Evaluation of Effects of Harvest on Alligator Populations in Louisiana

Biologists with the Louisiana Department of Wildlife and Fisheries, Louisiana, USA, have managed statewide annual harvest of alligators (Alligator mississippiensis) for 35 years (1981–present). We collected and analyzed harvest data for Louisiana alligators to determine the effects of harvest on the population structure, focusing on the larger size classes (≥274 cm) of this slow-growing species. Linear regression analyses revealed that body size-class structure, based on overall average size and the percentage of animals harvested in the larger size classes was relatively stable. Annual aerial alligator nest counts indicated a continual growth of the population, and over time harvested alligators maintained a constant average size. Analyses of population size (based on number of nests and population modeling) indicated that the current annual harvest represents approximately 3% of the population. Linear regression analysis showed that annual hunter success declined only slightly during the study period, and the scheduling of the hunt season after the hatch period and recommended hunting in areas not frequented by breeding females provides economic opportunities for hunters to participate in a sustainable harvest that preserves the larger size classes of alligators in the population. Strict enforcement of existing laws was a key factor responsible for the success of this harvest program. Comparison of alligator population size and number of harvest-related citations indicated that illegal harvest did not have a negative effect on population size, and linear regression analyses revealed that the rate of increase in citations was lower than the increase in populations over the study period. The results of this harvest program indicated that alligators can be hunted in a sustainable manner if hunting is conducted after the hatch period and occurs in areas that primarily exclude the harvest of adult females, and strict law enforcement curbs illegal activities that negatively affect populations. © 2021 The Authors. The Journal of Wildlife Management published by Wiley Periodicals LLC on behalf of The Wildlife Society.     

Symbiosis of cornulitids with the cystoporate bryozoan Fistulipora in the Pridoli of Saaremaa,Estonia

Cornulites sp. and Fistulipora przhidolensis formed a symbiotic association in the Pridoli (latest Silurian) of Saaremaa Island, Estonia. This Cornulites sp.–F. przhidolensis association is the youngest example of cornulitid–bryozoan symbiosis. Symbiosis is indicated by intergrowth of both organisms. The cornulitids are completely embedded within the cystoporate bryozoan colony, leaving only their apertures free on the growth surface of bryozoan. In terms of food competition, this association could have been slightly harmful to F. przhidolensis as Cornulites sp. may have been a kleptoparasite. There may have been a small escalation in the evolution of the endobiotic life mode of cornulitids as the number of such associations increased from the Ordovician to Silurian. It is likely that Palaeozoic bryozoan symbiosis reached its maximum in the Late Ordovician. Most of the symbiotic bryozoans in the Palaeozoic are trepostomes, and the diversity of symbiotic associations was also greatest among trepostomes.     

Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene

Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs.To determine the variants of SARS-CoV-2 circulating in the state of Nevada,specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform,which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads,without the need of culture-based amplification.High genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the outbreak.We report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine(F) from proline (P),in the first reported isolate of SARS-CoV-2,Wuhan-Hu-1.This 323F variant was present at a very high frequency in Northern Nevada.Structural modeling determined this mutation in the interface domain,which is important for the association of accessory proteins required for the polymerase.In conclusion,we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations,which is important for understanding the evolution and circulation of SARS-CoV-2variants of public health importance,while it circulates in humans.     

lra: A long read aligner for sequences and contigs

It is computationally challenging to detect variation by aligning single-molecule sequencing (SMS) reads, or contigs from SMS assemblies. One approach to efficiently align SMS reads is sparse dynamic programming (SDP), where optimal chains of exact matches are found between the sequence and the genome. While straightforward implementations of SDP penalize gaps with a cost that is a linear function of gap length, biological variation is more accurately represented when gap cost is a concave function of gap length. We have developed a method, lra, that uses SDP with a concave-cost gap penalty, and used lra to align long-read sequences from PacBio and Oxford Nanopore (ONT) instruments as well as de novo assembly contigs. This alignment approach increases sensitivity and specificity for SV discovery, particularly for variants above 1kb and when discovering variation from ONT reads, while having runtime that are comparable (1.05-3.76×) to current methods. When applied to calling variation from de novo assembly contigs, there is a 3.2% increase in Truvari F1 score compared to minimap2+htsbox. lra is available in bioconda (https://anaconda.org/bioconda/lra) and github (https://github.com/ChaissonLab/LRA).     

Correction to: Sex and race differences of cerebrospinal fluid metabolites in healthy individuals

Metabolomics - Metabolomics applications to the aquaculture research are increasing steadily. The use of standardized proton nuclear magnetic resonance (1H NMR) spectroscopy can provide the...     

Lichenochemical Screening and Antioxidant Capacity of Four Tunisian Lichen Species

The phenolic composition and antioxidant capacity of four Tunisian lichen species, Cladonia rangiformis, Flavoparmelia caperata, Squamarina cartilaginea and Xanthoria parietina, were determined in order to provide a better understanding of their lichenochemical composition. Powdered material of F. caperata was the richest in total phenolic content (956.68 μg GAE g⁻¹ DW) and S. cartilaginea in proanthocyanidin content (77.31 μg CE g⁻¹ DW), while the acetone extract of X. parietina showed the highest flavonoid content (9.56 μg CE g⁻¹ DW). The antioxidant capacity of all lichen extracts and crude material was evaluated by DPPH^. scavenging, iron-chelating, and iron-reducing powers. Results showed that methanol extracts of S. cartilaginea had the highest DPPH^. antioxidant capacity (IC₅₀=0.9 μg mL⁻¹) and the highest iron-reducing power was attributed to the acetone extract of this species. All extracts of all species were further screened by Fourier-transform infrared spectroscopy (FT-IR) and nuclear resonance spectroscopy (NMR); results showed an abundance of phenols, aromatic compounds, and fatty acids. Overall, our results showed that the investigated species are a rich source of potentially bioactive compounds with valuable properties.     

