Major Source Of Variation Research Articles

Population genetic structures of Puccinia triticina in five provinces of China

To understand the evolution of Puccinia triticina, we used single nucleotide polymorphisms (SNPs) to evaluate the P. triticina population genetic structure in five Chinese provinces, Gansu, Henan, Hubei, Shaanxi and Sichuan from 2013 to 2015. The populations exhibited characteristics of high haplotype diversity but low nuclear diversity. The gene flow was frequent between Gansu and Henan, Gansu and Sichuan and Sichuan and Henan. Genetic differentiation was significant among populations except between Henan and Gansu and between Henan and Sichuan (P < 0.05). The P. triticina isolates from the five provinces were grouped into two clusters: Gansu/Henan/Shaanxi/Sichuan and Hubei clusters. AMOVA analysis showed that the populations exhibited genetic variation; the variation percentage reached 87.45%, and the genetic variation within populations was the major source of variation. Our results suggest that the genetic diversity of P. triticina was high and that gene flow was frequent between populations. P. triticina population of China had experienced a rapid expansion, which caused some differences between populations. The Hubei population was different from other population due to genetic variation within populations.

Antioxidant potential of non-oil seed legumes of Indonesian’s ethnobotanical extracts

This study investigated the in vitro antioxidant properties (DPPH, ABTS, CUPRAC and FRAP), total phenolic content and flavonoid content of extracts from three non-oil seed legumes (Phaseolus lunatus red and white, and Canavalia ensiformis), local edible seeds from Indonesia, obtained using different solvent system (distilled water, 70% ethanol, and 100% ethanol). The variety of legume was a major source of variation in the phenolic contents, flavonoid content and antioxidant activity. HPLC analysis of the non-oil seed legume extracts identified gallic acid, epicatechin and coumaric acid. Among the varieties of non-oil seed legume extracts, the phenolic content varied from 15.21–38.60 mg gallic acid equivalents/g dry weight and the flavonoid content was 11.73–24.61 mg catechin equivalents/g dry weight. The antioxidant activity of the extracts suppressed the reactive oxygen species (ROS) generation and cellular damage induced by UV-B in HaCaT cells. These results showed that antioxidant activity (1.83–19.42% of inhibition DPPH; 2.99–37.29% of inhibition ABTS; 0.20–2.47 µM CUPRAC value; and 0.96–1.10 µM of FRAP value) of extracts possessed strong radical scavenging activity as well as inhibited ROS generation in a dose-dependent manner without showing any cytotoxicity. Collectively, the data presented that antioxidant of the extracts have potent antioxidant activity and decreasing ROS generation in HaCaT cells. It can be intimately used as alternative criterion for antioxidant and antiradical activities that can be utilized as a functional food and nutraceutical ingredients.

Consistency and reproducibility in atomic layer deposition

Atomic layer deposition (ALD) is a thin film synthesis technique that can provide exquisite accuracy and precision in film thickness and composition even on complex, large area substrates. Based on self-limiting surface chemistry, ALD can be insensitive to process conditions and reactor designs, allowing an ALD process developed in one lab to be easily reproduced in other labs. In practice, however, ALD is sometimes difficult to reproduce or replicate, and the results can vary substantially between ALD reactors and between labs. This is exemplified by large deviations in reports on the growth of, e.g., Al2O3, FeOx, and TiO2 given the same precursors under similar conditions. Furthermore, the problem of irreproducibility seems to be growing as ALD is adopted by more researchers and integrated into new applications. In this article, the authors highlight some of the major sources of variations and errors and common misconceptions related to ALD. In particular, the authors focus on issues related to precursors, substrates, and deposition tools. The authors illustrate these problems through examples from the literature, and they present results from numerical simulations that describe how nonidealities would manifest in thickness profiles in a typical cross-flow reactor. They also describe how reproducibility in ALD is linked to consistent experimental practice and reporting between labs. The authors’ hope is that by educating newcomers to ALD and advocating for consistent reporting of deposition conditions, they can minimize irreproducibility and enable ALD practitioners to realize the full potential afforded by self-limiting surface chemistry.

