Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards

Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long‐term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome‐wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long‐term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional‐scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.     

Can functional regions of proteins be predicted from their coding sequences? The case study of G-protein coupled receptors

A filter based on a set of unsupervised neural networks trained with a winner-take-all strategy discloses signals along the coding sequences of G-protein coupled receptors. By comparing with the existing experimental data it appears that these signals correlate with putative functional domains of the proteins. After protein alignment within subfamilies, signals cluster in protein regions which, according to the presently available experimental results, are described as possible functional domains of the folded proteins. The mapping procedure reveals characteristic regions in the coding sequences common and/or characteristic of the receptor subtype. This is particularly noticeable for the third cytoplasmic loop, which is likely to be involved in the molecular coupling of all the subfamilies with G-proteins. The results indicate that our mapping can highlight intrinsic representative features of the coding sequences which, in the case of G-protein coupled receptors, are characteristic of protein functional regions and suggest a possible application of the filter for predicting functional determinants in proteins starting from the coding sequence.     

Why flowers close at noon? A case study of an alpine species Gentianopsis paludosa (Gentianaceae)

Repeatable floral closure with diurnal rhythms, that is, flower opening in the morning and closing in the evening, was widely reported. However, the rhythm of flower opening in the morning but closing in the midday received much less attention. Gentianopsis paludosa, Gentianaceae, has an obvious petal movement rhythm opening in the morning and closing at noon at northeast of the Qinghai‐Tibetan Plateau. In this study, we examined the effects of temperature (T), relative humidity (RH), and illumination intensity (II) on G. paludosa''s flower closure. Furthermore, we monitored the environmental changes inside and outside of the flowers, aiming to test the effect of floral closure on the stability of microenvironment inside the flower. Finally, we artificially interrupted temporal petal closure and investigated its effects on reproductive fitness. The results showed that high/low temperature contributed more to the flower closure than low RH, while illumination intensity had no significant effect on it. The medium temperature, relative humidity and illumination intensity (environmental conditions at 10:00) did not delay flower closure when flowers at pre‐closing period or stimulate reopen when flowers full closed. Floral closure provided a stable temperature condition and a higher RH condition inside the flower. Meanwhile, compulsive opening and delayed closure of flowers decreased the seed‐set ratio while no effect was found when flowers were forced to close. We conclude that endogenous rhythm regulates floral closure. The rhythm of petal movement providing a stable microenvironment for G. paludosa, increasing the seed production and saving energy from flower opening maintenance, which might be an adaptive strategy to against unfavorable environmental conditions.     

Can species distribution modelling provide estimates of population densities? A case study with jaguars in the Neotropics

Aim To test the prediction that environmental suitability derived from species distribution modelling (SDM) could be a surrogate for jaguar local population density estimates. Location Americas. Methods We used 1409 occurrence records of jaguars to model the distribution of the species using 11 SDM methods. We tested whether models’ suitability is linearly correlated with jaguar population densities estimated from 37 different locations. We evaluated whether the relationship between density and suitability forms a constraint envelope, in which higher densities are found mainly in regions with high suitability, whereas low densities can occur in regions with variable suitability. We tested this using heteroscedasticity test and quantile regressions. Results A positive linear relationship between suitability and jaguar density was found only for four methods [bioclimatic envelope (BIOCLIM), genetic algorithm for rule set production (GARP), maximum entropy (Maxent) and generalized boosting models (GBM)], but with weak explanatory power. BIOCLIM showed the strongest relationship. Variance of suitability for lower densities values was larger than for higher values for many of the SDM models used, but the quantile regression was significantly positive only for BIOCLIM and random forests (RF). RF and GBM provided the most accurate models when measured with the standard SDM evaluation metrics, but possess poor relationship with local density estimates. Main conclusions Results indicate that the relationship between density and suitability could be better described as a triangular constraint envelope than by a straight positive relationship, and some of the SDM methods tested here were able to discriminate regions with high or low local population densities. Low jaguar densities can occur in areas with low or high suitability, whereas high values are restricted to areas where the suitability is greater. In high suitability areas but with low jaguar density estimates, we discuss how extrinsic factors driving abundance could act at local scales and then prevent higher densities that would be expected by the favourable regional environmental conditions.     

