Multivariate analysis of phyto-climatic patterns of the Croatian part of the eastern Adriatic coast

ABSTRACT

The present study analyses the climatic patterns of that part of the eastern Adriatic coast belonging to the Republic of Croatia and the narrow zone of the inlands. This area comprises a part of the Mediterranean phytogeographic region characterised by the Mediterranean climate type, and the transitional area towards the Eurosiberian phytogeographic region influenced by the continental climate type. The analysis was performed using multivariate numerical methods, cluster analysis following by the inertia analysis, and Principal Components Analysis with partitioning, considering the principal local climatic gradients in the data set. Six main climate classes were obtained. The results are biologically more interpretable than those obtained by using either numerical indices or the Walter climate diagram system. This suggests that multivariate numerical methods could be more efficient tools for detecting biologically significant climatic patterns on a small spatial scale.     

Impact of protein diversification on morphometric behavior of Andrographis paniculata Nees

Proteins are important biochemical parameters in genetic diversity and controlling morphological characteristics in plants. In this study, the proteomic and morphometric data of an important medicinal herb “Aci Pa?a” (Andrographis paniculata) were combined together to illustrate their impacts on genetic variation of the plant’s population and to realize the connection between protein patterns and phenotypic behavior of the species. We used three protein extraction buffers including Tris, potassium phosphate, and sodium citrate. The Tris buffer was significantly different (p ≤ 0.01) than other two in terms of the quality and quantity of protein bands by producing 15 types of proteins ranged from 13 to 105 kDa of which two of them were polymorphic. Consequently, a total of 12 accessions of A. paniculata were subjected to morpho-proteomic analyses. The unweighted pair group method with arithmetic average cluster analysis of the accessions based on the protein data and morphological characteristics generated three and four clusters, respectively, at a Euclidean distance of 2.53 for the morphological traits. Moreover, seed proteins analysis revealed that the two polymorphic protein bands sized 20.5 (protein “b”) and 30 kDa (protein “a”) effectively diversified the morphological characteristics and phylogenetic relationships among the 12 accessions of A. paniculata. Interestingly, the protein “b” acted as an activator agent for the number of branches, leaves and total dry weight, while the protein “a” performed a suppressive role for the same traits. Additionally, the two high-weighted faint bands “c” (75 kDa) and “d” (100 kDa) with a very low expression in accession 11228 proved their suppressive role along with the “a” band, while these bands were strongly expressed in the rest of the accessions. These findings suggest that these four proteins should be sequenced and perfectly established for further proteomic analyses. Ultimately, the mentioned proteins can be developed for any prospective breeding program or gene identification.     

Concepts of macro- and microevolution as related to the problem of origin and global expansion of the plague pathogen Yersinia pestis

The relationship between macro- and microevolutionary processes is considered with reference to the ecological scenario of the origin of the plague pathogen and its subsequent natural and anthropogenic global expansion. The macroevolutionary transformation of the ancestral pseudotuberculosis microbe clone into the initial plague microbe Yersinia pestis tarbagani occurred in Central Asia at the end of the Late Pleistocene by a “vertical” Darwinian way in an inadaptive heterothermal continual intermediate environment—the Mongolian marmot Marmota sibirica—flea Oropsylla silantiewi system—via a sequence of unstable and currently extinct intermediate forms. Its natural geographic expansion on the “oil spot” principle in the postglacial time led to the microevolutionary formation of 20–30 hostal subspecies circulating in populations of the background species of burrowing rodents and pikas in arid areas of Eurasia. The intercontinental spread of the “marmot” and “rat” pathogen subspecies in the past few centuries has been exclusively anthropogenic, with the involvement of synanthropic (ship) rats.     

Defining gait patterns using Parallel Factor 2 (PARAFAC2): A new analysis of previously published data

