Coalescence-based species delimitation using genome-wide data reveals hidden diversity in a cosmopolitan group of lichens

Although there is an abundance of species delimitation methods on the market, most approaches depend on predefined assignment of specimens to species or populations. Assignment-free methods, which can simultaneously infer boundaries and relationships among species, are of high importance in cases, when correct pre-assignment is difficult or not at all possible. In this study, we use assignment-free multispecies coalescent-based species delimitation (STACEY, tr2-delimitation, and BP&P), phylogenetic methods, and clustering algorithms to investigate the inter- and infraspecific relationships within a common and widespread group of lichens with contentious species boundaries. The Cetraria aculeata group presents a good example of extreme morphological variability and unclear species delimitation in lichens. Based on DNA-sequence data from 26 fungal loci and 10 microsatellite loci, as well as morphological and chemical data, our results provide evidence for the occurrence of five different taxa within the group and highlight the difficulties of morphologically distinguishing these species. We discovered a separate lineage (clade C) within C. aculeata s. str., which does not fully coincide with any of the a priori identified species C. aculeata, C. crespoae, or C. steppae and conclude that this clade constitutes a semi-cryptic, genetically isolated lineage within C. aculeata. We recognize this lineage at subspecific rank as C. aculeata subsp. steppae and synonymize Cetraria crespoae with C. aculeata subsp. aculeata. Epitypes are designated for all involved names to stabilize their usage. The PKS8 gene locus is recommended as a barcode for the separation of C. aculeata subsp. aculeata and subsp. steppae. We demonstrate the potential use of microsatellite data for species delimitation in lichens that might offer an alternative insight or be used to test species delimitation hypotheses, when dealing with closely related or potentially cryptic species. Our results also confirm the presence of an undescribed sister lineage to C. odontella previously misidentified as C. muricata and extend the known range of this lineage to Central Asia (Altay Mts.) and the Central European Alps (France, Switzerland), which calls for a critical reappraisal of records of C. aculeata and C. muricata from these mountain ranges.

     

High Prevalence of Bovine Tuberculosis in Dairy Cattle in Central Ethiopia: Implications for the Dairy Industry and Public Health

Background

Ethiopia has the largest cattle population in Africa. The vast majority of the national herd is of indigenous zebu cattle maintained in rural areas under extensive husbandry systems. However, in response to the increasing demand for milk products and the Ethiopian government''s efforts to improve productivity in the livestock sector, recent years have seen increased intensive husbandry settings holding exotic and cross breeds. This drive for increased productivity is however threatened by animal diseases that thrive under intensive settings, such as bovine tuberculosis (BTB), a disease that is already endemic in Ethiopia.

Methodology/Principal Findings

An extensive study was conducted to: estimate the prevalence of BTB in intensive dairy farms in central Ethiopia; identify associated risk factors; and characterize circulating strains of the causative agent, Mycobacterium bovis. The comparative intradermal tuberculin test (CIDT), questionnaire survey, post-mortem examination, bacteriology, and molecular typing were used to get a better understanding of the BTB prevalence among dairy farms in the study area. Based on the CIDT, our findings showed that around 30% of 2956 tested dairy cattle from 88 herds were positive for BTB while the herd prevalence was over 50%. Post-mortem examination revealed gross tuberculous lesions in 34/36 CIDT positive cattle and acid-fast bacilli were recovered from 31 animals. Molecular typing identified all isolates as M. bovis and further characterization by spoligotyping and MIRU-VNTR typing indicated low strain diversity within the study area.

Conclusions/Significance

This study showed an overall BTB herd prevalence of 50% in intensive dairy farms in Addis Ababa and surroundings, signalling an urgent need for intervention to control the disease and prevent zoonotic transmission of M. bovis to human populations consuming dairy products coming from these farms. It is suggested that government and policy makers should work together with stakeholders to design methods for the control of BTB in intensive farms in Ethiopia.     

Independent and Joint Effects of Prenatal Zinc and Vitamin A Deficiencies on Birthweight in Rural Sidama,Southern Ethiopia: Prospective Cohort Study

Background

The effects of prenatal Zinc Deficiency (ZD) and Vitamin A Deficiency (VAD) on birthweight are controversial and their interaction has not been investigated.

Objective

To assess the independent and interaction effects of prenatal zinc and vitamin A deficiencies on birthweight in rural Sidama, Southern Ethiopia.

