Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations.

Multiple sclerosis (MS) is a neuro-inflammatory and neurodegenerative disease that is most prevalent in Northern Europe. Although it is known that inherited risk for MS is located within or in close proximity to immune-related genes, it is unknown when, where and how this genetic risk originated1. Here, by using a large ancient genome dataset from the Mesolithic period to the Bronze Age2, along with new Medieval and post-Medieval genomes, we show that the genetic risk for MS rose among pastoralists from the Pontic steppe and was brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the steppe population and later in Europe, probably driven by pathogenic challenges coinciding with changes in diet, lifestyle and population density. This study highlights the critical importance of the Neolithic period and Bronze Age as determinants of modern immune responses and their subsequent effect on the risk of developing MS in a changing environment.

Effective population size mediates the impact of pollination services on pollen limitation.

Inadequate pollen receipt limits flowering plant reproduction worldwide. Ecological causes of pollen limitation (PL), like pollinator scarcity and low plant abundance, have been a primary research focus. The genetic diversity of plant populations could impact both quantity and quality components of PL in concert with ecological factors, yet empirical examples are lacking. We evaluated joint effects of ecological factors (flower abundance, pollinator visitation) and genetic effective population size (NE) on PL across 13 populations of the common herb Argentina anserina. We used a histological approach with 5504 styles from 1137 flowers to separate quantity and quality components of PL, and link these to reproductive output. NE and pollinator visitation interacted to shape PL, but NE had stronger direct effects. Effectively smaller populations experienced stronger quantity PL, and controlled crosses in a pollinator-free environment revealed that stigmatic pollen quantity was an intrinsic population-level attribute that increased with NE. Pollinator visitation enhanced pollen quality, but only in effectively larger populations. Quantity and quality PL negatively impacted fruit and seed set, respectively. Results highlight that PL is dictated by plant population genetic diversity in addition to commonly evaluated ecological factors. Efforts to support pollinators will more strongly enhance plant reproduction in genetically diverse populations.

Population Rescue through an Increase in the Selfing Rate under Pollen Limitation: Plasticity versus Evolution.

AbstractIncreased rates of self-fertilization offer reproductive assurance when plant populations experience pollen limitation, but self-fertilization may reduce fitness by exposing deleterious mutations. If an environmental change responsible for pollen limitation also induces plastic mating system shifts toward self-pollination, the reproductive assurance benefit and inbreeding depression cost of increased self-fertilization occur immediately, while the benefit and cost happen more gradually when increased self-fertilization occur through evolution. I built eco-evolutionary models to explore the demographic and genetic conditions in which higher self-fertilization by plasticity and/or evolution rescues populations, following deficits due to a sudden onset of pollen limitation. Rescue is most likely under an intermediate level of selfing rate increase, either through plasticity or evolution, and this critical level of selfing rate increase is higher under stronger pollen limitation. Generally, rescue is more likely through plasticity than through evolution. Under weak pollen limitation, rescue by enhanced self-fertilization may mainly occur through purging of deleterious mutations rather than reproductive assurance. The selfing rate increase conferring the highest rescue probability is lower when the initial population size is smaller. This article shows the importance of plasticity during plant population rescue and offers insights for future studies of the evolution of mating system plasticity.

Population Size Estimation of People Who Use Illicit Drugs and Alcohol in Iran (2015-2016).

BACKGROUND: Estimating the number of people using illicit drugs and alcohol is necessary for informing health policy and programming. However, it is often challenging to reliably estimate the size of these marginalized populations through direct methods. In this study, we estimated the population size of these groups using the indirect Network Scale-Up (NSU) method in Iran from 2015 to 2016. METHODS: Using a self-administered questionnaire, we asked 15 124 individuals (54% men) about the number of people they know who used different types of drugs at least once in the past 12 months. Prevalence estimates were reported per 100 000 population. The uncertainty level (UL) was calculated using the bootstrap method. RESULTS: The average age of the respondents was 33 years old, and 35.1% of them were unmarried. The most common drugs and their prevalence were as follows: opium (2534 [95% UL: 2467-2598]), hashish (849 [95% UL: 811-886]), stimulants (methamphetamine, ecstasy pills, cocaine, and Ritalin) (842 [95% UL: 802-879]), heroin/crack (578 [95% UL: 550-607]), and drug injection (459 [95% UL: 438-484]). Additionally, we estimated the prevalence of alcohol use as 2797 (95% UL: 2731-2861). On average, substance use was 5.23 times more prevalent among men than women. Opium use was more prevalent among individuals aged >50 years old. Moreover, alcohol use was more prevalent among participants between 18 and 30 years old (5164 per 100 000 population). CONCLUSION: Although opium continues to be the most prevalent illicit drug in Iran, the patterns of illicit drug use are heterogeneous among different age groups, genders, and provinces. Age-gender specific and culturally appropriate interventions are warranted to meet the needs of people in different subgroups.

