Evidence of a highly divergent novel parvovirus in Australia's critically endangered western ground parrot/kyloring (Pezoporus flaviventris).

Detecting pathogens in endangered animal populations is vital for understanding and mitigating threats to their survival. The critically endangered western ground parrot (Pezoporus flaviventris, WGP), with a population as low as 150 individuals in Australia, faces an imminent risk of extinction. Despite this urgency, research on viral pathogens in this species remains limited. This study aimed to identify and characterise viruses present in faecal samples from seven individual WGP using a viral metagenomic approach. Analysis of the sequenced datasets revealed the presence of a novel virus belonging to the Parvoviridae family, named psittaciform chaphamaparvovirus 7 (PsChPV-7). The genome of PsChPV-7 contains typical structural and functional gene sequences found in Parvoviridae but is highly divergent, indicating its classification as a distinct species. Phylogenetic analysis placed PsChPV-7 within a unique sub-clade of the Chaphamaparvovirus genus, suggesting its evolutionary significance as an ancient lineage within this group. These findings may contribute to the development of strategic management and biosecurity plans aimed at conserving this endangered WGP.

Variation in air sac morphology and postcranial skeletal pneumatization patterns in the African grey parrot.

The anatomy of the avian lower respiratory system includes a complex interaction between air-filled pulmonary tissues, pulmonary air sacs, and much of the postcranial skeleton. Hypotheses related to the function and phylogenetic provenance of these respiratory structures have been posed based on extensive interspecific descriptions for an array of taxa. By contrast, intraspecific descriptions of anatomical variation for these features are much more limited, particularly for skeletal pneumatization, and are essential to establish a baseline for evaluating interspecific variation. To address this issue, we collected micro-computed tomography (µCT) scans of live and deceased African grey parrots (Psittacus erithacus) to assess variation in the arrangement of the lungs, the air sacs, and their respective invasion of the postcranial skeleton via pneumatic foramina. Analysis reveals that the two pairs of caudalmost air sacs vary in size and arrangement, often exhibiting an asymmetric morphology. Further, locations of the pneumatic foramina are more variable for midline, non-costal skeletal elements when compared to other pneumatized bones. These findings indicate a need to better understand contributing factors to variation in avian postcranial respiratory anatomy that can inform future intraspecific and interspecific comparisons.

Research Note: Development of a reverse transcriptase recombinase-aided amplification method for detection of Parrot Borna Virus 4.

The Parrot Borna virus 4 (PaBV-4) is the primary causative agent of parrot developmental disorder (PDD), leading to symptoms such as bloating, undigested feed in stool, decreased appetite, diarrhea, and weight loss. Its impact on the parrot industry has been significant, therefore, it is imperative to develop a rapid detection method for PaBV-4. The detection of PaBV-4 was achieved through the development of an RT-RAA assay, which involved the design of specific probes and primers targeting the N gene. This method allows for detection at 41°C within 30 min and has a minimum detection threshold of 8.56 × 101 copies/µL. The RT-RAA method demonstrated specific detection of PaBV-4 without any cross-reactivity observed with H5N6, H7N9, H9N2 avian influenza virus, newcastle disease virus (NDV), avian infectious bronchitis virus (IBV) and Parrot Borna virus 2 (PaBV-2). The coefficient of variation for the 3 repeatability experiments was below 10%. Tissue samples from 28 suspected cases of PaBV related deaths in parrots were analyzed using both RT-RAA and RT-qPCR methods. The sensitivity and specificity of both methods were 100%, demonstrating perfect agreement between them as indicated by a kappa value of 1. In conclusion, this study created a RT-RAA method for PaBV-4 detection successfully.

Variation in Plumage Coloration of Rosy-Faced Lovebirds (Agapornis roseicollis): Links to Sex, Age, Nutritional Condition, Viral Infection, and Habitat Urbanization.