Morphological and Compositional Analysis of Two Walnut (Juglans regia L.) Cultivars Growing in China.

Two selected walnut cultivars (Xiangling and Jizhaomian) growing in China were analyzed in terms of proximate and mineral composition, fatty acid and amino acid profile. According to the higher kernel rate (61.22%), thinner shell (1.03mm), higher content of fat (66.93%), protein (20.97%), essential amino acids (29.31% of total amino acids) and minerals such as manganese, zinc and copper, Xiangling would be the more nutritive cultivar with more commercial value. However, Jizhaomian would be the more healthful cultivar based on the higher content of polyunsaturated fatty acids (79.39% of total fatty acids), and it would be more sensitive to rancidity. Jizhaomian also showed higher content in potassium, calcium, magnesium and iron. Genotype is the major source of variability in morphology and chemical compositions. Regardless of the cultivar, consumption of walnuts is desirably encouraged, since all of them contain compounds potentially beneficial to health.

Multi-Environment Evaluation and Genotype &amp;#215; Environment Interaction Analysis of Sorghum [&amp;lt;i&amp;gt;Sorghum bicolor&amp;lt;/i&amp;gt; (L.) Moench] Genotypes in Highland Areas of Ethiopia

Sorghum [Sorghum bicolor (L.) Moench] is a high-yielding, nutrient-use efficient, and drought tolerant crop that can be cultivated on over 80 per cent of the world’s agricultural land. However, a number of biotic and abiotic factors are limiting grain yield increase. Diseases (leaf and grain) are considered as one of the major biotic factors hindering sorghum productivity in the highland and intermediate altitude sorghum growing areas of Ethiopia. In addition, the yield performance of crop varieties is highly influenced by genotype × environment (G × E) interaction which is the major focus of researchers while generating improved varieties. In Ethiopia, high yielding and stable varieties that withstand biotic stress in the highland areas are limited. In line with this, the yield performance of 21 sorghum genotypes and one standard check were evaluated across 14 environments with the objectives of estimating magnitude G × E interaction for grain yield and to identify high yielder and stable genotypes across environments. The experiment was laid out using Randomized Complete Block Design with three replications in all environments. The combined analysis of variance across environments revealed highly significant differences among environments, genotypes and G × E interactions of grain yield suggesting further analysis of the G × E interaction. The results of the combined AMMI analysis of variance indicated that the total variation in grain yield was attributed to environments effects 71.21%, genotypes effects 4.52% and G × E interactions effects 24.27% indicating the major sources of variation. Genotypes 2006AN7010 and 2006AN7011 were high yielder and they were stable across environments and one variety has been released for commercial production and can be used as parental lines for genetic improvement in the sorghum improvement program. In general, this research study revealed the importance of evaluating sorghum genotypes for their yield and stability across diverse highland areas of Ethiopia before releasing for commercial production.

An Opsonophagocytic Killing Assay for the Evaluation of Group A Streptococcus Vaccine Antisera.

Group A Streptococcus (GAS) is a major cause of global mortality, yet there are no licensed GAS vaccines. Vaccine progress has been hampered, in part, by a lack of standardized assays able to quantify antibody function in test antisera. The most widely used assay was developed over 50years ago by Rebecca Lancefield and relies on human whole blood as a source of complement and neutrophils. Recently, an opsonophagocytic killing (OPK) assay has been developed for GAS by adapting the OPK methods utilized in Streptococcus pneumoniae vaccine testing. This assay uses dimethylformamide (DMF)-differentiated human promyelocytic leukemia cells (HL-60 cells) as a source of neutrophils and baby rabbit complement, thus removing the major sources of variation in the Lancefield assays. This protocol outlines methods for performing a GAS OPK assay including titering test sera to generate an opsonic index. This in vitro assay could aid in selecting vaccine candidates by demonstrating whether candidate-induced antibodies lead to complement deposition and opsonophagocytic killing.