How do different aspects of biodiversity change through time? A case study on an Australian bird community

The study of ecological communities through time can reveal fundamental ecological processes and is key to understanding how natural and human pressures will affect biodiversity. Most studies of ecological communities through time consider only one or a few summary measures (e.g. species richness, total abundance), which might neglect important aspects of community structure or function. We studied temporal variation in several measures of species diversity, size diversity, and species composition in an intensively sampled bird community to determine whether different biodiversity measures change synchronously. We used a novel function regression model, which supports the study of diversity measures that are distributions (e.g. species abundance distributions) alongside measures that are scalar values (e.g. species richness). Most diversity measures changed predictably within years, but inter‐annual changes in size diversity and species composition were not reflected in species diversity. Within and among years, there was considerable variation in distributional measures that was not captured in scalar measures. Predictable variation within years probably was related to seasonal variation in weather patterns or food availability, but variation in size diversity among years probably resulted from stochastic changes in species composition. These results suggest that species and size diversity may be decoupled, and that inferences on scalar diversity measures might not reflect fundamental changes to community structure or function. Our method supports the inclusion of size‐based measures and distributional measures in ecological analyses, and broader uptake of our approach is likely to provide new insight into the processes structuring ecological communities, and inform the links between structure and function in ecological communities.     

What factors influence the diversity of saproxylic beetles? A multiscaled study from a spruce forest in southern Norway

The diversity in different groups of obligate saproxylic beetles was related to ecological variables at three levels of spatial scale in mature spruce-dominated forest. The variables were connected to: (i) decaying wood, (ii) wood-inhabiting fungi, (iii) the level of disturbance, (iv) landscape ecology, and (v) vegetational structure. Several strong relationships were found at medium (1 km²) and large scales (4 km²), while only weak relationships were found at a small scale (0.16 ha; 1 ha=10⁴ m²). This may be explained by the local variations in habitat parameters and the high mobilities of many beetle species. Factors connected to decaying wood and wood-inhabiting fungi were clearly the most important factors at all scale levels. In particular, the variables diversity of dead tree parts, number of dead trees of large diameter and number of polypore fungi species increased the species richness of many groups and increased the abundance of many species. Eight species were absent below a certain density of decaying wood per 1 or 4 km². Former extensive cutting was a negative factor at large scale, probably because of decreasing recolonization with increasing distance to the source habitats. Thinning reduced the diversity of species associated with birch. The development of guidelines favouring the diversity of saproxylic beetles are discussed below.     

Can vegetation provide indications of ancient lake shorelines after more than one hundred years? A case study of Iskander-kul Lake,Tajikistan

Bioindication is a common approach to assess and evaluate environmental changes over both short or long periods of time. Here we attempt to highlight that vegetation can provide indications of the palaeoshoreline of Lake Iskander-kul, even after at least 150 years. It is an example of a dammed lake that was created by a huge mass rockfall as a result of a strong earthquake during the late Pleistocene. Applying the two way indicator species analysis (TWINSPAN) we found that the shrubby vegetation is the particular one that can still effectively thrive along the palaeoshoreline despite the lake downlift. Using the phi coefficient as a fidelity measure for certain vegetation type, we found, that Juniperus seravschanica, Lonicera seravschanica, Berberis integerrima, Seseli lehmannianum, Astragalus kabadianus and Ephedra intermedia have the highest indicator value for palaeoshoreline. Apart from the ancient palaeoshoreline, on the screes and slopes surrounding the lake, significantly different vegetation types developed on the screes and slopes dominated by steppe (Hyssopus servaschanica, Galium turkestanicum, Festuca valesiaca) and scree (Ferula foetidissima, Stipa drobovii or Ferula kuhistanica) vegetation types. Using the multivariate analysis (CCA) we show that the slope inclination and distance from the palaeoshorelines has considerable influence on species composition within the study plots.     