Expression of vibrant plumage color plays important communication roles in many avian clades, ranging from penguins to passerines, but comparatively less is known about color signals in parrots (order Psittaciformes). We measured variation in coloration from three plumage patches (red face, blue rump, red tail) in an introduced population of rosy-faced lovebirds (Agapornis roseicollis) in Phoenix, Arizona, USA and examined color differences between the sexes and ages as well as relationships with several indices of quality, including disease presence/absence (infection with beak and feather disease, Circovirus parrot, and a polyomavirus, Gammapolyomavirus avis), nutritional state (e.g., blood glucose and ketone levels), and habitat type from which birds were captured. We found that different plumage colors were linked to different quality indices: (a) adults had redder faces than juveniles, and birds with brighter faces had lower glucose levels and were less likely to have polyomavirus; (b) males had bluer rumps than females; and (c) birds caught farther from the city had redder and darker tail feathers than those caught closer to the urban center. Our findings reveal diverse information underlying variation in the expression of these disparate, ornate feather traits in an introduced parrot species, and suggest that these condition-dependent and/or sexually dichromatic features may serve important intraspecific signaling roles (i.e., mediating rival competitions or mate choices).

Distribution of lesions in psittacine birds naturally infected with parrot bornavirus in Japan.

Mononuclear cell infiltration of the central nervous system and ganglioneuritis are characteristic histopathological findings of proventricular dilatation disease (PDD) caused by parrot bornavirus (PaBV) infection. The purpose of this study was to clarify the link between the degree of inflammatory lesions and the distribution of the virus antigen in naturally PaBV-infected parrots. Pathological examination was performed on 18 PaBV-infected birds identified by reverse transcriptase-PCR. Dilatation of the crop, proventriculus, and ventriculus was observed in all 18 (100%) birds, and dilation of the right ventricle of the heart was observed in 14/18 (78%) birds. Cases were classified based on the scores for the distribution and degree of histological lesions into neural type, with severe brain lesions, digestive type, with severe gastric lesions, or nervous/digestive type, with severe lesions in both the brain and ventriculus. The PaBV immunohistological score correlated with the inflammatory lesion scores. Ganglioneuritis, myocarditis, and myocardial degeneration were frequently observed in the heart. Interestingly, macroscopic and microscopic lesions and virus antigen were detected in the hearts of all three histological types. The present study showed that parrots naturally infected with PaBVs can be grouped into three types based on the lesion distribution, and heart failure is an important symptom in PaBV-infected parrots.

Detection of Anxiety-Based Epileptic Seizures in EEG Signals Using Fuzzy Features and Parrot Optimization-Tuned LSTM.

In humans, epilepsy is diagnosed through electroencephalography (EEG) signals. Epileptic seizures (ESs) arise due to anxiety. The detection of anxiety-based seizures is challenging for radiologists, and there is a limited availability of anxiety-based EEG signals. Data augmentation methods are required to increase the number of novel samples. An epileptic seizure arises due to anxiety, which manifests as variations in EEG signal patterns consisting of changes in the size and shape of the signal. In this study, anxiety EEG signals were synthesized by applying data augmentation methods such as random data augmentation (RDA) to existing epileptic seizure signals from the Bonn EEG dataset. The data-augmented anxiety seizure signals were processed using three algorithms-(i) fuzzy C-means-particle swarm optimization-long short-term memory (FCM-PS-LSTM), (ii) particle swarm optimization-long short-term memory (PS-LSTM), and (iii) parrot optimization LSTM (PO-LSTM)-for the detection of anxiety ESs via EEG signals. The predicted accuracies of detecting ESs through EEG signals using the proposed algorithms-namely, (i) FCM-PS-LSTM, (ii) PS-LSTM, and (iii) PO-LSTM-were about 98%, 98.5%, and 96%, respectively.

An efficient improved parrot optimizer for bladder cancer classification.