Complexity and density of Hebrew verbs in preschool peer talk

AbstractHebrew verbs were analyzed in the peer talk produced by 36 Hebrew-speaking children in two age/schooling groups (4;0–5;0 and 5;0–6;0 years), and from two socio-economic backgrounds (SES), mid-high and low. Each of the four age/SES groups consisted of nine children in three triads, where each triad was recorded for 30 minutes while playing. The interface of lexical and morphological growth was demonstrated in the developing organization of verbs in terms of roots,binyanconjugations and derivational families. SES was found the major source of variation in all measures, indicating a smaller and less specific verb lexicon in the low SES groups. Network analyses, a novel methodological approach, revealed the internal structure of the verb category in each age/SES cell, pointing to a scarce and less complex verb lexicon of the low SES groups. These measures also accounted for the growth potential of the network, increasing from the younger low SES group at one pole and peaking in the older mid-high SES at the other pole. These quantitative and qualitative differences in the morphological make-up of the verb lexicon and its usage patterns in preschool peer talk have implications for the impact of SES on verb learning in Hebrew.

Exploration of the effect of farm, breed, sex and animal on detailed mineral profile of beef and their latent explanatory factors

SummaryMinerals in meat vary with different extrinsic and intrinsic sources; therefore, we aimed to quantify different sources of variation in mineral profile of beef. Longissimus thoracis muscle (N.182) from young bulls and heifers was analysed using ICP‐OES for 6 macrominerals, 5 essential microminerals and 9 environmental microminerals. Results of mixed models show that breed and sex have little effect on mineral profile. Major sources of variation, such as farm, individual animal within farm and side/sample within animal, differed markedly from mineral to mineral, affecting reproducibility coefficients. Multivariate factor analysis revealed that five latent factors explained 69% of the co‐variance of 20 minerals. The first was a quantitative factor, followed by others based on Na‐Fe‐Cu, on K‐B‐Pb, on Fe‐Mn and on Zn content, respectively. In conclusion, minerals’ major source of variation depends on complex relationships between the animal’s genetics, physiology, farm environment, management and feeding, whose understanding is favoured by latent factor analyses.

EEG Theta/Beta Ratio Calculations Differ Between Various EEG Neurofeedback and Assessment Software Packages: Clinical Interpretation.

The quantitative electroencephalographic (QEEG) theta/beta power ratio (TBR) has been shown to have an association with attention-deficit hyperactivity disorder (ADHD), with a previous tacit assumption of equivalence across hardware and software systems. Therefore, the International Collaborative ADHD Neurofeedback (ICAN) randomized clinical trial used a fixed TBR ≥ 4.5 cutoff as measured by the Thought Technology Monastra-Lubar Assessment Suite as an inclusion criterion, 1.5 SD above norms collected with that system. However, a difference was noted between the TBR calculated by that assessment suite and the TBR computed by EEGer, the neurofeedback software used for treatment, leading us to investigate the discrepancy. The difference may arise from different calculation methods. This article explains and compares various computational methods used to calculate and display EEG values, including TBR, elucidating why the values are not equivalent across equipment and software programs. Two major sources of variance are (1) how "spectral leakage" at the ends of bands is handled and (2) whether voltages of bins within a band are first averaged and then squared to get bandwidth power or are first squared to get power (turning negative voltages into positive power) and then averaged to get the bandwidth power; the latter method results in higher band power. This article compares methods of computing the TBR. Biofeedback practitioners and investigators should be aware of the algorithms their systems use when interpreting TBRs and require normative comparison data collected with the same system.

Relationships of a Detailed Mineral Profile of Meat with Animal Performance and Beef Quality.