An exploratory method to determine the plant characteristics affecting the final yield of Echium amoenum Fisch. & C.A. Mey. under fertilizers application and plant densities.

Employing of advanced statistical methods to quantify agricultural information has helped to carry out targeted planning to alleviate the problems of farmers, researchers and policy section. One of these exploratory methods, is multivariate statistical analysis that examines and models the relationship between variables. Considering the importance of Echium amoenum and its use growing trend in traditional medicine and the pharmaceutical industry, also the lack of information on the correlations between its yield and morpho physiological traits, the objective of this study was to determine the causality path in which the Echium amoenum characteristics affects the yield of Echium amoenum as regards of application of organic and chemical fertilizers under different plant densities. The employed method revealed that organic fertilizers increased flower yield compared with the control. The flower yield as a result of application of compost, vermicompost and cattle manure were increased by 25, 28, and 27% compared with the control, respectively. The results of multiple regression showed that variables of plant height, shoot dry weight, flower number per plant were the main factors affected the flower yield. The relative contribution of shoot dry weight was 16 and 25% more than plant height and flower number per plant, respectively. Causality analysis identified that shoot dry weight per plant had indirect effect on flower yield in different paths, as mainly was imposed through plant height considering the path coefficients. This study suggests that optimum production of Echium amoenum with application of ecological inputs along with effective agronomical managements of the causal paths of flower yield forming, including increase in shoot yield and plant height could be achieved through an ecological cropping system with reduced costs and no health concerning due to agrochemicals residual.

The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato.

Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.

The critical role of natural forest as refugium for generalist species in oil palm-dominated landscapes.

In Borneo, oil palm plantations have replaced much of natural resources, where generalist species tend to be the principal beneficiaries, due to the abundant food provided by oil palm plantations. Here, we analyse the distribution of the Asian water monitor lizard (Varanus salvator) population within an oil palm-dominated landscape in the Kinabatangan floodplain, Malaysian Borneo. By using mark-recapture methods we estimated its population size, survival, and growth in forest and plantation habitats. We compared body measurements (i.e. body weight and body length) of individuals living in forest and oil palm habitats as proxy for the population's health status, and used general least squares estimation models to evaluate its response to highly fragmented landscapes in the absence of intensive hunting pressures. Contrary to previous studies, the abundance of lizards was higher in the forest than in oil palm plantations. Recruitment rates were also higher in the forest, suggesting that these areas may function as a source of new individuals into the landscape. While there were no morphometric differences among plantation sites, we found significant differences among forested areas, where larger lizards were found inhabiting forest adjacent to oil palm plantations. Although abundant in food resources, the limited availability of refugia in oil palm plantations may intensify intra-specific encounters and competition, altering the body size distribution in plantation populations, contrary to what happens in the forest. We conclude that large patches of forest, around and within oil palm plantations, are essential for the dynamics of the monitor lizard population in the Kinabatangan floodplain, as well as a potential source of individuals to the landscape. We recommend assessing this effect in other generalist species, as well as the impact on the prey communities, especially to reinforce the establishment of buffer zones and corridors as a conservation strategy within plantations.

From Green Spaces to Squares: Mapping the Distribution of Taijiquan Organizations in London.

