Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo
Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the FIS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.
Soara et al. (2022) Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo. PeerJ 10:e12637 https://doi.org/10.7717/peerj.12637
Galapagos land iguanas as ecosystem engineers
Background Declines of large-bodied herbivorous reptiles are well documented, but the consequences for ecosystem function are not. Understanding how large-bodied herbivorous reptiles engineer ecosystems is relevant given the current interest in restoration of tropical islands where extinction rates are disproportionately high and reptiles are prominent as herbivores. Methods In this study, we measured the ecosystem-level outcomes of long-term quasi-experiment represented by two adjacent islands within the Galapagos Archipelago, one with and the other without Galapagos land iguanas (Conolophus subcristatus), large-bodied herbivores known to feed on many plant species. We characterized plant communities on each island by developing high-resolution (<1 cm2) aerial imagery and delineating extent of plant associations and counting individual plants on each. Results In the presence of iguanas there was dramatically less woody plant cover, more area with seasonal grasses, and many fewer cacti. Cacti had a more clumped distribution where iguanas were absent than where iguanas were present. Discussion This study provided strong evidence that Galapagos land iguanas can substantially engineer the structure of terrestrial plant communities; therefore, restoration of large-bodied reptilian herbivores, such as land iguanas and giant tortoises, should be regarded as an important component of overall ecosystem restoration, especially for tropical islands from which they have been extirpated.
Tapia et al. (2022) Galapagos land iguanas as ecosystem engineers. PeerJ 10:e12711 https://doi.org/10.7717/peerj.12711
Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems
Ecosystem Design (ED) is an approach for constructing habitats that places human needs for ecosystem services at the center of intervention, with the overarching goal of establishing self-sustaining habitats which require limited management. This concept was originally developed for use in mangrove ecosystems, and is understandably controversial, as it markedly diverges from other protection approaches that assign human use a minor priority or exclude it. However, the advantage of ED lies within the considered implementation of these designed ecosystems, thus preserving human benefits from potential later disturbances. Here, we outline the concept of ED in tropical carbonate depositional systems and discuss potential applications to aid ecosystem services such as beach nourishment and protection of coastlines and reef islands at risk from environmental and climate change, CO2 sequestration, food production, and tourism. Biological carbonate sediment production is a crucial source of stability of reef islands and reef-rimmed coastlines. Careful implementation of designed carbonate depositional ecosystems could help counterbalance sea-level rise and manage documented erosion effects of coastal constructions. Importantly, adhering to the core ethos of ED, careful dynamic assessments which provide a balanced approach to maximizing ecosystem services (e.g., carbonate production), should identify and avoid any potential damages to existing functioning ecosystems.
Westphal et al. (2022) Ecosystem design as an avenue for improving services provided by carbonate producing marine ecosystems. PeerJ 10:e12785 https://doi.org/10.7717/peerj.12785
Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?
As linear mixed-effects models (LMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of the grouping variable associated with a random effect. Having so few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one’s ability to estimate fixed effects terms—which are often of primary interest in ecology. Here, I simulate datasets and fit simple models to show that having few random effects levels does not strongly influence the parameter estimates or uncertainty around those estimates for fixed effects terms—at least in the case presented here. Instead, the coverage probability of fixed effects estimates is sample size dependent. LMMs including low-level random effects terms may come at the expense of increased singular fits, but this did not appear to influence coverage probability or RMSE, except in low sample size (N = 30) scenarios. Thus, it may be acceptable to use fewer than five levels of random effects if one is not interested in making inferences about the random effects terms (i.e. when they are ‘nuisance’ parameters used to group non-independent data), but further work is needed to explore alternative scenarios. Given the widespread accessibility of LMMs in ecology and evolution, future simulation studies and further assessments of these statistical methods are necessary to understand the consequences both of violating and of routinely following simple guidelines.
Gomes (2022) Should I use fixed effects or random effects when I have fewer than five levels of a grouping factor in a mixed-effects model?. PeerJ 10:e12794 https://doi.org/10.7717/peerj.12794
Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean
Background Strigolactones (SLs) play a key role in modulating plant root growth, shoot branching, and plant-symbiont interaction. However, despite their significance, the components of SL biosynthesis and signaling in soybean and their role in soybean-rhizobia interaction is unknown. Methods In this study, we identified and functionally characterized the GmD53a from soybean. The GmD53a ORFs were amplified from root cDNA using primers for GmD53a RNA interference. To induce transgenic hairy roots of soybean, electric shock was used to transform pB7WG1WG2 vectors containing GmD53a knockdown and GUS into K599 strains of Agrobacterium rhizogenes. The hairy roots and nodules were collected and examined for root nodules ratio and RNA was extracted after 4 weeks of rhizobia inoculation. Results A tissue-specific expression assay showed that GmD53a was differentially expressed in plant parts, predominantly in the stem and nodule. Furthermore, its expression was significantly up-regulated during rhizobia infection and varied with nodule formation. The GmD53a-knockdown chimerical plants were produced to further check its role in soybean nodulation in comparison with control GUS. In knockdown lines, the GmD53a (suppressor of strigolactone MAX2) has a higher number of nodules compared to control lines. Furthermore, the expression levels of several nodulation genes essential for initiation and formation of nodules were altered in GmD53a-knockdown lines. Conclusion The results revealed that SL biosynthesis and signaling are not conserved but also have close interaction between SL and legume rhizobia.