Bladder Cancer (BC) is a common disease that comes with a high risk of morbidity, death, and expense. Primary risk factors for BC include exposure to carcinogens in the workplace or the environment, particularly tobacco. There are several difficulties, such as the requirement for a qualified expert in BC classification. The Parrot Optimizer (PO), is an optimization method inspired by key behaviors observed in trained Pyrrhura Molinae parrots, but the PO algorithm becomes stuck in sub-regions, has less accuracy, and a high error rate. So, an Improved variant of the PO (IPO) algorithm was developed using a combination of two strategies: (1) Mirror Reflection Learning (MRL) and (2) Bernoulli Maps (BMs). Both strategies improve optimization performance by avoiding local optimums and striking a compromise between convergence speed and solution diversity. The performance of the proposed IPO is evaluated against eight other competitor algorithms in terms of statistical convergence and other metrics according to Friedman's test and Bonferroni-Dunn test on the IEEE Congress on Evolutionary Computation conducted in 2022 (CEC 2022) test suite functions and nine BC datasets from official repositories. The IPO algorithm ranked number one in best fitness and is more optimal than the other eight MH algorithms for CEC 2022 functions. The proposed IPO algorithm was integrated with the Support Vector Machine (SVM) classifier termed (IPO-SVM) approach for bladder cancer classification purposes. Nine BC datasets were then used to confirm the effectiveness of the proposed IPO algorithm. The experiments show that the IPO-SVM approach outperforms eight recently proposed MH algorithms. Using the nine BC datasets, IPO-SVM achieved an Accuracy (ACC) of 84.11%, Sensitivity (SE) of 98.10%, Precision (PPV) of 95.59%, Specificity (SP) of 95.98%, and F-score (F1) of 94.15%. This demonstrates how the proposed IPO approach can help to classify BCs effectively. The open-source codes are available at https://www.mathworks.com/matlabcentral/fileexchange/169846-an-efficient-improved-parrot-optimizer.

Visitation patterns of endangered grey parrots (Psittacus erithacus) in a forest clearing in the Democratic Republic of the Congo.

The grey parrot (Psittacus erithacus), once abundant, has become increasingly threatened due to the combined effects of capture for the global pet trade and habitat loss. Although grey parrots are well studied in captivity, effective conservation efforts require a better understanding of their ecological requirements in the wild. The aim of this paper is to quantify grey parrot behaviours across the annual cycle. To do that, we studied groups of grey parrots gathering in a natural forest clearing in the Nkuba Conservation Area, eastern Democratic Republic of the Congo. Using parrot counts and focal sampling, combined with descriptive statistics, we found that an average of 40 grey parrots visited the clearing each day, following a regular pattern in which they first perched in the trees surrounding the clearing, vocalizing loudly, until the group landed in the clearing to feed, drink and interact with each other. Generalized linear models (GLMs) and generalized additive models (GAMs) showed that the time at which parrots arrived, landed at, and left clearings was influenced by the weather, seasonality and the month of the year. We also found that parrots shortened their visits when disturbed by predators or the presence of humans. Although the underlying mechanisms for grey parrot visits to forest clearings remains unclear, the consistency of this behaviour observed elsewhere in Africa and the feeding observed in the clearing in this study suggest that these area support important foraging habitat for the wild grey parrots. Therefore, ensuring the availability of such clearings is paramount to the long-term survival of the species. We suggest that future efforts to protect grey parrots in their native habitats focus on identifying clearings visited by parrots, monitoring these clearings and allowing parrots to visit them without disturbance or risk of capture.

Widespread cultural change in declining populations of Amazon parrots.

Species worldwide are experiencing anthropogenic environmental change, and the long-term impacts on animal cultural traditions such as vocal dialects are often unknown. Our prior studies of the yellow-naped amazon (Amazona auropalliata) revealed stable vocal dialects over an 11-year period (1994-2005), with modest shifts in geographic boundaries and acoustic structure of contact calls. Here, we examined whether yellow-naped amazons maintained stable dialects over the subsequent 11-year time span from 2005 to 2016, culminating in 22 years of study. Over this same period, this species suffered a dramatic decrease in population size that prompted two successive uplists in IUCN status, from vulnerable to critically endangered. In this most recent 11-year time span, we found evidence of geographic shifts in call types, manifesting in more bilingual sites and introgression across the formerly distinct North-South acoustic boundary. We also found greater evidence of acoustic drift, in the form of new emerging call types and greater acoustic variation overall. These results suggest cultural traditions such as dialects may change in response to demographic and environmental conditions, with broad implications for threatened species.