What triggers seizures in neurocysticercosis? A MRI-based study in pig farming community from a district of North India

Colloidal and calcified cysts are considered responsible for seizure in neurocysticercosis (NCC); however, calcified cysts have also been reported in asymptomatic individuals. We carried out a MRI-based study in a rural pig farming community of North India to detect the various stages, locations and numbers of the cyst in asymptomatic individuals and compared them with symptomatic NCC cases to see its association with occurrence of seizures. A total of 107 asymptomatic family members of 29 symptomatic NCC confirmed cases were evaluated clinically, immunologically and by neuroimaging for NCC. MRI-based staging of the parasite was done in both groups, and compared to look for the differences, if any. Thirty-one (29.0%) asymptomatic family members of symptomatic cases were diagnosed to have NCC. There was no difference in proportion of colloidal/degenerating and calcified stages of the parasite between symptomatic and asymptomatic groups; however, significantly higher proportion of the asymptomatic populations had vesicular stage of the parasite (P = 0.029). Our findings show that a large number of individuals harboring different stages of cysticerci in their brain remain symptoms free and question the belief that the degenerating/calcified stages of the parasite are primarily responsible for seizure occurrence in NCC.     

A pilot study of angiogenin in heart failure with preserved ejection fraction: a novel potential biomarker for diagnosis and prognosis?

Characteristics of heart failure with preserved ejection fraction (HFPEF) have not yet been fully understood. The objectives of this pilot study are to detect protein expression profile in the sera of HFPEF patients, and to identify potential biomarkers for the disease. Five hundred and seven proteins were detected in the sera of healthy volunteers and patients with either HFPEF or hypertension using antibody microarrays (three in each group). The results showed that the serum concentrations of 17 proteins (e.g. angiogenin, activin A and artemin) differed considerably between HFPEF and non‐HFPEF patients (hypertensive patients and healthy controls), while a protein expression pattern distinct from that in non‐HFPEF patients was associated with HFPEF patients. The up‐regulation of angiogenin in both HFPEF patients with LVEF ≥50% (P = 0.004) and a subset of HFPEF patients with LVEF = 41–49% (P < 0.001) was further validated in 16 HFPEF patients and 16 healthy controls. Meanwhile, angiogenin distinguished HFPEF patients from controls with a mean area under the receiver operating characteristic curve of 0.88 (P < 0.001) and a diagnostic cut‐off point of 426 ng/ml. Moreover, the angiogenin levels in HFPEF patients were positively correlated with Lg(N‐terminal pro‐B‐type natriuretic peptide, NT‐proBNP) (P < 0.001). In addition, high angiogenin level (≥426 ng/ml) was a predictor of all‐cause death within a short‐term follow‐up duration, but not in the longer term of 36 months. This pilot study indicates that the aforementioned 17 potential biomarkers, such as angiogenin, may hold great promise for both diagnosis and prognosis assessment of HFPEF.     

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone

The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long‐standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M. galloprovincialis, across a well‐studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best‐supported scenario was a long period of allopatric isolation during the first three‐quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.     

Premature ventricular contractions of the right ventricular outflow tract: is there an incipient underlying disease? New insights from a speckle tracking echocardiography study