Simply SummaryMinerals play direct or indirect role in different biological process of animals. These biological processes finally affect the meat quality. Therefore, analysis of minerals in cattle’s diet is important for assessing potential effects on beef quality. However, minerals profile and concentration in beef are affected by several factors such as animals rearing practices, age, environment, breed etc. Hence, we analyzed 20 minerals in 192 beef samples and studied the different sources of variation which affect the minerals profile in beef. In order to understand the complex and intriguing relations of beef qualities and minerals, we utilized correlation and factor analysis with 16 traits related to animal performance and beef quality. Our analysis shows many significant associations of minerals in beef with animal performance and beef qualities. Five groups of minerals (latent factors) were associated with almost all quality traits of beef. The knowledge about the mineral contents in beef is important to understand the complex interrelationships of animal rearing, farm management, environmental conditions with regard to animal performance and beef quality.The mineral profile of beef is a subject of human health interest, but also animal performance and meat quality. This study analyzes the relationships of 20 minerals in beef inductively coupled plasma-optical emission spectrometry (ICP-OES) with three animal performance and 13 beef quality traits analyzed on 182 samples of Longissimus thoracis. Animals’ breed and sex showed limited effects. The major sources of variation (farm/date of slaughter, individual animal within group and side/sample within animal) differed greatly from trait to trait. Mineral contents were correlated to animal performance and beef quality being significant 52 out of the 320 correlations at the farm/date level, and 101 out of the 320 at the individual animal level. Five latent factors explained 69% of mineral co-variation. The most important, “Mineral quantity” factor correlated with age at slaughter and with the beef color traits. Two latent factors (“Na + Fe + Cu” and “Fe + Mn”) correlated with performance and beef color traits. Two other (“K-B-Pb” and “Zn”) correlated with beef chemical composition and the latter also with carcass weight and daily gain, and beef color traits. Beef cooking losses correlated with “K-B-Pb”. Latent factor analysis appears be a useful means of disentangling the very complex relationships that the minerals in beef have with animal performance and beef quality traits.

The Influence of Mitochondria Enzyme Activity on Beef Tenderness

ObjectivesAmong all eating quality attributes, tenderness is often described as the most important factor dictating the overall acceptance of cooked beef, as well as, future decision to repeat purchase. While many intrinsic and extrinsic factors impact end-product tenderness, variation in tenderness is usually attributed to the extent of postmortem proteolysis occurring during meat aging. Evidence from the literature indicates that muscle fiber type composition is a major source of variation in the rate and extent of postmortem proteolysis. One of the major differences that distinguishes muscle fibers is the content of mitochondria. Typically, red muscle (slow-oxidative) is characterized by greater amounts of mitochondria than white muscle (fast-glycolytic). As part of the calcium buffering system, mitochondria sequester large quantities of calcium to maintain a constant cytosolic calcium level. We hypothesized that mitochondria may delay the activation of µ-calpain, the major protease responsible for postmortem proteolysis, through preventing the increase in cytosolic calcium concentration.Materials and MethodsTo test our hypothesis, beef longissimus thoracis muscle samples were collected at 30 min and 16 d postmortem. The 30 min samples were immediately snap frozen in liquid nitrogen and stored at – 80°C, while the 16 d samples were used to determine Warner-Bratzler shear force (WBSF) values. Based on WBSF values, the samples were allocated into less tender (average WBSF = 5.3 kg; n = 8) or more tender (average WBSF = 2.3 kg; n = 8) categories. Succinate dehydrogenase (SDH) abundance, citrate synthase (CS) activity, phosphofructokinase (PFK) activity, and glycogen phosphorylase (GP) activity were compared between the two categories using the 30 min samples. Collected data were analyzed using a Student’s t test and considered significant at P ≤ 0.05.ResultsOur results showed that SDH abundance and CS activity (mitochondrial biomarkers) were significantly greater (P = 0.01 and 0.003, respectively) in less tender samples when compared to more tender samples. On the other hand, PFK and GP activities (glycolytic biomarkers) were greater (P &lt; 0.05) in the more tender than less tender steaks.ConclusionWhile not a cause and effect relationship, these data indicate that mitochondria content likely plays a role in development of beef tenderness.