Subclinical peripheral inflammation has systemic effects impacting central nervous system proteome in budgerigars.

Regulation of neuroimmune interactions varies across avian species. Little is presently known about the interplay between periphery and central nervous system (CNS) in parrots, birds sensitive to neuroinflammation. Here we investigated the systemic and CNS responses to dextran sulphate sodium (DSS)- and lipopolysaccharide (LPS)-induced subclinical acute peripheral inflammation in budgerigar (Melopsittacus undulatus). Three experimental treatment groups differing in DSS and LPS stimulation were compared to controls. Individuals treated with DSS showed significant histological intestinal damage. Through quantitative proteomics we described changes in plasma (PL) and cerebrospinal fluid (CSF) composition. In total, we identified 180 proteins in PL and 978 proteins in CSF, with moderate co-structure between the proteomes. Between treatments we detected differences in immune, coagulation and metabolic pathways. Proteomic variation was associated with the levels of pro-inflammatory cytokine mRNA expression in intestine and brain. Our findings shed light on systemic impacts of peripheral low-grade inflammation in birds.

Feathered Lectures-Evidence of Perceptual Factors on Social Learning in Kea Parrots (Nestor notabilis).

Social learning describes the acquisition of knowledge through observation of other individuals, and it is fundamental for the development of culture and traditions within human groups. Although previous studies suggest that Kea (Nestor notabilis) benefit from social learning, experimental evidence has been inconclusive, as in a recent two-action task, all perceptual factors were ignored. The present study attempts to address this by investigating social learning in Kea with a focus on social enhancement processes. In an experiment with a captive group of Kea, we investigated whether individuals that had the opportunity to observe a conspecific performing a simple task subsequently show better performance in that task than a control group without prior demonstration. This study provides a strong tendency of greater success in skill acquisition in Kea as a result of social learning. Kea that observed a conspecific solving a task showed clear evidence of perceptual factors drawing attention to the relevant parts of the experimental apparatus and manipulated these significantly more (100% of trials) than control birds (77.8% of trials). Combined with a strong trend (p = 0.056) of the test subjects solving the task more than the control subjects, this shows conclusively that Kea, at least when required to solve a task, do attend to perceptual factors of a demonstrated action.

Comparing the productive vocabularies of grey parrots (Psittacus erithacus) and young children.

Due to their outstanding ability of vocal imitation, parrots are often kept as pets. Research has shown that they do not just repeat human words. They can use words purposefully to label objects, persons, and animals, and they can even use conversational phrases in appropriate contexts. So far, the structure of pet parrots' vocabularies and the difference between them and human vocabulary acquisition has been studied only in one individual. This study quantitatively analyses parrot and child vocabularies in a larger sample using a vocabulary coding method suitable for assessing the vocabulary structure in both species. We have explored the composition of word-like sounds produced by 21 grey parrots (Psittacus erithacus) kept as pets in Czech- or Slovak-speaking homes, and compared it to the composition of early productive vocabularies of 21 children acquiring Czech (aged 8-18 months), who were matched to the parrots by vocabulary size. The results show that the 'vocabularies' of talking grey parrots and children differ: children use significantly more object labels, activity and situation labels, and emotional expressions, while parrots produce significantly more conversational expressions, greetings, and multiword utterances in general. These differences could reflect a strong link between learning spoken words and understanding the underlying concepts, an ability seemingly unique to human children (and absent in parrots), but also different communicative goals of the two species.

Exploration-Based Planning for Multiple-Target Search with Real-Drone Results.

