The hidden side of diversity: Effects of imperfect detection on multiple dimensions of biodiversity

1. Studies on ecological communities often address patterns of species distribution and abundance, but few consider uncertainty in counts of both species and individuals when computing diversity measures.
2. We evaluated the extent to which imperfect detection may influence patterns of taxonomic, functional, and phylogenetic diversity in ecological communities.
3. We estimated the true abundance of fruit‐feeding butterflies sampled in canopy and understory strata in a subtropical forest. We compared the diversity values calculated by observed and estimated abundance data through the hidden diversity framework. This framework evaluates the deviation of observed diversity when compared with diversities derived from estimated true abundances and whether such deviation represents a bias or a noise in the observed diversity pattern.
4. The hidden diversity values differed between strata for all diversity measures, except for functional richness. The taxonomic measure was the only one where we observed an inversion of the most diverse stratum when imperfect detection was included. Regarding phylogenetic and functional measures, the strata showed distinct responses to imperfect detection, despite the tendency to overestimate observed diversity. While the understory showed noise for the phylogenetic measure, since the observed pattern was maintained, the canopy had biased diversity for the functional metric. This bias occurred since no significant differences were found between strata for observed diversity, but rather for estimated diversity, with the canopy being more clustered.
5. We demonstrate that ignore imperfect detection may lead to unrealistic estimates of diversity and hence to erroneous interpretations of patterns and processes that structure biological communities. For fruit‐feeding butterflies, according to their phylogenetic position or functional traits, the undetected individuals triggered different responses in the relationship of the diversity measures to the environmental factor. This highlights the importance to evaluate and include the uncertainty in species detectability before calculating biodiversity measures to describe communities.

     

Changes in stable isotopic signatures of soil nitrogen and carbon during 40 years of forest development

Understanding what governs patterns of soil δ¹⁵N and δ¹³C is limited by the absence of these data assembled throughout the development of individual ecosystems. These patterns are important because stable isotopes of soil organic N and C are integrative indicators of biogeochemical processing of soil organic matter. We examined δ¹⁵N of soil organic matter (δ¹⁵N_SOM) and δ¹³C_SOM of archived soil samples across four decades from four depths of an aggrading forest in southeastern USA. The site supports an old-field pine forest in which the N cycle is affected by former agricultural fertilization, massive accumulation of soil N by aggrading trees over four decades, and small to insignificant fluxes of N via NH₃ volatilization, nitrification, and denitrification. We examine isotopic data and the N and C dynamics of this ecosystem to evaluate mechanisms driving isotopic shifts over time. With forest development, δ¹³C_SOM became depth-dependent. This trend resulted from a decline of ~2‰ in the surficial 15 cm of mineral soil to −26.0‰, due to organic matter inputs from forest vegetation. Deeper layers exhibited relatively little trend in δ¹³C_SOM with time. In contrast, δ¹⁵N_SOM was most dynamic in deeper layers. During the four decades of forest development, the deepest layer (35–60 cm) reached a maximum δ¹⁵N value of 9.1‰, increasing by 7.6‰. The transfer of >800 kg ha⁻¹ of soil organic N into aggrading vegetation and the forest floor and the apparent large proportion of ectomycorrhizal (ECM) fungi in these soils suggest that fractionation via microbial transformations must be the major process changing δ¹⁵N in these soils. Accretion of isotopically enriched compounds derived from microbial cells (i.e., ECM fungi) likely promote isotopic enrichment of soils over time. The work indicates the rapid rate at which ecosystem development can impart δ¹⁵N_SOM and δ¹³C_SOM signatures associated with undisturbed soil profiles.     

Targeted metabolite profiling provides a functional link among eucalypt taxonomy, physiology and evolution

Adaptation to aridity is considered a major factor in the evolution of the genus Eucalyptus. For the first time, targeted metabolite profiling has uncovered a quantitative yet discrete phytochemical link with eucalypt taxonomy. The distribution of cyclitols among Eucalyptus species, and a range of other Australian tree genera, support their proposed functions in plant tissues and provide putative links with the acclimation of trees to arid environments.     