Gender and age-specific reference intervals of common biochemical analytes in Chinese population: Derivation using real laboratory data.

BackgroundIndirect sampling methods are not only inexpensive but also efficient for establishing reference intervals (RIs) using clinical data. This study was conducted to select fully normal records to establish ageand gender-specific RIs for common biochemical analytes by laboratory data mining.MethodsIn total, 280,206 records from 2014 to 2018 were obtained from Peking Union Medical College Hospital. Common biochemical analytes total protein, albumin, total bilirubin (TBil), direct bilirubin (DBil), alanine aminotransferase (ALT), glutamyltranspeptidase (GGT), alkaline phosphatase (ALP), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), potassium, sodium, chlorine, calcium, urea, glucose, uric acid (UA), inorganic phosphorus, creatinine (Cr), total cholesterol, triglyceride, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol] were measured using an automatic analyzer. Sources of variation were identified by multiple regression analysis. The 2.5th and 97.5th percentiles were calculated as the lower and upper limits of the RIs, respectivelyResultsGender was the major source of variation among the 13 common biochemical analytes with an rp > 0.15. In contrast to the value listed in the WS/T 404, nearly all RIs established in this study were significantly narrower. Furthermore, age-specific RIs should be determined for DBil, LDH, and urea, whereas gender-specific RIs are suggested for GGT, LDH, and urea.ConclusionsWe recommend that gender-specific RIs should be established for ALT, AST, GGT, DBil, TBil, UA, and Cr as well as genderand age-specific RIs for urea and ALP. Through indirect sampling, ageand gender-specific RIs for common biochemical analytes were established and analyzed.

Prediction of meat quality traits in the abattoir using portable and hand-held near-infrared spectrometers

The use of near-infrared spectrometers (NIRS) for predicting meat quality traits directly in the abattoir was tested with three trials. For the calibration trial, spectra were acquired from the cross-cut surface of the Longissimus thoracis muscle on 1166 carcasses of Piemontese young bulls with a portable visible-near-infrared spectrometer (Vis-NIRS) and with a small hand-held instrument (Micro-NIRS). A sample of the same muscle was analyzed to provide the reference. Validation statistics of the two instruments were similar. Predictabilities of meat color and purge loss were good, whereas for the other traits they were less promising. The repeatability trial showed that post-slaughter factors, not predictable by NIR spectra collected in the abattoir, affect reference meat quality values. A trial under operative conditions showed that both spectrometers were able to capture the major sources of variation in most of the meat quality traits. Overall, NIRS could be used to predict the animals' “native” characteristics exploitable for genetic improvement of meat quality traits.

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium

Accurate analysis of gene expression in human tissues using RNA sequencing is dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lay the foundation for understanding RNA regulation post-mortem and provide novel insights into RNA metabolism in the tissues of the mammalian eye.

Quantifying vocal effort from the shape of the one-third octave long-term-average spectrum of speech.

Vocal effort is a major source of variability in speech processing. The present study examines its spectral effects from calibrated data recorded in 1977. The 97 talkers were instructed to vary their vocal effort in five degrees. Each sequence was represented by its sound level and its 1/3 octave long-term-average spectrum. After normalization to a common arbitrary level, comparing each spectrum to the others demonstrated that the original sound level could be recovered within a 5 dB error margin. A principal component analysis brought out several spectral features involved in the quantitative relationship between spectral shape and sound level.