Specialized soil types affect host acceptability and performance of weed biocontrol candidates: implications for host specificity assessments

The Eurasian gall-forming weevil Ceutorhynchus cardariae Korotyeav (Coleoptera: Curculionidae) is a biological control candidate for the invasive Eurasian Lepidium draba L. (Brassicaceae) in the western USA. Among 157 nontarget plant species that have been tested, some North American Caulanthus and Streptanthus species, confamilial with Lepidium, were found to be at potential risk of attack by C. cardariae. Many Caulanthus and Streptanthus species grow on serpentine soils, which are characterized by low nutrient content and high concentrations of various combinations of heavy metals. Some of these species accumulate heavy metals, which have been shown to act as deterrents against insect herbivory. Standard pre-release host specificity tests with C. cardariae used plants propagated on horticultural soils, which could have inflated performance by C. cardariae on Caulanthus and Streptanthus species. To examine this possibility, we assessed the performance of C. cardariae on three Caulanthus species, the federally listed threatened and endangered Streptanthus glandulosus ssp. albidus, and Lepidium draba, on plants propagated in horticultural soil or in native serpentine soil. Our study showed that native serpentine soil influenced C. cardariae attack. All plant species, including L. draba, received less feeding damage and gall formation when grown in serpentine soil. In addition, feeding by C. cardariae was much less and fewer galls were formed on the confamilial species than on L. draba, regardless of soil type. Our data show that native confamilial species restricted to specialized soil types may be at less risk of herbivore attack than predicted based on tests conducted in horticultural soil.

     

Lake morphometry determines Dreissena invasion dynamics

Predicting the ecosystem effects of invasive species and the best control strategies requires understanding population dynamics and population regulation. Invasive bivalves zebra and quagga mussels (Dreissena spp.) are considered the most aggressive invaders in freshwaters and have become major drivers of ecosystem processes in the Laurentian Great Lakes. Combining all lake-wide studies of Dreissena spp. conducted in the Great Lakes, we found that invasion dynamics are largely governed by lake morphometry. Where both species are present, quagga mussels generally become dominant in 8–13 years. Thereafter, zebra mussels remain common in shallow lakes and embayments and lake-wide Dreissena density may remain similar, while in deep lakes quagga led to a near-complete displacement of zebra mussels and an ensuing dramatic increase in overall dreissenid density. In deep lakes, overall Dreissena biomass peaked later and achieved?~?threefold higher levels than in shallow lakes. Comparison with 21 waterbodies in North America and Europe colonized by both dreissenids confirmed that patterns of invasion dynamics found in the Great Lakes are very consistent with other waterbodies, and thus can be generalized to other lakes. Our biophysical model predicted that the long-term reduction in primary producers by mussel grazing may be fourfold less in deep compared to shallow lakes due to thermal stratification and a smaller proportion of the epilimnion in contact with the bottom. While this impact remains greatest in shallow areas, we show that when lakes are vertically well-mixed, dreissenid grazing impact may be greatest offshore, revealing a potentially strong offshore carbon and phosphorus sink.

     

Aquatic models of human ciliary diseases

Cilia are microtubule‐based structures that either transmit information into the cell or move fluid outside of the cell. There are many human diseases that arise from malfunctioning cilia. Although mammalian models provide vital insights into the underlying pathology of these diseases, aquatic organisms such as Xenopus and zebrafish provide valuable tools to help screen and dissect out the underlying causes of these diseases. In this review we focus on recent studies that identify or describe different types of human ciliopathies and outline how aquatic organisms have aided our understanding of these diseases.     

Punishment is strongly motivated by revenge and weakly motivated by inequity aversion

There are two broad functional explanations for second-party punishment: fitness-leveling and deterrence. The former suggests that people punish to reduce fitness differences, while the latter suggests that people punish in order to reciprocate losses and deter others from inflicting losses on them in the future. We explore the relative roles of these motivations using a pre-registered, two-player experiment with 2426 US participants from Amazon Mechanical Turk. Participants played as the “responder” and were assigned to either a Take or Augment condition. In the Take condition, the “partner” could steal money from the responder's bonus or do nothing. In the Augment condition, the partner could augment the responder's bonus by giving them money at no cost to themselves or do nothing. We also manipulated the responders' starting endowments, such that after the partner's decision, responders experienced different payoff outcomes: advantageous inequity, equality, or varying degrees of disadvantageous inequity. Responders then decided whether to pay a cost to punish the partner. Punishment was clearly influenced by theft and was most frequent when theft resulted in disadvantageous inequity. However, people also punished in the absence of theft, particularly when confronted with disadvantageous inequity. While the effect of inequity on punishment was small, our results suggest that punishment is motivated by more than just the desire to reciprocate losses. These findings highlight the multiple motivations undergirding punishment and bear directly on functional explanations for the existence of punishment in human societies.