Collapse of a new living species of giant clam in the Red Sea

Giant clams are among the most spectacular but also the most endangered marine invertebrates. Their large size and easy accessibility has caused overfishing and collapse of the natural stocks in many places and local extinction in some of the species [1, 2]. The diversity of giant clams is extremely low because of reliction in this Tethyan group [3, 4]. The latest additions of living species date back almost two decades [5-7], fixing the number of extant Tridacna at seven species [3]. Here, we report the discovery of a new species of giant clam: Tridacna costata sp. nov. features characteristic shells with pronounced vertical folds, is genetically distinct, and shows an earlier and abbreviated reproduction than its Red Sea congeners. This species represents less than 1% of the present stocks but up to >80% of the fossil shells. The decline in proportion and shell size (20x) indicates overharvesting [8] dating back to the early human occupation of the Red Sea >125,000 years ago [9]. This earliest depletion reported so far of a shallow-water megafaunal invertebrate has important ramifications for human dispersal out of Africa [10]. Its oversight in one of the best-investigated reef provinces [11-13] illustrates the dearth of knowledge on marine biodiversity.     

Taurolithocholic acid-3 sulfate impairs insulin signaling in cultured rat hepatocytes and perfused rat liver.

BACKGROUND/AIMS: The role of bile acids for insulin resistance in cholestatic liver disease is unknown. METHODS: The effect of taurolithocholic acid-3 sulfate (TLCS) on insulin signaling was studied in cultured rat hepatocytes and perfused rat liver. RESULTS: TLCS induced insulin resistance at the level of insulin receptor (IR) beta Tyr(1158) phosphorylation, phosphoinositide (PI) 3-kinase activity and protein kinase (PK)B Ser(473) phosphorylation in cultured hepatocytes. Consistently, the insulin stimulation of the PI 3-kinase-dependent K(+) uptake, hepatocyte swelling and proteolysis inhibition was blunted by TLCS in perfused rat liver. The PKC inhibitor Go6850 and tauroursodeoxycholate (TUDC) counteracted the suppression of insulin-induced IRbeta and PKB phosphorylation by TLCS. Rapamycin and dibutyryl-cAMP, which inhibited basal signaling via mammalian target of rapamycin (mTOR), restored insulin-induced PKB- but not IRbeta phosphorylation. In livers from 7 day bile duct-ligated rats PKB Ser(473) phosphorylation was decreased by about 50%. CONCLUSION: TLCS induces insulin resistance by a PKC-dependent suppression of insulin-induced IRbeta phosphorylation and the PI 3-kinase/PKB path. This can in part be compensated by a decrease of mTOR activity, which may release insulin-sensitive components downstream of the insulin receptor from tonic inhibition. The data suggest that retention of hydrophobic bile acids confers insulin resistance on the cholestatic liver.     

Expression, purification and fluorine-18 radiolabeling of recombinant S100 proteins--potential probes for molecular imaging of receptor for advanced glycation endproducts (RAGE) in vivo

Data concerning the pathophysiological role of the interaction of circulating S100 proteins, a multigenic family of Ca(2+)-modulated proteins, with the receptor for advanced glycation endproducts (RAGE) in cardiovascular diseases, inflammatory processes, and tumorigenesis in vivo are scarce. One reason is the shortage of suitable radiotracer methods. We report a novel methodology using recombinant human S100A1, S100B, and S100A12 as potential probes for molecular imaging of this interaction. Therefore, human S100 proteins were cloned as GST fusion proteins in the bacterial expression vector pGEX-6P-1 and expressed in E. coli strain BL21. Purified recombinant human S100 proteins were radiolabeled with the positron emitter fluorine-18 ((18)F) by conjugation with N-succinimidyl-4-[(18)F]fluorobenzoate ([(18)F]SFB). The radiolabeled recombinant S100 proteins ((18)F-S100) were used in biodistribution experiments and small animal positron emission tomography (PET) studies in rats. The tissue-specific distribution of (18)F-S100 proteins in vivo correlated well with the anatomical localization of RAGE, e.g., in lungs and in the vascular system. These findings indicate circulating S100A1, S100B, and S100A12 proteins to be ligands for RAGE in rats in vivo. The approach allows the use of small animal PET and provides novel probes to delineate functional expression of RAGE under normal and pathophysiological conditions in rodent models of disease.     