Methodology

A community-based prospective cohort study design was employed. Six hundred fifty pregnant women in their second or third trimester were randomly selected and their serum zinc and retinol concentrations were determined. About 575 subjects were successfully followed until delivery and birthweight was measured within 72 hours after delivery. The association between the exposures and birthweight was examined using log-binomial and liner regression analyses. Potential interaction between ZD and VAD was examined using Synergy Index (SI).

Results

The mean birthweight (± standard deviation) was 2896 g (±423). About 16.5% (95% CI: 13.5–19.6%) of the babies had Low Birthweight (LBW). Prenatal ZD and VAD were not significantly associated to LBW with Adjusted Relative Risk (ARR) of 1.25 (95 CI: 0.86–1.82) and 1.27 (95% CI: 0.86–1.87), respectively. Stratified analysis on the basis of gestational trimester showed that the occurrence of the deficiencies neither in the second nor third trimester were associated to LBW. The deficiencies did not show synergetic interaction in causing LBW [SI = 1.04 (95% CI: 0.17–6.28)]. Important risk factors of LBW were maternal illiteracy [RR = 1.80 (95% CI: 1.11–2.93)], female sex of the newborn [RR = 1.79 (95% CI: 1.19–2.67)], primiparity [RR = 1.16 (95% CI: 1.02–1.35)], short maternal stature [RR = 1.63 (95% CI: 1.06–2.51)] and maternal thinness [RR = 1.52 (95% CI: 1.03–2.25)]. In the linear regression model, elevated CRP was also negatively associated to birthweight.

Conclusion

LBW is of public health significance in the locality. The study did not witness any independent or interaction effect of prenatal ZD and VAD on birthweight.     

An integrated restriction fragment length polymorphism--amplified fragment length polymorphism linkage map for cultivated sunflower.

Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2 population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 x HA372 F2 progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 x HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 x HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.     

Ecological succession and its impact on malaria vectors and their predators in borrow pits in western Ethiopia

Soil pits excavated for home construction are important larval habitats for malaria vectors in certain parts of Africa. Borrow pits in diverse stages of ecological succession in a maize‐farming region of Western Ethiopia were surveyed to assess the relationships between stage of succession and the structure and composition of invertebrate and plant communities, with particular attention to Anopheles gambiae s.l. and An. coustani, the primary local malaria vectors. An array of 82 borrow pits was identified in a multi‐lobed drainage basin in the community of Woktola. Each pit was evaluated on its physical features and by faunal and floral surveys during August, 2011, at the height of the longer rainy season (kiremt). Anopheles gambiae s.l. and An. coustani were the sole immature anophelines collected, often coexisting with Culex spp. Sedges were the most common plants within these pits, and included Cyperus elegantulus, C. flavescens, C. erectus and C. assimilis. The legume Smithia abyssinica, Nile grass (Acroceras macrum), cutgrass (Leersia hexandra), clover (Trifolium spp.), and the edible herb Centella asiatica, were also common in these habitats. No plant species in particular was strongly and consistently predictive of the presence or absence of mosquito immatures, particularly with regard to An. coustani. The presence of An.gambiae s.l. immatures in borrow pit habitats was negatively correlated with the presence of backswimmers (Notonectidae) (Z = −2.34, P = 0.019). Young (freshly excavated) borrow pits more likely contained immature An. gambiae s.l. (Z =‐2.86, P=0.004). Ecological succession was apparent in older pits, and as they aged, they became less likely to serve as habitats for An. gambiae s.l. (Z=0.26, P=0.796), and more likely to support An. coustani (Z=0.728, P=0.007). As borrow pits age they become less suitable for An. gambiae s.l. breeding and more likely to harbor An. coustani. The abundance of notonectids in habitats was a negative indicator for An. gambiae s.l. abundance. Plant species are not reliable indicators for the presence or absence of malaria vectors in borrow pits.     

Short- and long-term outcomes in infective endocarditis patients: a systematic review and meta-analysis

Background

Despite advances in medical knowledge, technology and antimicrobial therapy, infective endocarditis (IE) is still associated with devastating outcomes. No reviews have yet assessed the outcomes of IE patients undergoing short- and long-term outcome evaluation, such as all-cause mortality and IE-related complications. We conducted a systematic review and meta-analysis to examine the short- and long-term mortality, as well as IE-related complications in patients with definite IE.