Three-dimensional gait analysis (3D–GA) is commonly used to answer clinical questions of the form “which joints and what variables are most affected during when”. When studying high-dimensional datasets, traditional dimension reduction methods (e.g. principal components analysis) require “data flattening”, which may make the ensuing solutions difficult to interpret. The aim of the present study is to present a case study of how a multi-dimensional dimension reduction technique, Parallel Factor 2 (PARAFAC2), provides a clinically interpretable set of solutions to typical biomechanical datasets where different variables are collected during walking and running. Three-dimensional kinematic and kinetic data used for the present analyses came from two publicly available datasets on walking (n = 33) and running (n = 28). For each dataset, a four-dimensional array was constructed as follows: Mode A was time normalized cycle points; mode B was the number of participants multiplied by the number of speed conditions tested; mode C was the number of joint degrees of freedom, and mode D was variable (angle, velocity, moment, power). Five factors for walking and four factors for running were extracted which explained 79.23% and 84.64% of their dataset’s variance. The factor which explains the greatest variance was swing-phase sagittal plane knee kinematics (walking), and kinematics and kinetics (running). Qualitatively, all extracted factors increased in magnitude with greater speed in both walking and running. This study is a proof of concept that PARAFAC2 is useful for performing dimension reduction and producing clinically interpretable solutions to guide clinical decision making.     

A method for decomposing multivariate time series into a causal hierarchy within specific frequency bands

We propose a method - Frequency extracted hierarchical decomposition (FEHD) - for studying multivariate time series that identifies linear combinations of its components that possess a causally hierarchical structure - the method orders the components so that those at the “top” of the hierarchy drive those below. The method shares many of the features of the “hierarchical decomposition” method of Repucci et al. (Annals of Biomedical Engineering, 29, 1135–1149, 2001) but makes a crucial advance - the proposed method is capable of determining this causal hierarchy over arbitrarily specified frequency bands. Additionally, a novel minimization strategy is used to generate the decomposition resulting in an increase in stability, reliability, and an improvement in the sensitivity to model parameters. We demonstrate the utility of the method by applying it to both artificial time series constructed to have specific causal graphs, and to the EEG of healthy volunteers and patient subjects who are recovering from a severe brain injury.     

Highly diversified population structure of the spider <Emphasis Type="Italic">Lycosa ishikariana</Emphasis> inhabiting sandy beach habitats

Sandy beach ecosystems are decreasing worldwide and organisms living there are becoming threatened. The burrowing wolf spider Lycosa ishikariana is one such example. To establish effective conservation strategies under habitat fragmentation, we examined population genetic structure of L. ishikariana from mitochondrial cytochrome oxidase I gene and 6 microsatellite loci. Mitochondrial sequence data revealed 6 population subgroups with very high fixation indices, indicating that L. ishikariana has a clear phylogeographic structure and that the level of differentiation among regions is considerable. In particular, one subgroup in the western Honshu mainland (clade G) has a highly distinct genetic structure, despite having no clear geographic barriers from its parapatric population. Moreover, the distribution ranges of the other two subgroups (clades D and E) were highly restricted, suggesting their vulnerability to local human impacts and highlighting their high conservation priorities. Microsatellite data revealed 10 subgroups that were compatible with the clades identified from the mitochondrial data. Fixation indices among these groups were very high, indicating a limited gene flow induced by male spiders. Based on these results, we proposed six conservation units of L. ishikariana and effective conservation/restoration strategies in the face of ongoing coastal armoring.     

Assessing the impact of plant invasions on soil seed bank communities: use of univariate and multivariate statistical approaches

Questions: Are soil seed banks affected by invasions of alien plants? How can we rigorously assess alterations in seed bank communities associated with invasive species and account for the high spatial variability of seed bank data? How do multivariate approaches compare with more traditional approaches based on analysis of variance? Location: Three riparian sites, Ireland. Methods: A protocol based on a combination of multivariate techniques was used to characterize soil seed bank communities associated with the herbaceous invasive species Heracleum mantegazzianum in May and October. Permutational multivariate analysis of variance (PERMANOVA) was used to test the effects of the factors “invasion”, “site”, “plot” and “depth” on the soil seed bank, while multivariate analysis of dispersion (PERMDISP) provided a measure of the variability of seed bank data at different spatial scales. Similarity percentages analysis (SIMPER) was used to identify the species that contributed most to the differences between invaded and uninvaded communities. A comparison between the results of PERMANOVA and ANOVA analyses was also made. Results: The composition of seed bank communities invaded by H. mantegazzianum differed significantly from that of uninvaded seed banks. Invaded seed banks were less diverse and had reduced abundance, and were dominated by only a few species, such as Urtica dioica and Juncus effusus. Such patterns were recorded at each of three depth categories, indicating that invasive plants can affect both the transient and the more persistent component of the soil seed bank. Seed bank variability was significantly higher within uninvaded areas, supporting the notion that invasions tend to lead to more homogeneous communities. Conclusion: The analytical protocol used in this study was effective in quantifying the effect of plant invasions, at different spatial scales, providing a statistically robust analysis of alterations in soil seed bank communities. Compared to ANOVA, this protocol provided more biological information and was more appropriate for analysis of the data. This approach is therefore recommended in soil seed bank and invasion ecological studies.     

