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Researchers in ecology and evolutionary biology are increasingly dependent on computational code to conduct research. Hence, the use of efficient methods to share, reproduce, and collaborate on code as well as document research is fundamental. GitHub is an online, cloud-based service that can help researchers track, organize, discuss, share, and collaborate on software and other materials related to research production, including data, code for analyses, and protocols. Despite these benefits, the use of GitHub in ecology and evolution is not widespread. To help researchers in ecology and evolution adopt useful features from GitHub to improve their research workflows, we review 12 practical ways to use the platform. We outline features ranging from low to high technical difficulty, including storing code, managing projects, coding collaboratively, conducting peer review, writing a manuscript, and using automated and continuous integration to streamline analyses. Given that members of a research team may have different technical skills and responsibilities, we describe how the optimal use of GitHub features may vary among members of a research collaboration. As more ecologists and evolutionary biologists establish their workflows using GitHub, the field can continue to push the boundaries of collaborative, transparent, and open research.

Cadra cautella (Walker) (Lepidoptera: Pyralidae) is a pest in barn, and its eggs are often utilized as an alternative prey or as hosts for mass production of insect predators and parasitoids. To aid in developing a mass-rearing system for C. castella, the suitability of using an artificial diet based on brown rice flour and whole brown rice was compared using the age-stage, 2-sex life table. Compared with those reared on brown rice, the insects reared on an artificial diet had a shorter preadult period (32.08 vs 37.38 d), higher fecundity (468.14 vs 356.20 eggs/female), greater intrinsic rate of increase (0.1509 vs 0.1145 d−1), and higher net reproductive rate (199.28 vs 103.52 offspring). Small populations were required to rear the moth on an artificial diet to achieve the same daily production of C. cautella. Still, the food expense was only 60.2% of that of C. cautella reared on brown rice. Approximately 99.44% of the eggs in each rearing procedure could be supplied as alternative prey for predators, with the remainder served to maintain the colonies for subsequent batches. Only eggs laid within 6 d would be utilized to ensure the high quality of alternative prey for the mass production of predacious bugs. Additionally, a multifunctional device was designed for moth rearing and egg collection, reducing labor input and minimizing health risks for workers coping with inhaled scales. To encourage the production of natural enemies, a cost-effective diet for maintaining a sustainable colony, and a system for daily egg-harvesting of alternative prey were proposed. [ABSTRACT FROM AUTHOR]

Simple Summary: Aphis gossypii Glover is an economically important sap-sucking insect pest that causes severe damage worldwide. The flonicamid has been widely used for controlling sap-sucking insect pests, but its intergenerational sublethal effects on key demographic parameters of A. gossypii have not been fully studied. The age-stage, two-sex life table analysis was conducted to investigate the sublethal effects of flonicamid on the biological parameters of adult A. gossypii (F0) and its subsequent intergenerational effects on the offspring (F1 generation). The results showed that the sublethal concentrations of flonicamid significantly decreased the longevity, fecundity, and reproductive days of F0 A. gossypii. Moreover, flonicamid induced intergenerational sublethal effects on the subsequent progeny generation (F1) by impacting the key biological and demographic parameters of A. gossypii. Taken together, these results demonstrated that sublethal concentrations of flonicamid negatively affect the demographic parameters of A. gossypii, resulting in the suppression of population growth. Flonicamid is a novel systemic insecticide widely used against aphids. However, the intergenerational sublethal effects of flonicamid on cotton aphid, Aphis gossypii, have not been fully studied. This study aimed to evaluate the sublethal effects of flonicamid on the biological parameters of adult A. gossypii (F0) and its subsequent intergenerational effects on the offspring (F1 generation) through age-stage, two-sex life table analysis. The results of the bioassays indicate that flonicamid exhibits significant toxicity toward adult A. gossypii, as evidenced by an LC50 value of 0.372 mg L−1 after a 48-h exposure period. The longevity, fecundity, and reproductive days of adult cotton aphids (F0) were significantly decreased when treated with the sublethal concentrations of flonicamid. The pre-adult stage exhibited an increase, whereas the adult longevity, total longevity, and fecundity experienced a notable decrease in F1 aphids after the exposure of F0 aphids to sublethal concentrations of flonicamid. Furthermore, the key demographic parameters, including r, λ, R0, and RPd, showed a significant decrease, while the total pre-reproductive period (TPRP) experienced a significant increase in the F1 generation. Collectively, our findings indicate that sublethal concentrations of flonicamid impact the demographic parameters of A. gossypii, resulting in suppression of population growth. This study presents comprehensive information on the overall impact of flonicamid on A. gossypii, which could potentially aid in managing this major pest. [ABSTRACT FROM AUTHOR]