Rehman et al. (2022) Knockdown of GmD53a confers strigolactones mediated rhizobia interaction and promotes nodulation in soybean. PeerJ 10:e12815 https://doi.org/10.7717/peerj.12815
Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants
Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
Shu et al. (2022) Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C4 and crassulacean acid metabolism plants. PeerJ 10:e12828 https://doi.org/10.7717/peerj.12828
Fast, low-memory detection and localization of large, polymorphic inversions from SNPs
Background Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. Methods We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. Results When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. Conclusion With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
Nowling et al. (2022) Fast, low-memory detection and localization of large, polymorphic inversions from SNPs. PeerJ 10:e12831 https://doi.org/10.7717/peerj.12831
Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills
Background Attention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder affecting numerous executive functioning skills, such as organizational skills. While the relationship between the inattention aspect of ADHD and poor organizational skills is well documented, it is still unclear if lower organizational skills are only associated with ADHD or if they are also associated with other comorbid disorders commonly diagnosed in conjunction with ADHD. The purpose of the present study is to investigate the relationship between organizational skills and ADHD in adults, as well as the impact of comorbid disorders on ADHD in relation to organizational skills. Methods Four hundred seven (n = 201 with a diagnosis of ADHD) adults from the general population were recruited online. Participants completed a measure of organizational skills, measures assessing levels of ADHD, depression, and anxiety, and extensive demographic information related to their diagnosis of ADHD or other possible diagnosis. Results Participants with a diagnosis of ADHD were significantly more likely to have a comorbid diagnosis of depression and/or anxiety. Organizational skills were significantly lower in individuals who reported having received a diagnosis of ADHD, but not in those with a past diagnosis of depression and anxiety. However, organizational skills were lower in individuals currently experiencing higher levels of depression and anxiety. The results of regression analyses suggest that levels of organizational skills are most strongly predicted by inattention and more weakly predicted by comorbid disorders. Discussion These results highlight the centrality of organizational skills deficit in ADHD as well as the influence of the inattention component over other components commonly observed in ADHD on organizational skills. Suggestions for treatment of ADHD in adults are discussed.
Durand et al. (2022) Exploring the relationship between ADHD, its common comorbidities, and their relationship to organizational skills. PeerJ 10:e12836 https://doi.org/10.7717/peerj.12836
Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups
Fire and herbivores are two important drivers of changes in vegetation composition, quality and dynamics and both are highly related to each other. Herbivores are known to respond to fire both in terms of foraging decisions and distribution. However, little is known about the actual changes in plant chemistry following a fire event and how long these changes will last. We investigated the effect of fire on two different plant functional groups (grasses and woody species) in a woodland savanna of southern Africa. We studied chemical compounds known to be important for palatability of five perennial grass and seven woody species (trees and shrubs) common in the woodland savanna and known to be utilized by herbivores. We wanted to know if plant chemistry differs between a recently burned site (burned 2 years ago) and a control site, burned 16 years ago, and if grasses and woody species show similar relative differences between sites (i.e., the plants’ response to fire). We found a clear difference in chemical composition patterns between the plant functional groups, with an almost homogenous response to fire among woody species, but higher variability in response among grass species. Furthermore, we found that woody species maintained a higher nutritional value even 2 years after burning, whereas grasses did not show clear differences among the two investigated sites. Hence, few years after burning, woody plants might still serve as an attraction for herbivores, especially browsers, in contrast to grasses. The knowledge about these differences between the two functional groups in response to fire is beneficial for the development of management strategies for large herbivores whether domestic or wild.
Stolter et al. (2022) Effect of fire on the palatability of plants in an African woodland savanna: varying impacts depending on plant functional groups. PeerJ 10:e12721 https://doi.org/10.7717/peerj.12721
Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods
Background Many coral reefs worldwide are experiencing declines in hard corals, resulting in other benthic organisms, e.g., soft corals, becoming more dominant. As such, more studies on the ecophysiology of soft corals are needed. Despite many methods for asexual reproduction of hard corals, effective methods for soft corals, i.e., without a hard skeleton, are scarce. This study, thus, assessed four fragmentation methods, the glue, rubber band, tunnel mesh, and plug mesh method for the pulsating soft coral Xenia umbellata that is widely distributed in the tropical Indo-Pacific. Methods Methods were comparatively assessed by determining the required time and labor for the fragmentation plus the health status of the fragmented corals by measuring their oxygen fluxes and pulsation rates, i.e., a special feature of this soft coral that can be used as a proxy for its health. Results There were no significant health status differences between methods. This was indicated by similar gross photosynthesis (between 7.4 to 9.7 μg O2 polyp−1 h−1) and pulsating rates (between 35 and 44 pulses min−1) among methods. In terms of time/labor intensity and success rates, i.e., the percentage of fragments attached to the desired surface, the plug mesh method was the most efficient method with a significantly higher success rate (95 ± 5%), while the others had a success rate between 5 ± 5 and 45 ± 15%. The time needed for fragmentation, though not significant, was also the shortest (78 ± 11 s fragment−1), while other methods required between 84 ± 14 and 126 ± 8 s frag−1. The plug mesh method may thus be a valuable tool related to the reproduction of soft corals for use in subsequent experimental work.
Kim et al. (2022) Effective asexual reproduction of a widespread soft coral: comparative assessment of four different fragmentation methods. PeerJ 10:e12589 https://doi.org/10.7717/peerj.12589