Contributing to Taijiquan studies, this research uses spatial analysis tools in ArcGIS 10.3 and SPSS 23.0 to map out the spatial distributional pattern of the Taijiquan organizations in London, and then explores factors attributing to the spatial distribution of Taijiquan culture. The result shows that the distribution of Taijiquan organizations in London generally presents a spatial distribution structure of "dense center + sparse periphery"; the spatial distribution is unbalanced, showing a cohesive distribution; the directional distribution tends to be obvious in areas that are proximate to urban traffic arteries and afforestation in London. Through multivariate hierarchical regression analysis, the study explores the influential factors for the spatial distribution of Taijiquan organizations in London. The results show that: population size, economic level, and education level have little influence on the spatial distribution of Taijiquan organizations; however, the population density of people over 65 years old, the accessibility of public service facilities such as green spaces, and public urban traffic has a significant impact on the spatial distribution of Taijiquan organizations.

Benthic jellyfish dominate water mixing in mangrove ecosystems.

Water mixing is a critical mechanism in marine habitats that governs many important processes, including nutrient transport. Physical mechanisms, such as winds or tides, are primarily responsible for mixing effects in shallow coastal systems, but the sheltered habitats adjacent to mangroves experience very low turbulence and vertical mixing. The significance of biogenic mixing in pelagic habitats has been investigated but remains unclear. In this study, we show that the upside-down jellyfish Cassiopea sp. plays a significant role with respect to biogenic contributions to water column mixing within its shallow natural habitat ([Formula: see text] m deep). The mixing contribution was determined by high-resolution flow velocimetry methods in both the laboratory and the natural environment. We demonstrate that Cassiopea sp. continuously pump water from the benthos upward in a vertical jet with flow velocities on the scale of centimeters per second. The volumetric flow rate was calculated to be 212 L⋅h-1 for average-sized animals (8.6 cm bell diameter), which translates to turnover of the entire water column every 15 min for a median population density (29 animals per m2). In addition, we found Cassiopea sp. are capable of releasing porewater into the water column at an average rate of 2.64 mL⋅h-1 per individual. The release of nutrient-rich benthic porewater combined with strong contributions to water column mixing suggests a role for Cassiopea sp. as an ecosystem engineer in mangrove habitats.

Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences.

The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

Características clínico-epidemiológicas de pacientes cubanos residentes en La Habana afectados por la COVID-19 / Clinical-epidemiological characteristics of patients affected by COVID-19 residing in Havana

Introducción: La Habana fue el territorio más complejo a nivel nacional en el enfrentamiento al primer brote de la COVID-19. Su condición de capital, la densidad poblacional, la escasa delimitación geográfica entre sus municipios, el elevado flujo intermunicipal e interprovincial de personas, sumado a que es la provincia que mayor número de viajeros recibe procedentes del extranjero, confirieron a este territorio particularidades en el enfrentamiento a la pandemia. Objetivo: Determinar las principales características clínico-epidemiológicas de pacientes cubanos residentes en La Habana afectados por la COVID-19. Métodos: Se realizó un estudio observacional, analítico, de corte transversal. La muestra quedó formada por 431 pacientes, mayores de un año, de alta epidemiológica de la infección por SARS-CoV-2. Para la recolección de información se aplicó un cuestionario a través de una entrevista. Resultados: La edad promedio de la muestra fue de 45 años. Más de la mitad de los casos evolucionaron de modo sintomático (no grave o grave). La fiebre fue la manifestación clínica más frecuente. Los individuos incluidos en la muestra, con grupo sanguíneo O, o con antecedentes de asma, mostraron menos riesgo de presentar formas sintomáticas de la enfermedad. Conclusiones: Los resultados sugieren que la edad constituye el principal factor de riesgo para desarrollar formas sintomáticas (no graves o graves) de la COVID-19. De modo contrario, el grupo sanguíneo O y el antecedente de asma son factores de protección para estas formas de evolución clínica(AU)

Introduction: Havana city was the most complex territory at the national level facingthe first outbreak of COVID-19. Its condition of capital, the population density, the limited geographical delimitation between its municipalities, the high inter-municipal and inter-provincial flow of people, added to the fact that it is the province that receives the largest number of travelers from abroad, conferred particularities on this territory. Objective: To determine the main clinical-epidemiological characteristics of patients affected by COVID-19 living in Havana. Methods: An observational, analytical, cross-sectional study was carried out. The sample contained 431 patients, older than one year, with epidemiological discharge from the SARS-CoV-2 infection. To collect information, a questionnaire was applied through an interview. Results: The average age of the sample was 45 years. More than half of the cases evolved in a symptomatic way (not serious or serious). Fever was the most frequent clinical manifestation. The individuals included in the sample, with blood group O or with a background of asthma, showed less risk of presenting symptomatic forms of the disease. Conclusions: The results suggest that age is the main risk factor for developing symptomatic forms (not severe or severe) of COVID-19. On the contrary, blood group O and a history of asthma are protective factors for these forms of clinical evolution(AU)