ContextPremature ventricular contractions (PVCs) originating in the right ventricular outflow tract (RVOT) are traditionally considered idiopathic and benign. Echocardiographic conventional measurements are typically normal.AimsTo assess whether right ventricle longitudinal strain, determined by two-dimensional speckle tracking echocardiography, differ between RVOT PVCs patients (treated with catheter ablation) and healthy controls.MethodsWe retrospectively selected patients with PVCs from the RVOT who underwent electrophysiological study and catheter ablation between 2016 and 2019. Patients with documented structural heart disease were excluded. Transthoracic echocardiography was performed and right ventricle global longitudinal strain (RV-GLS), free wall longitudinal strain (RVFW-LS) and left ventricle global longitudinal strain (LV-GLS) were determined as well as conventional ultrasound measurements of RV and LV function.ResultsWe studied 21 patients with RVOT PVCs and 13 controls. Patients with PVCs from the RVOT had lower values of RV-GLS and RVFW-LS compared with the control group (?19.4% versus ?22.5%, P = 0.015 and ?22.1% versus ?25.5, P = 0.041, respectively). They also had lower values of LV-GLS, although still within the normal range (?19.1% versus ?20.9%, P = 0.047). Regarding RVOT PVCs patients only, RV-GLS and RVFW-LS had no correlation with the PVCs burden prior to catheter ablation and they did not differ between the patients in whom the catheter ablation was successful and those in whom it was not. RV-GLS also had a positive correlation with RVOT proximal diameter (r = 0.487, P = 0.025).ConclusionsIn this group of RVOT PVCs patients, we found worse RV longitudinal strain values (and therefore sub-clinical myocardial dysfunction) when compared to healthy controls.     

Can captive populations function as sources of genetic variation for reintroductions into the wild? A case study of the Arabian oryx from the Phoenix Zoo and the Shaumari Wildlife Reserve,Jordan

The Arabian oryx (Oryx leucoryx) historically ranged across the Arabian Peninsula and neighboring countries until its extirpation in 1972. In 1963–1964 a captive breeding program for this species was started at the Phoenix Zoo (PHX); it ultimately consisted of 11 animals that became known as the ‘World Herd’. In 1978–1979 a wild population was established at the Shaumari Wildlife Reserve (SWR), Jordan, with eight descendants from the World Herd and three individuals from Qatar. We described the mtDNA and nuclear genetic diversity and structure of PHX and SWR. We also determined the long-term demographic and genetic viability of these populations under different reciprocal translocation scenarios. PHX displayed a greater number of mtDNA haplotypes (n = 4) than SWR (n = 2). Additionally, PHX and SWR presented nuclear genetic diversities of \(\bar{N}_{\text{A}}\) = 2.88 vs. 2.75, \(\bar{H}_{\text{O}}\) = 0.469 vs. 0.387, and \(\bar{H}_{\text{E}}\) = 0.501 vs. 0.421, respectively. Although these populations showed no signs of inbreeding (\(\bar{F}_{\text{IS}}\) ≈ 0), they were highly differentiated (\(G^{\prime\prime}_{\text{ST}}\) = 0.580; P < 0.001). Migration between PHX and SWR (Nm = 1, 4, and 8 individuals/generation) increased their genetic diversity in the short-term and substantially reduced the probability of extinction in PHX during 25 generations. Under such scenarios, maximum genetic diversities were achieved in the first generations before the effects of genetic drift became predominant. Although captive populations can function as sources of genetic variation for reintroduction programs, we recommend promoting mutual and continuous gene flow with wild populations to ensure the long-term survival of this species.     

A novel gene encoding a ras-like GTP-binding protein from Trypanosoma brucei: an evolutionary ancestor of the ras and rap genes of higher eukaryotes?

The ras superfamily of GTP binding proteins encompasses a wide range of family members, related by conserved amino-acid motifs, and act as molecular binary switches that play key roles in cellular processes. Gene duplication and divergence has been postulated as the mechanism by which such family members have evolved their specific functions. We have cloned and sequenced a ras-like gene, tbrlp, from the primitive eukaryote Trypanosoma brucei. The gene encodes a protein of 227 amino acids and contains the six conserved subdomains that designate it as a ras/rap subfamily member. However, the presence of key diagnostic residues characteristic of both the ras and rap families of GTP confuse the familial classification of this gene. Phylogenetic analysis of the GTP binding domain places its origins at the divergence point of the ras/rap families and suggests that tbrlp is an ancestral gene to the ras/rap genes of higher eukaryotes.     