Methods

A computerized systematic literature search was carried out in PubMed, Scopus and Google Scholar from 2000 to August, 2016. Included studies were published studies in English that assessed short-and long-term mortality for adult IE patients. Pooled estimations with 95% confidence interval (CI) were calculated with DerSimonian-Laird (DL) random-effects model. Sensitivity and subgroup analyses were also performed. Publication bias was evaluated using inspection of funnel plots and statistical tests.

Results

Twenty five observational studies (retrospective, 14; prospective, 11) including 22,382 patients were identified. The overall pooled mortality estimates for IE patients who underwent short- and long-term follow-up were 20% (95% CI: 18.0–23.0, P?<?0.01) and 37% (95% CI: 27.0–48.0, P?<?0.01), respectively. The pooled prevalence of cardiac complications in patients with IE was found to be 39% (95%CI: 32.0–46.0) while septic embolism and renal complications accounted for 25% (95% CI: 20.0–31) and 19% (95% CI: 14.0–25.0) (all P?<?0.01), respectively.

Conclusion

Irrespective of the follow-up period, a significantly higher mortality rate was reported in IE patients, and the burden of IE-related complications were immense. Further research is needed to assess the determinants of overall mortality in IE patients, as well as well-designed observational studies to conform our results.

     

Age,growth, maturity and mortality of the tapetail anchovy Coilia brachygnathus (Engraulidae) in Lake Honghu,China

The tapertail anchovy Coilia brachygnathus, a commercially important species mainly distributed along the mid-lower Chang-Jiang basin, is by far the most dominant species in Lake Honghu. To figure out its success in this semiclosed lake, some basic biological parameters of this anchovy were analysed based on samples seasonally collected from October 2020 to December 2021. The results demonstrated that the age classes of fished individuals varied from 0.5 to 3.5, with the majority (97.36%) being between 0.5 and 3 years old. The size at 50% maturity of 17.2 cm total length (TL) for females and 19.0 cm TL for males corresponded to 1 and 1.6 years, respectively. Coilia brachygnathus has a short life span, early sexual maturity and a relatively fast growth rate. The flourishing of the fish in the lake is mainly attributed to its short life span, early maturity, fast growth rate, closed fishing, pelagic spawners, the availability of plenty of food and low predation effect on it. Age 3.5 year occurs in an extremely small percentage of the total (<3%), indicating that a large number of larger-sized or older fish died after spawning, which is probably one of the major sources of water pollution if the closed fishing measure is adopted in Lake Honghu. Thus, individuals older than 2 years or more than 20.0 cm TL should be harvested. These findings have important management implications for the fish resources in Lake Honghu and beyond.     

Fuzziness and Heterogeneity of Benthic Metacommunities in a Complex Transitional System

We propose an extension to the metacommunity (MC) concept and a novel operational methodology that has the potential to refine the analysis of MC structure at different hierarchical levels. We show that assemblages of species can also be seen as assemblages of abstract subregional habitat-related metacommunities (habMCs). This intrinsically fuzzy concept recognizes the existence of habMCs that are typically associated with given habitats, while allowing for the mixing and superposition of different habMCs in all sites and for boundaries among subregions that are neither spatially sharp nor temporally constant. The combination of fuzzy clustering and direct gradient analysis permits us to 1) objectively identify the number of habMCs that are present in a region as well as their spatial distributions and relative weights at different sites; 2) associate different subregions with different biological communities; and 3) quantitatively assess the affinities between habMCs and physical, morphological, biogeochemical, and environmental properties, thereby enabling an analysis of the roles and relative importance of various environmental parameters in shaping the spatial structure of a metacommunity. This concept and methodology offer the possibility of integrating the continuum and community unit concepts and of developing the concept of a habMC ecological niche. This approach also facilitates the practical application of the MC concept, which are not currently in common use. Applying these methods to macrophytobenthic and macrozoobenthic hard-substrate assemblages in the Venetian Lagoon, we identified a hierarchical organization of macrobenthic communities that associated different habMCs with different habitats. Our results demonstrate that different reference terms should be applied to different subregions to assess the ecological status of a waterbody and show that a combination of several environmental parameters describes the spatial heterogeneity of benthic communities much better than any single property can. Our results also emphasize the importance of considering heterogeneity and fuzziness when working in natural systems.     

Correction to: Coalescence-based species delimitation using genome-wide data reveals hidden diversity in a cosmopolitan group of lichens

Organisms Diversity & Evolution - The publisher regrets that the Table 3 of the original published version of this article is incorrect thus the table is now presented correctly. The original...