The pest kill rate of thirteen natural enemies as aggregate evaluation criterion of their biological control potential of Tuta absoluta.

Ecologists study how populations are regulated, while scientists studying biological pest control apply population regulation processes to reduce numbers of harmful organisms: an organism (a natural enemy) is used to reduce the population density of another organism (a pest). Finding an effective biological control agent among the tens to hundreds of natural enemies of a pest is a daunting task. Evaluation criteria help in a first selection to remove clearly ineffective or risky species from the list of candidates. Next, we propose to use an aggregate evaluation criterion, the pest kill rate, to compare the pest population reduction capacity of species not eliminated during the first selection. The pest kill rate is the average daily lifetime killing of the pest by the natural enemy under consideration. Pest kill rates of six species of predators and seven species of parasitoids of Tuta absoluta were calculated and compared. Several natural enemies had pest kill rates that were too low to be able to theoretically reduce the pest population below crop damaging densities. Other species showed a high pest reduction capacity and their potential for practical application can now be tested under commercial crop production conditions.

A rhamnolipid biosurfactant increased bacterial population size but hindered hydrocarbon biodegradation in weathered contaminated soils.

Surfactants are used to enhance the bioavailability of recalcitrant residual petroleum contamination during bioremediation. However, surfactants in some cases inhibit biodegradation, which is often attributed to their toxicity. Herein, we show that a rhamnolipid biosurfactant likely served as a carbon source and exhibited physiological inhibition on petroleum biodegradation. The addition of biosurfactants in mixed, batch, slurry bioreactors with soils from a petroleum-contaminated site led to a dose-dependent shift in the microbial community with a decrease in diversity and increase in population size and delayed biodegradation. Microbial community analysis indicated the enrichment of Alphaproteobacteria affiliated taxa such as Sphingomonadaceae in systems amended with biosurfactant. The diversity was significantly lower in systems with higher doses of biosurfactants compared to systems without biosurfactant. Droplet Digital PCR indicated a 30-90 fold increase in 16S rRNA copy numbers in systems with higher doses of biosurfactant than control systems without surfactant and nutrients, whereas the nutrient amendment alone led to a two-fold increase in population size. Total petroleum hydrocarbon analysis showed that the biodegradation extent was negatively impacted by rhamnolipid at the highest dose compared to lower doses (23% vs. 40%) or without the biosurfactant. Indigenous isolates cultivated from the oil-amended soil exhibited growth on rhamnolipid as a sole carbon source. A novel insight gained is how dose-dependent responses of microbial communities to biosurfactants alter the biodegradation time profile of hydrocarbons. The study highlights the significance of microbial assessment prior to surfactant-mediated bioremediation practices.

Population decline in a ground-nesting solitary squash bee (Eucera pruinosa) following exposure to a neonicotinoid insecticide treated crop (Cucurbita pepo).

Insect pollinators are threatened by multiple environmental stressors, including pesticide exposure. Despite being important pollinators, solitary ground-nesting bees are inadequately represented by pesticide risk assessments reliant almost exclusively on honeybee ecotoxicology. Here we evaluate the effects of realistic exposure via squash crops treated with systemic insecticides (Admire-imidacloprid soil application, FarMore FI400-thiamethoxam seed-coating, or Coragen-chlorantraniliprole foliar spray) for a ground-nesting bee species (Hoary squash bee, Eucera pruinosa) in a 3-year semi-field experiment. Hoary squash bees provide essential pollination services to pumpkin and squash crops and commonly nest within cropping areas increasing their risk of pesticide exposure from soil, nectar, and pollen. When exposed to a crop treated at planting with soil-applied imidacloprid, these bees initiated 85% fewer nests, left 5.3 times more pollen unharvested, and produced 89% fewer offspring than untreated controls. No measurable impacts on bees from exposure to squash treated with thiamethoxam as a seed-coating or foliage sprayed with chlorantraniliprole were found. Our results demonstrate important sublethal effects of field-realistic exposure to a soil-applied neonicotinoid (imidacloprid) on bee behaviour and reproductive success. Soil must be considered a potential route of pesticide exposure in risk assessments, and restrictions on soil-applied insecticides may be justified, to mitigate impacts on ground-nesting solitary bee populations and the crop pollination services they provide.