Genetic parameters for linear type traits including locomotion in Italian Jersey cattle breed

This study aimed to estimate genetic parameters for 19 linear type traits related to frame, udder, and feet and legs, and for final score of 10,305 first-parity Jersey cows evaluated between 2004 and 2016. Since scoring of locomotion in Jersey breed started in 2009, a subset of 6853 animals was extracted from the original data and used to investigate sources of variation and heritability of locomotion score, and its associations with the other traits. Univariate animal models were used to estimate variance components of type traits and bivariate analyses were implemented to obtain genetic correlations between traits. Fixed effects were herd-year-classifier, season of evaluation, stage of lactation at scoring and age at calving, and the random effects were additive genetic animal and the residual. Herd-year-classifier was the major source of variation affecting the traits. Heritabilities were low with the only exception of a moderate heritability (0.32 ± 0.02) for stature. The lowest heritabilities were estimated for feet and legs traits with values between 0.04 ± 0.02 (rear leg set side view, rear leg set rear view and locomotion) and 0.07 ± 0.02 (foot angle). The final score had heritability of 0.20 ± 0.02. Genetic correlations were generally stronger than their phenotypic counterparts. Overall, frame traits were weakly correlated with feet and legs, and udder traits, except for rump width, which showed moderate correlations with almost all traits, and angularity which showed the greatest correlations with rear udder height (0.61 ± 0.10) and rear udder width (0.62 ± 0.11). Genetic correlations between locomotion and frame traits ranged from 0.08 ± 0.22 (angularity) to 0.32 ± 0.16 (stature). The strongest correlations were estimated between locomotion and other feet and legs traits, but also with front teat placement (0.97 ± 0.19) and with rear teat placement (0.88 ± 0.17). Results of the present study will be used to enhance genetic evaluation of linear type traits in Jersey cattle breed.

Population-dependent reproducible deviation from natural bread wheat genome in synthetic hexaploid wheat.

Sequence elimination is one of the main mechanisms that increases the divergence among homoeologous chromosomes after allopolyploidization to enhance the stability of recently established lineages, but it can cause a loss of some economically important genes. Synthetic hexaploid wheat (SHW) is an important source of genetic variation to the natural hexaploid wheat (NHW) genepool that has low genetic diversity. Here, we investigated the change between SHW and NHW genomes by utilizing a large germplasm set of primary synthetics and synthetic derivatives. Reproducible segment elimination (RSE) was declared if a large chromosomal chunk (>5cM) produced no aligned reads in more than five SHWs. RSE in five genomic regions was the major source of variation between SHW and NHW. One RSE eliminated almost the complete short arm of chromosome 1B, which contains major genes for flour quality, disease resistance and different enzymes. The occurrence of RSE was highly dependent on the choice of diploid and tetraploid parental lines, their ancestral subpopulation and admixture, e.g. SHWs derived from Triticum dicoccon or from one of two Aegilops tauschii subpopulations were almost free of RSE, while highly admixed parents had higher RSE rates. The rate of RSE in synthetic derivatives was almost double that in primary synthetics. Genome-wide association analysis detected four loci with minor effects on the occurrence of RSE, indicating that both parental lines and genetic factors were affecting the occurrence of RSE. Therefore, pre-pre-breeding strategies should be applied before introducing SHW into pre-breeding programs to ensure genomic stability and avoid undesirable gene loss.

Detailed macro- and micromineral profile of milk: Effects of herd productivity, parity, and stage of lactation of cows of 6 dairy and dual-purpose breeds