The human mitochondrial ribosome recycling factor is essential for cell viability

The molecular mechanism of human mitochondrial translation has yet to be fully described. We are particularly interested in understanding the process of translational termination and ribosome recycling in the mitochondrion. Several candidates have been implicated, for which subcellular localization and characterization have not been reported. Here, we show that the putative mitochondrial recycling factor, mtRRF, is indeed a mitochondrial protein. Expression of human mtRRF in fission yeast devoid of endogenous mitochondrial recycling factor suppresses the respiratory phenotype. Further, human mtRRF is able to associate with Escherichia coli ribosomes in vitro and can associate with mitoribosomes in vivo. Depletion of mtRRF in human cell lines is lethal, initially causing profound mitochondrial dysmorphism, aggregation of mitoribosomes, elevated mitochondrial superoxide production and eventual loss of OXPHOS complexes. Finally, mtRRF was shown to co-immunoprecipitate a large number of mitoribosomal proteins attached to other mitochondrial proteins, including putative members of the mitochondrial nucleoid.     

Bohunician technology and thermoluminescence dating of the type locality of Brno-Bohunice (Czech Republic)

Results of thermoluminescence (TL) dating of 11 heated flint artifacts from the 2002 excavation at Brno-Bohunice, Czech Republic, are presented. The samples are from the eponym locality for the Bohunician, an industrial type considered technologically transitional between Middle and Upper Paleolithic core reduction strategies. The Bohunician is the first early Upper Paleolithic technocomplex in the Middle Danube of Central Europe and, therefore, is implicated in several issues related to the origins of modern humans in Europe. The Bohunician provides an example of how one technological strategy combines crested blade initiation of a core with the surficial (almost Levalloisian) reduction of blanks as blades and points. As the Middle Danube lacks antecedents of the behavioral steps within this technology, several hypotheses of inter-regional cultural transmission, with and without hominin gene flow, could explain the appearance of the Bohunician. The elucidation of the temporal context of Bohunician assemblages is, therefore, a critical step in understanding the behavioral, and potentially biological, succession in this region. Radiocarbon age estimates from charcoal associated with Bohunician sites suggest a wide age range between 33 and 41 ka ¹⁴C BP, which is also observed for individual sites. TL dating of heated flint artifacts provides ages on the calendric time scale of an archeological event, the firing. The weighted mean of 48.2 ± 1.9 ka BP_TL for 11 heated flint samples from Brno-Bohunice provides the first non-radiocarbon data on archeological material from the Bohunician. The TL dating, in conjunction with the archeological and sedimentological analysis, allows the evaluation of the integrity of this new type-collection. The hypothetical possibility of the incorporation of Szeletian artifacts (i.e., leaf points) into the site formation processes can therefore be refuted.     

Chemical differences between seeds and elaiosomes indicate an adaptation to nutritional needs of ants

Ant-dispersed plants usually produce seeds with appendages (elaiosomes) as reward for ants. Plants that produce high-quality elaiosomes benefit because ants preferentially disperse their diaspores. We therefore hypothesized that seeds and elaiosomes differ in chemical composition in ways that make elaiosomes of high nutritional quality for ants, capable of providing essential dietary components that explain the increased fitness and higher gyne production documented for colonies with elaiosome consumption. To test the hypothesis we analysed the content and composition of lipids, amino acids, soluble carbohydrates, proteins and starch in seeds and elaiosomes of 15 central European ant-dispersed plants. After separating the different fractions, total lipids were determined gravimetrically, fatty acids and soluble carbohydrates were detected by gas chromatography (GC) and GC–mass spectrometry, free amino acids by an amino acid analyser while starch and protein were analysed photometrically. Seeds accumulated high molecular weight compounds such as proteins and starch, whereas elaiosomes accumulated more easily digestible low molecular weight compounds such as amino acids and monosaccharides. Analysis of similarities and similarity percentages analysis demonstrated that the composition of fatty acids, free amino acids and carbohydrates differed markedly between elaiosomes and seeds. The most important difference was in total amino acid content, which was on average 7.5 times higher in elaiosomes than in seeds. The difference was especially marked for the nitrogen-rich amino acid histidine. The availability of essential nutrients and, in some species, the higher nitrogen content in elaiosomes suggest that their nutritional value for larvae plays a key role in this interaction. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.