Effects of alpha-lipoic acid on the behavior, serum indicators, and bone quality of broilers under stocking density stress.

The objective of present study was to investigate the effects of alpha-lipoic acid (ALA) dietary supplementation on the behavior, physiological and oxidant stress indicators, and bone quality in broilers under high stocking density (HSD) stress. A total of one thousand eight hundred 22-day-old Arbor Acres male broiler chicks were randomly allocated to 18 pens (2.97 × 2.03 m) in 3 groups: 14 birds/m2 (NSD, normal stocking density) or 18 birds/m2 (HSD) or 18 birds/m2 plus 300 mg/kg ALA dietary supplement (HSD + ALA, high stocking density + alpha-lipoic acid). Each treatment had 6 replicates, and the experiment lasted 3 wk. The HSD group was significantly lower than the NSD group (P < 0.05) in the frequency of eating, walking, and preening behavior. The alkaline phosphatase activity and serum calcium content were significantly higher, and the parathyroid hormone (PTH) level was significantly lower in the HSD group than in the NSD group (P < 0.05). When compared with the NSD group, the HSD group showed an increase (P < 0.05) in serum heterophil/lymphocyte ratio (H/L ratio), corticosterone (CORT), malondialdehyde (MDA) content, and catalase (CAT) activity, whereas a decrease (P < 0.05) in total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) concentrations. The HSD group was also significantly lower (P < 0.05) than the NSD group in the tibia and femur breaking strength, bone mineral density, and BMC. Importantly, the addition of ALA into the diets of the HSD group enabled the HSD + ALA group to recover to the levels of NSD group (P > 0.05) in the standing and preening behavior, alkaline phosphatase activity, PTH concentration, H/L ratio, CAT, T-AOC, MDA, SOD, and GSH-Px. These results indicate that the increase of stocking density lowered the bone quality, increased the physiological and oxidative stress indicators, and modified the behavior of broilers, whereas ALA dietary supplementation could counteract the reduction in the performance and physiological responses of broilers under high-density environmental stress.

Recent effective population size in Eastern European plain Russians correlates with the key historical events.

Effective population size reflects the history of population growth, contraction, and structuring. When the effect of structuring is negligible, the inferred trajectory of the effective population size can be informative about the key events in the history of a population. We used the IBDNe and DoRIS approaches, which exploit the data on IBD sharing between genomes, to reconstruct the recent effective population size in two population datasets of Russians from Eastern European plain: (1) ethnic Russians sampled from the westernmost part of Russia; (2) ethnic Russians, Bashkirs, and Tatars sampled from the Volga-Ural region. In this way, we examined changes in effective population size among ethnic Russians that reside in their historical area at the West of the plain, and that expanded eastward to come into contact with the indigenous peoples at the East of the plain. We compared the inferred demographic trajectories of each ethnic group to written historical data related to demographic events such as migration, war, colonization, famine, establishment, and collapse of empires. According to IBDNe estimations, 200 generations (~6000 years) ago, the effective size of the ancestral populations of Russians, Bashkirs, and Tatars hovered around 3,000, 30,000, and 8,000 respectively. Then, the ethnic Russians exponentially grew with increasing rates for the last 115 generations and become the largest ethnic group of the plain. Russians do not show any drop in effective population size after the key historical conflicts, including the Mongol invasion. The only exception is a moderate drop in the 17th century, which is well known in Russian history as The Smuta. Our analyses suggest a more eventful recent population history for the two small ethnic groups that came into contact with ethnic Russians in the Volga-Ural region. We found that the effective population size of Bashkirs and Tatars started to decrease during the time of the Mongol invasion. Interestingly, there is an even stronger drop in the effective population size that coincides with the expansion of Russians to the East. Thus, 15-20 generations ago, i.e. in the 16-18th centuries in the trajectories of Bashkirs and Tatars, we observe the bottlenecks of four and twenty thousand, respectively. Our results on the recent effective population size correlate with the key events in the history of populations of the Eastern European plain and have importance for designing biomedical studies in the region.