The aim of this study was to quantify the major sources of variation in the levels of 15 minerals in individual milk samples collected from cows raised in multibreed dairy herds. The herds (n = 27) were classified into 2 categories, according to milk productivity. Milk productivity was based on the net energy of lactating cows' average daily milk yield. Milk samples were collected from 240 cows of 6 different breeds: 3 specialized dairy (Holstein-Friesian, Brown Swiss, and Jersey) and 3 dual-purpose (Simmental, Rendena, and Alpine Grey). The samples were analyzed for macro-elements (Na, Mg, P, S, K, and Ca), essential micro-elements (Mn, Fe, Cu, Zn, and Se), and environmental micro-elements (B, Si, Sr, and Sn), using inductively coupled plasma-optical emission spectrometry. Data were analyzed using a linear mixed model that included fixed effects of days in milk (DIM), parity, breed, and herd productivity, and a random effect of herd-date within productivity level. Results showed that the effect of herd-date varied across minerals. It was especially large for environmental minerals (ranging from 47 to 91% of total variance) and ranged from 11 to 61% for macrominerals and essential microminerals. Milk samples collected from farms with a high level of herd productivity had a richer mineral profile than samples from low-productivity herds. Parity only influenced macrominerals, with the exception of S and Ca, while DIM influenced almost all minerals, with a few exceptions among the environmental elements. Differences in mineral profile were small between specialized and dual-purpose breeds, but they were large within the group of the specialized cows. These breed differences were reduced after adjusting for milk quality and yield, particularly in the case of milk Mg, S, Ca, Mn, and Zn levels. Milk samples from the Jersey and Brown Swiss cows had higher mineral levels (Sn excluded) than milk from the Holstein-Friesian cows; the other breeds of Alpine origin produced milk of intermediate quality. Our findings suggest that breed has a stronger effect on macrominerals and some of the essential microminerals than herd productivity, parity, and DIM. The modification of the mineral profile in milk seems possible for many minerals, but it likely depends on genetics (e.g., breed, selection) and on environmental and management factors in variable proportions according to the mineral considered.

Drivers of Late Pleistocene human survival and dispersal: an agent-based modeling and machine learning approach

Understanding Late Pleistocene human dispersals from Africa requires understanding a multifaceted problem with factors varying in space and time, such as climate, ecology, human behavior, and population dynamics. To understand how these factors interact to affect human survival and dispersal, we have developed a realistic agent-based model that includes geographic features, climate change, and time-varying vegetation and food resources. To enhance computational efficiency, we further apply machine learning algorithms. Our approach is new in that it is designed to systematically evaluate a large-scale agent-based model, and identify its key parameters and sensitivities. Results show that parameter interactions are the major source in generating variability in human dispersal and survival/extinction scenarios. In realistic scenarios with geographical features and time-evolving climatic conditions, random fluctuations become a major source of variability in arrival times and success. Furthermore, parameter settings as different as 92% of maximum possible difference, and occupying more than 30% of parameter space can result in similar dispersal scenarios. This suggests that historical contingency (similar causes – different effects) and equifinality (different causes – similar effects) are primary constituents of human dispersal scenarios. While paleoanthropology, archaeology and paleogenetics now provide insights into patterns of human dispersals at an unprecedented level of detail, elucidating the causes underlying these patterns remains a major challenge.

Macroinvertebrate functional feeding group alterations in response to habitat degradation of headwater Austral streams

Protecting the structural and functional integrity of lotic ecosystems is becoming increasingly important as many ecological systems face escalating pressures from human population growth and environmental impacts. Knowledge on the functional composition of macroinvertebrates in austral temperate streams is generally lacking hindering the design and implementation of water management and restoration goals. Therefore, this study examined the effects of urban land–use activities on the benthic macroinvertebrate functional feeding guild structure among different stream orders in an austral river system (Bloukrans River) in the Eastern Cape Province of South Africa. Water quality and macroinvertebrate community data were collected across two seasons from 18 sites in two different stream order categories (i.e. 1, 2 + 3), following standard methods. We separated macroinvertebrates into functional feeding groups (FFGs), which we then used to assess the effects of riparian condition on FFG organization. Linear mixed effects model (LMM) results demonstrated that total dissolved solids (TDS), canopy cover, phosphate and channel width were the key variables that described the major sources of variation in macroinvertebrate FFGs. Based on FFG proportions, collector–gatherers were the most abundant in the Bloukrans River and represented 71.3% of the macroinvertebrate assemblages. The FFG ratios indicated that all the eighteen sites were strongly heterotrophic (i.e. streams received additional sources of energy from leaf litter and other organic matter), showed below expected linkage with riparian input and stable substrates were limited. The FFG ratios offered some insights into the overall functioning of Bloukrans River system. Our results highlight the importance of including macroinvertebrate functional diversity as a complementary approach to assess the ecological integrity in management and restoration plans of river systems.