Consider a drone that aims to find an unknown number of static targets at unknown positions as quickly as possible. A multi-target particle filter uses imperfect measurements of the target positions to update an intensity function that represents the expected number of targets. We propose a novel receding-horizon planner that selects the next position of the drone by maximizing an objective that combines exploration and target refinement. Confidently localized targets are saved and removed from consideration along with their future measurements. A controller with an obstacle-avoidance component is used to reach the desired waypoints. We demonstrate the performance of our approach through a series of simulations as well as via a real-robot experiment in which a Parrot Mambo drone searches from a constant altitude for targets located on the floor. Target measurements are obtained on-board the drone using segmentation in the camera image, while planning is done off-board. The sensor model is adapted to the application. Both in the simulations and in the experiments, the novel framework works better than the lawnmower and active-search baselines.

Surveillance of Parrot Bornavirus in Taiwan Captive Psittaciformes.

Parrot bornavirus (PaBV) is an infectious disease linked with proventricular dilatation disease (PDD) with severe digestive and neurological symptoms affecting psittacine birds. Despite its detection in 2008, PaBV prevalence in Taiwan remains unexplored. Taiwan is one of the leading psittacine bird breeders; hence, understanding the distribution of PaBV aids preventive measures in controlling spread, early disease recognition, epidemiology, and transmission dynamics. Here, we aimed to detect the prevalence rate of PaBV and assess its genetic variation in Taiwan. Among 124 psittacine birds tested, fifty-seven were PaBV-positive, a prevalence rate of 45.97%. Most of the PaBV infections were adult psittacine birds, with five birds surviving the infection, resulting in a low survival rate (8.77%). A year of parrot bornavirus surveillance presented a seasonal pattern, with peak PaBV infection rates occurring in the spring season (68%) and the least in the summer season (25%), indicating the occurrence of PaBV infections linked to seasonal factors. Histopathology reveals severe meningoencephalitis in the cerebellum and dilated cardiomyopathy of the heart in psittacine birds who suffered from PDD. Three brain samples underwent X/P gene sequencing, revealing PaBV-2 and PaBV-4 viral genotypes through phylogenetic analyses. This underscores the necessity for ongoing PaBV surveillance and further investigation into its pathophysiology and transmission routes.

Antimicrobial Sensitivity Profile in Psittacine Birds at an Avian Teaching Hospital: A Retrospective Study, 2015-2022.

Veterinary hospitals house patient populations with diverse infectious statuses, microbiota, and histories of prior antibiotic therapy. Choanal swabs are commonly used for assessing the upper respiratory tract of birds for bacterial disease, with the samples submitted for cytologic testing and/or culture and antimicrobial sensitivity testing. The aim of this retrospective study was to identify and quantify bacteria isolated from choanal swabs collected from psittacine patients at a veterinary teaching hospital in Mexico City, Mexico. Data regarding bacterial isolates from choanal swabs were obtained from the medical records of companion psittacines suspected of upper respiratory bacterial disease that presented between November 2015 and December 2022. A total of 47.8% (175 of 366) of the bacterial isolates were from specimens obtained from red-lored Amazons (Amazona autumnalis). Gram-negative bacteria predominated, with 27 different genera identified. Klebsiella, Staphylococcus, and Escherichia were the most frequently isolated genera. A total of 90.4% (331 of 366) of the isolates were resistant to at least 1 antibiotic tested in the sensitivity panel, and a single Klebsiella isolate was resistant to 13 different antibiotics. Gentamicin had a high percentage of efficacy (79.5%; 182 of 229) against the bacterial isolates, whereas isolates tested against sulfonamide-trimethoprim (46.7%, 98 of 210), streptomycin (43.8%; 88 of 201), and clindamycin (12.9%; 15 of 116) had susceptibilities <50%. This is the first study to report common bacterial isolates and their antimicrobial susceptibility patterns from choanal swab samples collected from companion psittacines suspected of upper respiratory disease in Mexico. Clinicians can use the information presented in this study as a guide for therapeutic decision-making when managing upper respiratory bacterial infections in companion psittacine patients.

Convergent evolution of parrot plumage coloration.