Black widows as plastic wallflowers: female choosiness increases with indicators of high mate availability in a natural population.

Female choice is an important driver of sexual selection, but can be costly, particularly when choosy females risk remaining unmated or experience delays to reproduction. Thus, females should reduce choosiness when mate encounter rates are low. We asked whether choosiness is affected by social context, which may provide reliable information about the local availability of mates. This has been demonstrated in the lab, but rarely under natural conditions. We studied western black widow spiders (Latrodectus hesperus) in the field, placing experimental final-instar immature females so they were either 'isolated' or 'clustered' near naturally occurring conspecifics (≥10 m or ≤1 m, respectively, from a microhabitat occupied by at least one other female). Upon maturity, females in both treatments were visited by similar numbers of males, but clustered females were visited by males earlier and in more rapid succession than isolated females, confirming that proximity to conspecifics reduces the risk of remaining unmated. As predicted, isolated females were less choosy in staged mating trials, neither rejecting males nor engaging in pre-copulatory cannibalism, in contrast to clustered females. These results demonstrate that exposure of females to natural variation in demography in the field can alter choosiness of adults. Thus, female behaviour in response to cues of local population density can affect the intensity of sexual selection on males in the wild.

Effect of dietary 25-hydroxycholecalciferol supplementation and high stocking density on performance, egg quality, and tibia quality in laying hens.

This study was conducted to determine the effects of 25-hydroxycholecalciferol (25-OH-D3) on performance, egg quality, tibia quality, and serum hormones concentration in laying hens reared under high stocking density. A total of 800 45-week-old Lohmann laying hens were randomly allotted into a 2 × 2 factorial design with 2 levels of dietary 25-OH-D3 levels (0 and 69 µg/kg) and 2 rates of stocking densities [506 (low density) and 338 (high density) cm2/hen]. Laying hens were monitored for 16 wk. High stocking density decreased laying rate, egg weight, and feed intake compared with low stocking density (P < 0.01) during 1 to 8 wk and 1 to 16 wk. Overall, high stocking density increased eggshell lightness value and decreased shell redness and yellowness value, strength, thickness, and relative weight compared with low stocking density (P < 0.05). Dietary supplementation with 25-OH-D3 reduced the value of the eggshell lightness and increased its yellowness and eggshells weight (P ≤ 0.05). The increase in eggshell thickness was more pronounced when 25-OH-D3 was supplemented to layers under high stocking density (interaction, P < 0.05). Layers under high stocking density had lower ash content and calcium content in the tibia than layers under low stocking density (P = 0.04); dietary 25-OH-D3 increased tibia strength compared with no addition (P = 0.05). Layers under high stocking density had higher serum concentrations of 25-OH-D3, corticosterone (CORT), lipopolysaccharide (LPS), and osteocalcin (OC; P < 0.05), lower content of parathyroid hormone (PTH) compared with layers under low stocking density (P < 0.01). Dietary 25-OH-D3 increased serum concentration of 25-OH-D3, carbonic anhydrase (CA), and calcitonin (CT) (P < 0.01) and reduced corticosterone, lipopolysaccharide and osteocalcin concentration (P ≤ 0.05). The increase effect in PTH was more pronounced when 25-OH-D3 was supplemented to layers under high stocking density (interaction, P = 0.05). Overall, the results gathered in this study indicate that high stocking density result in reducing production performance, shell color and quality, and tibia health, whereas dietary 25-OH-D3 was able to maintain tibia health and to mitigate the negative impact of high stocking density on productive performance.

Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences.

BACKGROUND: Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and organization. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including the familiar table, leaf (chard), fodder, and sugar beet crop types. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between accessions based on identity-by-state metrics and shared genetic variation among lineages. RESULTS: Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages. CONCLUSIONS: A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between table and sugar groups, perhaps the result of less intensive selection for end use.