50 por cento mais espécies por isca que transectos com iscas distantes a 2,5 e 3,4 m entre si. Nossos resultados sugerem que nesta área, a amostragem mais eficiente desse método de coleta seria distribuir 450 iscas a cada 10 m ou 20 m no solo da floresta.

Baits are widely used to investigate the activity of terrestrial and arboreal ants, but also can be used to estimate the ant abundance and species richness. Despite the fact that baiting are cheap and easy to implement, many factors, such as the distance between baits, may influence the estimate of ant species richness and abundance. In this study, we evaluated the effects of bait spacing on abundance and the number of ant species. We also demonstrate which distance between baits showed the best relationship between costs and number of ant species sampled. We sampled 30 transects of 100 m with bait spacing ranging from 2.5 to 20 m, spread over 1 km² of a "terra-firme" forest situated at North of Manaus. The bait spacing did not affect the ant diversity estimative. Regardless bait spacing, the number of species collected every five baits was around 8, and the average abundance was approximately 50 individuals. However the number of species per bait was higher in transects with larger bait spacing. Transects with bait spacing of 10 m and 20 m, collected 50 percent more species than transects with baits placed 2.5 m and 3.4 m apart. Our results suggest that at this forest, the most efficient sampling design using only baits would be place 450 baits every 10 m or 20 m at the forest floor.