This paper reviews and introduces innovative research pertaining to the age-stage, two-sex life table. The main topics discussed are: (1) Analysis of data involving group-reared life table studies. We address the rationale behind the data analysis used when constructing a group-reared life table. Proper analysis of grouped-reared life table data enables the collection of realistic and applicable data for ecological studies, devising efficient mass-rearing programs and formulating pest management routines using time- and labor-saving group-rearing methods. (2) The bootstrap-match technique. This novel technique is applicable to those instances when constructing a complete life table involves collecting the immature independently from the adult data. (3) Application of the set theory in life table research. This procedure enables a mathematical description of the population structure and bootstrap samples. (4) Application of the multinomial theorem. Using the multinomial theorem enables calculation of the exact probability of bootstrap samples. (5) Inclusion of infertile bootstrap samples. Because it is impossible to calculate the intrinsic rates of increase for infertile samples, they are normally omitted in life table analysis. Inclusion of these infertile bootstrap samples produces an unbiased life table analysis. (6) The Cartesian product. The Cartesian product of two sets produces the complete coverage of all possible differences. We compared the paired bootstrap test, the Cartesian paired test based on bootstrap results, and the Cartesian paired test based on the multinomial theorem. (7) Integration of life table data with predation data. This procedure, which is especially relevant to biological control programs, enables a comprehensive study of the predator-prey relationship. (8) Computer simulation based on life tables. Population projection based on the age-stage, two-sex life table not only provides the means to predict the dynamics of stage structures of a given pest population, but also provides an insight into the dynamics of predation capacity of the predator population. (9) Problems in life table research. Each of the subjects discussed is crucial for the theoretical advancement and practical applications of scientific demographic research. [ABSTRACT FROM AUTHOR]

Many publications lack sufficient background information (e.g. location) to be interpreted, replicated, or reused for synthesis. This impedes scientific progress and the application of science to practice. Reporting guidelines (e.g. checklists) improve reporting standards. They have been widely taken up in the medical sciences, but not in ecological and agricultural research. Here, we use a community-centred approach to develop a reporting checklist (AgroEcoList 1.0) through surveys and workshops with 23 experts and the wider agroecological community. To put AgroEcoList in context, we also assessed the agroecological community's perception of reporting standards in agroecology. A total of 345 researchers, reviewers, and editors, responded to our survey. Although only 32% of respondents had prior knowledge of reporting guidelines, 76% of those that had said guidelines improved reporting standards. Overall, respondents agreed on the need of AgroEcolist 1.0; only 24% of respondents had used reporting guidelines before, but 78% indicated they would use AgroEcoList 1.0. We updated AgroecoList 1.0 based on respondents' feedback and user-testing. AgroecoList 1.0 consists of 42 variables in seven groups: experimental/sampling set-up, study site, soil, livestock management, crop and grassland management, outputs, and finances. It is presented here, and is also available on github (https://github.com/AgroecoList/Agroecolist). AgroEcoList 1.0 can serve as a guide for authors, reviewers, and editors to improve reporting standards in agricultural ecology. Our community-centred approach is a replicable method that could be adapted to develop reporting checklists in other fields. Reporting guidelines such as AgroEcoList can improve reporting standards and therefore the application of research to practice, and we recommend that they are adopted more widely in agriculture and ecology. [ABSTRACT FROM AUTHOR]