Genetic Diversity,Genotype Discrimination,and Population Structure of Mexican <Emphasis Type="Italic">Opuntia</Emphasis> sp., Determined by SSR Markers

The Opuntia (prickly pear) genus, an important horticultural crop in Mexico, is essentially a fruit crop with two variants: sweet (“tunas”) or acid (“xoconostles”) fruits; it is also a source of vegetables “nopalitos” or fodder for livestock, among other uses. Its taxonomical classification has been reported as complex, although few studies on the genetic structure of Mexican Opuntia are available, and genetic differences between the two types of fruits are unknown. Opuntia genotype identification and classification are still mainly based on morphological characters. In this study, the genetic diversity of Mexican Opuntia germplasm with agronomic and economic importance was revealed, using 88 accessions and 13 SSR markers, in an attempt to explore the genetic relationships among them. A total of 159 alleles were detected ranging from 7 to 23 per locus with an average of 12.2. The SSR markers generated unique fingerprints for each Opuntia accession confirming their usefulness for genetic analysis. The accessions’ grouping was defined by several complementary clustering methods, and the moderate incongruences between the different methods did not influence the overall clustering. DAPC and STRUCTURE analyses grouped the accessions into five groups, thus confirming the incorrect delimitation of species in this genus. The following species had no clear boundaries: Opuntia ficus-indica, Opuntia albicarpa, Opuntia megacantha, Opuntia streptacantha, Opuntia lasiacantha, and Opuntia hyptiacantha. However, Opuntia robusta was separated from the rest of the species. Opuntia joconostle and Opuntia matudae, which produce acid fruits, tended to differ from the others. Median-joining simulation classified all genotypes into a complex network, and both linear and reticular ties between Mexican Opuntia genotypes were revealed. The genetic distance revealed in the present study shows the importance of Mexican accessions for conservation and use in breeding programs.     

川产淫羊藿属（Epimedium）药用植物的无性系构件特征和生物量配置比较

在构件水平上,对川产的3种药用淫羊藿属植物（淫羊藿（Epimedium brevicornu）、箭叶淫羊藿（E.sagittatum）、柔毛淫羊藿（E.pubescens））的无性系构件特征、克隆构型及构件生物量配置进行比较,结果表明在野生状态下：该属3个种无性系构件的形态特征差异显著,且存在较大的变异性,变异系数范围在29.29%~48.31%之间;箭叶淫羊藿更趋于“游击型”克隆构型,而淫羊藿和柔毛淫羊藿则更趋于“密集型”克隆构型;该属3个种都将高比例生物量配置到叶片或者根茎,其次为茎,再其次为根。柔毛淫羊藿具有更强的克隆繁殖能力,单位面积上各构件生物量均最大,应作为人工引种栽培的首选种。     

A bibliometric analysis of research trends in bat echolocation studies between 1970 and 2021

Bats are among the few mammals that have acquired a sophisticated echolocation ability, attracting considerable attention for their uniqueness. Over the past 50 years, numerous research projects have been designed to study bat echolocation. The overall trend is complex and the dynamics of those publications are difficult to capture. In this study, we conducted quantitative bibliometric analyses of academic articles to identify global research trends in bat echolocation. Data were retrieved from the Web of Science, with 2914 articles sampled in our dataset from 1970 to 2021. We analyzed the global research trends in terms of annual publications, active journals, authors, institutions, and countries. We identified growth trends in the past 50 years, to which the United States was found to be the largest contributor. The University of Bristol, the University of Munich, and the Smithsonian Institute were the representative institutions of publication records. Meanwhile, Acta Chiropterologica, Journal of Experimental Biology, and Journal of the Acoustical Society of America were the top three active platforms for bat echolocation research. Co-occurrence analysis of keywords identified five clusters that correspond to five major research topics in bat echolocation: “habitat use and conservation,” “evolution,” “physiology and nervous system,” “communication and social call,” and “hunting and predation.” The overlay visualization indicated that studies on the evolution of bat echolocation had become the latest research trend, which we summarized and reviewed. Lastly, based on the results obtained, we discussed the importance of future directions for integrative multi-omics studies to uncover the mechanisms and evolution of bat echolocation.     