Can a benthic diatom community complement chemical analyses and discriminate between disturbed and undisturbed saline wetland habitats? A study of seven soda pans in Serbia

Soda pans are protected in the European Union as Natura 2000 areas in the category of “Pannonic saline steppes and marshes”. There are at least six soda pans of reference status in Serbia and only a half have strict legal protection. The number of similar, but disturbed (modified) habitats that could be reconstructed is still unknown. We conducted sampling in five natural and two disturbed soda pans aiming to compare a difference in physical and chemical water properties and benthic diatom communities. In addition, we tried to apply recently developed Diatom Index for Soda Pans (DISP) and Trait-based index (TBI) to test the applicability of taxonomic and trait-based approaches in ecological status assessment of soda pans in the southern part of the Carpathian Basin. In contrast to natural soda pans, lower pH and nutrients levels were recorded in disturbed pans. A total of 86 taxa of benthic diatoms, including 11 new for diatom flora of Serbia, were identified. A lower species richness and Shannon index was recorded in natural soda pans. Nitzschia austriaca, N. supralitorea, Navicula veneta and N. wiesneri were dominant diatoms in soda pans of the reference status. Both diatom indices were in average lower in disturbed pans, and this difference was statistically significant for DISP index. We concluded that two indices, supplemented with indicator values for some local diatom species, can be a promising tool for soda pan conservation in this part of the Carpathian Basin.

     

Is an Idea Different from Cake: Can You Have It and Eat It,Too? A Violation of Permanence in Information Consumption

One of the basic features of information is permanence. This feature states that the consumption of information by one consumer does not affect the availability of that information to other consumers. We present examples in two studies indicating that both laymen and experts of information exchange may be motivated to make choices that violate the permanence feature in accepting (Study 1) and offering (Study 2) information. When they possess, but have not yet consumed information, people may suffer from the appearance of wastefulness. This apparent wastefulness may provide a potential explanation for the observed violation of the permanence feature. Our findings indicate that, as the material age evolves into the information age, information-exchange behavior has not evolved significantly away from material-exchange behavior.     

Can markers injected into a single-loop anterior cruciate ligament graft define the axes of the tibial and femoral tunnels? A cadaveric study using roentgen stereophotogrammetric analysis

Lengthening of a soft-tissue anterior cruciate ligament (ACL) graft construct over time, which leads to an increase in anterior laxity following ACL reconstruction, can result from relative motions between the graft and fixation devices and between the fixation devices and bone. To determine these relative motions using Roentgen stereophotogrammetry (RSA), it is first necessary to identify the axes of the tibial and femoral tunnels. The purpose of this in vitro study was to determine the error in using markers injected into the portions of a soft-tissue tendon graft enclosed within the tibial and femoral tunnels to define the axes of these tunnels. Markers were injected into the tibia, femur, and graft in six cadaveric legs the knees of which were reconstructed with single-loop tibialis grafts. The axes of the tunnels were defined by marker pairs that were injected into the bones on lines parallel to the walls of the tibial and femoral tunnels (i.e., standard). By using marker pairs injected into the portions of the graft enclosed within the tibial and femoral tunnels and the marker pairs aligned with the tunnel axes, the directions of vectors were determined by using RSA, while a 150 N anterior force was transmitted at the knee. The average and standard deviations of the angle between the two vectors were 5.5+/-3.3 deg. This angle translates into an average error and standard deviation of the error in lengthening quantities (i.e., relative motions along the tunnel axes) at the sites of fixation of (0.6+/-0.8)%. Identifying the axes of the tunnels by using marker pairs in the graft rather than marker pairs in the walls of the tunnels will shorten the surgical procedure by eliminating the specialized tools and time required to insert marker pairs in the tunnel walls and will simplify the data analysis in in vivo studies.