Methyl benzoate (MBe), a volatile organic molecule, has been shown to have insecticidal effects on a variety of agricultural, stored products, and urban arthropod pests in recent investigations. However, the toxicity of MBe against nontarget organisms has rarely been investigated. This study investigated the lethal and sublethal effects of MBe on the generalist predator Orius laevigatus (Fieber) (Hemiptera: Anthocoridae) via different exposure routes. This species is an important natural enemy of thrips, aphids, and mites in biological control programs globally. Acute toxicity bioassays conducted on O. laevigatus showed that the lethal median concentration (LC50) values of MBe for topical and residual toxicity were 0.73 and 0.94%, respectively, after 24 hr of exposure. Importantly, a sublethal concentration of MBe (LC30 = 0.51%) did not affect the survival and reproduction of O. laevigatus. In addition, prey consumption by O. laevigatus under different exposure conditions with varying densities of Aphis gossypii (Glover) (Hemiptera: Aphididae) adults demonstrated a good fit for a Type II functional response. The sublethal concentration of MBe did not affect the attack rate and handling time of O. laevigatus compared to untreated insects, nor did it affect the longevity and fecundity of O. laevigatus females. Thus, according to the International Organization for Biological Control, the sublethal MBe concentration for O. laevigatus is categorized as harmless and may be used in conjunction with this predator species for integrated control of many agricultural insect pests. Graphical Abstract [ABSTRACT FROM AUTHOR]

Short note on TWOSEX-MSChart: the key tool for life table research and education. [ABSTRACT FROM AUTHOR]

The bootstrap technique has been widely used to estimate the variances, standard errors, and confidence intervals (CI) of life table parameters, while the paired bootstrap test has been used to compare life table parameters between treatments by assessing the CI of differences. Although a great number of resamplings (B = 1,000 ~ 100,000) has been suggested for the application of the bootstrap technique, each computer simulation will generate different results because the bootstrap sampling with replacement is based on a stochastic process. In order to determine the theoretical and true confidence intervals of population parameters, and thereby, achieve an accurate assessment of differences between treatments, we introduce an innovative application of set theory, Cartesian product, and multinomial theorem for a mathematical formulation of demographic analysis. Moreover, when a bootstrap sample is composed of individuals that cannot produce offspring (i.e., an infertile bootstrap sample), the intrinsic rate of increase (r) and finite rate of increase (?) cannot be calculated. Omitting these infertile bootstrap samples will result in biased estimates. This problem of infertile bootstrap samples in demographic research has not been resolved. The integrated application of the set theory, Cartesian products, and multinomial theorem enables the detection of all possible combinations of bootstrap samples, the true CIs of population parameters, and the CIs of differences between treatments; furthermore, the probabilities of both fertile and infertile bootstrap samples can also be calculated. The life table data of the well-known cosmopolitan pest, Myzus persicae (Sulzer) (Hemiptera: Aphididae), were collected and used as examples. [ABSTRACT FROM AUTHOR]

Frankliniella intonsa (Trybom) (Thysanoptera: Thripidae) is an important pest of numerous horticultural and agricultural crops in Taiwan. Orius strigicollis (Poppius) (Hemiptera: Anthocoridae) is a predator with high predation capacity against many pests of legumes and flowers. We used the age-stage, two-sex life table method to integrate the life table data with the predation rate of O. strigicollis fed on F. intonsa. The preadult duration, adult longevity, net reproductive rate, intrinsic rate of increase, and finite rate of increase for O. strigicollis were 13.6 d, 12.5 d, 18.8 offspring/individual, 0.1437 d-1, and 1.1546 d-1, respectively. The total predation of O. strigicollis during their preadult and adult stages was 60.4 and 107.3 thrips, respectively. The net predation rate was 101 prey/individual. To demonstrate the effect of releasing predators of different stages on the population growth and predation capacity, we used population projection to evaluate the predation potential of O. strigicollis, and the uncertainty of predation potential was determined by using the life tables from the 0.025th and 0.975th bootstrap percentiles of the finite rate of increase. Releasing third instars or adults of O. strigicollis can effectively control the pest sooner than releasing O. strigicollis eggs. In biological control, both predator and prey populations are age-stage-structured and (in most instances) individuals of both sexes are present. It is imperative that the agestage, two-sex life table be used to precisely incorporate the variability that occurs in the developmental rate, stage differentiation, survival rates, and predation rates among individuals and between sexes. Our results demonstrate that integrating life table and predation rate data generated by using the age-stage, two-sex life table is an important technique for improving biological control programs by refining the timing and estimating the release of natural enemies. Moreover, by using the multinomial theorem, we demonstrated that a large resampling (B =100,000) is necessary to obtain more precise estimates of population parameters in applications of the bootstrap technique. [ABSTRACT FROM AUTHOR]