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data,and a revised phylogeny for Sceloporus

Phrynosomatid lizards are among the most common and diverse groups of reptiles in western North America, Mexico, and Central America. Phrynosomatidae includes 136 species in 10 genera. Phrynosomatids are used as model systems in many research programs in evolution and ecology, and much of this research has been undertaken in a comparative phylogenetic framework. However, relationships among many phrynosomatid genera are poorly supported and in conflict between recent studies. Further, previous studies based on mitochondrial DNA sequences suggested that the most species-rich genus (Sceloporus) is possibly paraphyletic with respect to as many as four other genera (Petrosaurus, Sator, Urosaurus, and Uta). Here, we collect new sequence data from five nuclear genes and combine them with published data from one additional nuclear gene and five mitochondrial gene regions. We compare trees from nuclear and mitochondrial data from 37 phrynosomatid taxa, including a “species tree” (from BEST) for the nuclear data. We also present a phylogeny for 122 phrynosomatid species based on maximum likelihood analysis of the combined data, which provides a strongly-supported hypothesis for relationships among most phrynosomatid genera and includes most phrynosomatid species. Our results strongly support the monophyly of Sceloporus (including Sator) and many of the relationships within it. We present a new classification for phrynosomatid lizards and the genus Sceloporus, and offer a new tree with branch lengths for use in comparative studies.     

Mismatch negativity to changes in a continuous tone with regularly varying frequencies

By using the mismatch negativity (MMN) component of the event-related potential, it was demonstrated that changes within a repetitively presented tone pattern can be automatically (i.e., involuntarily and attention-independently) detected by the human brain. Patterns consisting of 5 tones, immediately succeeding one another and differing in frequency, were delivered to subjects reading a self-selected book. There was a frequent , “standard” (P = 0.90) and an infrequent, “deviant” (P = 0.10) pattern presented in random order. The deviant pattern elicited the MMN even when the auditory stimulation was continuous, that is, no empty between-pattern interval indicated the beginning of a tone pattern. It may be concluded that the MMN mechanism is not necessarily timed by an “external” reference but is able to use “internal” units extracted from the repetitive structure inherent in the incessant flow of acoustic signals. The MMN paradigm seems to provide a tool to illuminate the organization of acoustic signals into auditory units.     

Mechanisms of spatial competition in marine soft-bottom communities

Two kinds of biogenic structures, roots of seagrasses and tubes of invertebrates, were found to reduce the mobility of a variety of burrowing species, including two polychaetes (Abarenicola pacifica Healy & Wells, A. claparedii Healy & Wells), two bivalves (Macoma nasuta Conrad, Clinocardium nuttalliiConrad), two crustaceans (Upogebia pugettensis (Dana), Callianassa californiensis Dana), a holothurian (Leptosynapta clarkii Heding), and an echinoid (Dendraster excentricus (Eschscholtz)). Comparisons of burrowing in similar sediments showed that: (a) all species had about a two-fold increase in mean time to burial in dense tube-mats of polychaetes and crustaceans; (b) hard-bodied taxa were particularly restricted by roots of Zostera marina L. and were often incapable of penetrating them; (c) roots and tubes together had the greatest impact, with mobility 3 to 37 times slower; and (d) burrowing ability increased when sediments were “pre-burrowed” for 1 day. Comparisons of burrowing rates in different sediments showed effects of physical origin (sediment compaction or sorting). Overall these physical effects were second to those of purely biogenic origin, sediment binding and cohesion by roots and tubes. Nonetheless, physical effects exceeded those of extremely high densities of tube-builders (3160 individuals ·0.01 m^?2). In all substrata the movement of larger individuals, and the larger of morphologically similar pairs of species (listed second above), were more restricted by roots and tubes than were smaller ones. The results suggest a general mechanism by which dense assemblages of tube-builders and seagrasses may restrict older and larger burrowing organisms. Because physical properties of the sediment and the abundance of other burrowers are also factors affecting mobility, it is not now possible to predict what situations will render this mechanism of interaction important to natural communities.     