Parrots have remarkable plumage coloration that result in part from a unique ability to produce pigments called psittacofulvins that yield yellow to red feather colors. Little is known about the evolution of psittacofulvin-based pigmentation. Widespread color mutations of captive-bred parrots provide perfect opportunities to study the genetic basis of this trait. An earlier study on blue budgerigars, which do not possess psittacofulvins, reveals the involvement of an uncharacterized polyketide synthase (MuPKS) in yellow psittacofulvin synthesis. The blue phenotype had repeatedly appeared in different parrot species, similar to independent experimental replications allowing the study of convergent evolution and molecular mechanism of psittacofulvin-based pigmentation. Here, we investigated the genetic basis of the blue phenotypes in two species of Agapornis parrots, Fischer's lovebird (A. fischeri) and Yellow-collared lovebird (A. personatus). Using whole-genome data, we identified a single genomic region with size <2 Mb to be strongly associated with the color difference between blue and wild-type (WT) birds in both species. Surprisingly, we discovered that the mutation associated with the blue Agapornis phenotype was identical to the previously described substitution causing the functional change of MuPKS in budgerigars. Together with the evidence of shared blue-associated haplotypes and signatures of a selective sweep in this genomic region in both species, we demonstrated both de novo mutation and interspecific introgression play a role in the evolution of this trait in different Agapornis species. The convergent substitution in the same gene in both lovebirds and budgerigars also indicates a strong evolutionary constraint on psittacofulvin-based coloration.

Parrot optimizer: Algorithm and applications to medical problems.

Stochastic optimization methods have gained significant prominence as effective techniques in contemporary research, addressing complex optimization challenges efficiently. This paper introduces the Parrot Optimizer (PO), an efficient optimization method inspired by key behaviors observed in trained Pyrrhura Molinae parrots. The study features qualitative analysis and comprehensive experiments to showcase the distinct characteristics of the Parrot Optimizer in handling various optimization problems. Performance evaluation involves benchmarking the proposed PO on 35 functions, encompassing classical cases and problems from the IEEE CEC 2022 test sets, and comparing it with eight popular algorithms. The results vividly highlight the competitive advantages of the PO in terms of its exploratory and exploitative traits. Furthermore, parameter sensitivity experiments explore the adaptability of the proposed PO under varying configurations. The developed PO demonstrates effectiveness and superiority when applied to engineering design problems. To further extend the assessment to real-world applications, we included the application of PO to disease diagnosis and medical image segmentation problems, which are highly relevant and significant in the medical field. In conclusion, the findings substantiate that the PO is a promising and competitive algorithm, surpassing some existing algorithms in the literature. The supplementary files and open source codes of the proposed Parrot Optimizer (PO) is available at https://aliasgharheidari.com/PO.html and https://github.com/junbolian/PO.

Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot.

Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.

Spontaneous tempo production in cockatiels (Nymphicus hollandicus) and jungle crows (Corvus macrorhynchos).

Musical and rhythmical abilities are poorly documented in non-human animals. Most of the existing studies focused on synchronisation performances to external rhythms. In humans, studies demonstrated that rhythmical processing (e. g. rhythm discrimination or synchronisation to external rhythm) is dependent of an individual measure: the individual tempo. It is assessed by asking participants to produce an endogenous isochronous rhythm (known as spontaneous motor tempo) without any specific instructions nor temporal cue. In non-human animal literature, studies describing spontaneous and endogenous production of motor tempo without any temporal clue are rare. This exploratory study aims to describe and compare the spontaneous motor tempo of cockatiels and jungle crows. Data were collected on spontaneous beak drumming behaviours of birds housed in laboratory. Inter beak strokes intervals were calculated from sound tracks of videos. The analyses revealed that inter beak strokes intervals are non-randomly distributed intervals and are isochronous. Recorded spontaneous motor tempos are significantly different among some cockatiels. Since we could only conduct statistical analysis with one corvid, we cannot conclude about this species. Our results suggest that cockatiels and jungle crows have individual tempos, thus encouraging further investigations.