Genetic structure among sorghum landraces as revealed by morphological variation and microsatellite markers in three agroclimatic regions of Burkina Faso

Diversity among 124 sorghum landraces from 10 villages surveyed in 3 regions of Burkina Faso covering different agroecological zones was assessed by 28 agromorphological traits and 29 microsatellite markers. 94.4% of the landraces collected belonged to the botanical race guinea (consisting of 96.6% guinea gambicum and 3.4% guinea margaritiferum), 74.2% had white kernels, 13.7% had orange and 12.1% had red kernels. Compared to the “village nested within zone” factor, the “variety nested within village within zone” factor predominately contributed to the diversity pattern for all nine statistically analysed quantitative traits. The multivariate analyses performed on ten morphological traits identified five landrace groups, and of these, the red kernel sorghum types appeared the most homogenous. 2 to 17 alleles were detected per locus with a mean 4.9 alleles per locus and a gene diversity (He) of 0.37. Landraces from the sub-Sahelian zone had the highest gene diversity (He = 0.38). Cluster analysis revealed that the diversity was weakly stratified and could not be explained by any biophysical criteria. One homogenous guinea margaritiferum group was distinguished from other guinea landraces. The red kernel type appeared to be genetically distinct from all other guinea landraces. The kernel colour was the principal structuring factor. This is an example of a homogeneous group of varieties selected for a specific use (for local beer preparation), mainly grown around the households in compound fields, and presenting particular agromorphological and genetic traits. This is the most original feature of sorghum diversity in Burkina Faso and should be the focus of special conservation efforts.     

Family Dinner and Adolescent Overweight

Objective: The purpose of this study was to examine both cross‐sectional and longitudinal associations between frequency of family dinner and overweight status in a large sample of 9‐ to 14‐year‐old children. Research Methods and Procedures: We studied a cohort of 7784 girls and 6647 boys, 9 to 14 years of age at baseline in 1996, participating in the Growing Up Today Study. From annual mailed surveys, we calculated BMI from self‐reported height and weight and assessed frequency of family dinner over the previous year. We defined “overweight” as age‐ and sex‐specific BMI >85th percentile. We performed multiple logistic regression analyses; the longitudinal analyses assessed the association of previous year family dinner consumption with 1‐year incidence of becoming overweight, using prospective data from 1996 through 1999. Results: At baseline in 1996, 16% of participants had family dinner “never or some days,” 40% on “most days,” and 44% “every day.” Across these categories, overweight prevalence for girls was 19.4%, 16.6%, and 16.7% and for boys was 24.6%, 23.3%, and 22.7%, respectively. In cross‐sectional analyses, adjusting for potential confounders, the odds of being overweight was 0.85 [95% confidence interval (CI): 0.76, 0.96] among children who ate family dinner on “most days” or “every day” compared with those who ate family dinner “never or some days.” In longitudinal multivariate models, the odds ratios between previous year frequency of eating family dinner and 1‐year incidence of becoming overweight were 0.95 (95% CI: 0.78, 1.16) and 1.04 (95% CI: 0.85, 1.27) for children who ate family dinner on “most days” and “every day,” respectively, compared with those who ate family dinner “never or some days.” Discussion: The frequency of eating family dinner was inversely associated with overweight prevalence at baseline but not with likelihood of becoming overweight in longitudinal analyses.     

Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon

We applied constrained ordination numerical ecology methods to data produced with a human intestinal tract-specific phylogenetic microarray (the Aus-HIT Chip) to examine the microbial diversity associated with matched biopsy tissue samples taken from the caecum, transverse colon, sigmoid colon and rectum of 10 healthy patients. Consistent with previous studies, the profiles revealed a marked intersubject variability; however, the numerical ecology methods of analysis allowed the subtraction of the subject effect from the data and revealed, for the first time, evidence of a longitudinal gradient for specific microbes along the colorectum. In particular, probes targeting Streptococcus and Enterococcus spp. produced strongest signals with caecal and transverse colon samples, with a gradual decline through to the rectum. Conversely, the analyses suggest that several members of the Enterobacteriaceae increase in relative abundance towards the rectum. These collective differences were substantiated by the multivariate analysis of quantitative PCR data. We were also able to identify differences in the microarray profiles, especially for the streptococci and Faecalibacterium prausnitzii, on the basis of gender. The results derived by these multivariate analyses are biologically intuitive and suggest that the biogeography of the colonic mucosa can be monitored for changes through cross-sectional and/or inception cohort studies.