Donald J. Brightsmith

Molecular characterization of the cloacal microbiota of wild and captive parrots.

The gastrointestinal microbiota plays a fundamental role in health and disease. Only limited data are available about the composition of the intestinal microbiota of captive animals compared to those of wild animals. The aim of the present study was to characterize the cloacal microbiota of apparently healthy wild and captive parrots. A total of 16 parrots, 8 wild and 8 captive, belonging to 3 different species, were used in this study. Cloacal material was collected via cloacal swabbing. DNA was extracted and 16S rRNA genes were amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. A total of 518 clones were analyzed, and 49 operational taxonomic units (OTUs) were identified. The OTUs were classified in 4 bacterial phyla: Firmicutes (72.9%), Proteobacteria (14.9%), Actinobacteria (12%), and Bacteroidetes (0.2%). Bacterial diversity was significantly lower in wild birds than in captive birds. Principal component analysis based on the Unifrac distance metric indicated that the cloacal microbiota differed between wild and captive parrots. Staphylococcus saprophyticus was significantly more abundant in wild birds, while Escherichia coli was significantly more abundant in captive birds. In conclusion, wild and captive parrots appear to have differences in the composition of their cloacal bacterial microbiota. The clinical significance of these differences remains to be determined.

PARROT NESTING IN SOUTHEASTERN PERU: SEASONAL PATTERNS AND KEYSTONE TREES

Abstract Parrots that inhabit tropical lowland forests are difficult to study, are poorly known, and little information is available on their nesting habits, making analysis of community-wide nesting patterns difficult. I present nesting records for 15 species of psittacids that co-occur in southeastern Peru. The psittacid breeding season in this area lasted from June to April, with smaller species nesting earlier than larger species. Why smaller species bred earlier is uncertain, though it may be related to interspecific competition for nest sites or variations in food availability. This study identified two keystone plant resources used by nesting parrots: Dipteryx micrantha (Fabaceae) and Mauritia flexuosa (Arecaceae). Local threats to these plant species are discussed.

EFFECTS OF WEATHER ON PARROT GEOPHAGY IN TAMBOPATA, PERU

Abstract Geophagy is widespread and well documented for mammals, but avian geophagy has only recently become the subject of serious scientific investigation. I analyzed data from 606 mornings of observations at a large avian geophagy site or “clay lick” in the southwestern Amazon Basin to examine the effects of weather on bird lick use. Birds used the clay lick on 94% of the mornings without precipitation or fog. Parrots dominated the site in both numbers of species (17) and individuals (>99%). Weather conditions were significantly correlated with total lick use: there was greater use on sunny mornings and less on rainy mornings. Fog and overnight rain were correlated with low lick use. Sun, rain, fog, and overnight rain were recorded on 47, 25, 20, and 8% of the mornings, respectively. I estimated that inclement weather caused an annual 29% reduction in geophagy for all bird species combined. When early morning rain prevented species from using the lick, they did not return later in the day nor did they compensate for rainy mornings by increasing lick use on subsequent days. The timing of lick use and the lack of compensation suggest that neutralization of toxins could be driving lick use in this system.

A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

Data deposition to NCBI Genomes This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.

Nutritional content of the diets of free-living scarlet macaw chicks in southeastern Peru.

Abstract To provide novel information on psittacine diets, we analyzed the texture, crude protein, crude fat, Ca, P (total), Mg, K, Na, S, Cu, Fe, and Zn concentrations of crop contents from 10 free-living scarlet macaw (Ara macao) chicks from lowland forests of southeastern Peru. We compared our results with nutrient concentrations of known wild parrot foods and published psittacine dietary recommendations to highlight similarities and differences and suggest future avenues of research. The diets were much coarser textured than those recommended for hand feeding. Soil in the diet provided an important source of Na, but Na levels were still lower than all recommendations. Concentrations of protein, Zn, K, Cu, and P (total) were near to or within the range of recommendations for captive psittacine birds. Fat, Ca, and Mg concentrations were greater in crop contents than in the average food plants and greater than published recommendations. The Na∶K ratios were only one-twentieth of those recommended for young poultry. Future analyses should investigate the bioavailability of Fe, Ca, and Zn in these diets and the effects of varying concentrations of fat, Na, Ca, Mg, and Na∶K ratio on psittacine growth and development.

Dietary modification of omega-3 fatty acids for birds with atherosclerosis.

Vet Med Today: Timely Topics in Nutrition 523 A is characterized by hardening of the arteries and plaque formation and is widely reported in humans, other mammals, and birds. A high intake of cholesterol or an imbalance in dietary fatty acids can accelerate the development of atherosclerosis. Because many avian species naturally develop or are easily induced to develop atherosclerosis, they are frequently used in the study of this disease. However, lipid metabolism of birds differs in some respects from lipid metabolism of mammals. A key difference is the existence of portomicrons, rather than chylomicrons, that form in response to consumption of a meal that contains fats. Many studies have explored the effect of providing supplemental UFAs in an attempt to reduce atherosclerosis, with omega-3 fatty acids providing the most promising results. The purpose of the information provided here is to review atherosclerosis in birds, lipid metabolism in birds, and the effect that dietary UFAs may have on atherosclerosis.

A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene.

Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.

Error Properties of Argos Satellite Telemetry Locations Using Least Squares and Kalman Filtering

Study of animal movements is key for understanding their ecology and facilitating their conservation. The Argos satellite system is a valuable tool for tracking species which move long distances, inhabit remote areas, and are otherwise difficult to track with traditional VHF telemetry and are not suitable for GPS systems. Previous research has raised doubts about the magnitude of position errors quoted by the satellite service provider CLS. In addition, no peer-reviewed publications have evaluated the usefulness of the CLS supplied error ellipses nor the accuracy of the new Kalman filtering (KF) processing method. Using transmitters hung from towers and trees in southeastern Peru, we show the Argos error ellipses generally contain <25% of the true locations and therefore do not adequately describe the true location errors. We also find that KF processing does not significantly increase location accuracy. The errors for both LS and KF processing methods were found to be lognormally distributed, which has important repercussions for error calculation, statistical analysis, and data interpretation. In brief, “good” positions (location codes 3, 2, 1, A) are accurate to about 2 km, while 0 and B locations are accurate to about 5–10 km. However, due to the lognormal distribution of the errors, larger outliers are to be expected in all location codes and need to be accounted for in the user’s data processing. We evaluate five different empirical error estimates and find that 68% lognormal error ellipses provided the most useful error estimates. Longitude errors are larger than latitude errors by a factor of 2 to 3, supporting the use of elliptical error ellipses. Numerous studies over the past 15 years have also found fault with the CLS-claimed error estimates yet CLS has failed to correct their misleading information. We hope this will be reversed in the near future.

Cultivable bacterial microbiota of northern bobwhite (Colinus virginianus): a new reservoir of antimicrobial resistance?

The northern bobwhite (Colinus virginianus) is an ecologically and economically important avian species. At the present time, little is known about the microbial communities associated with these birds. As the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and DNA sequencing approach. A total of 414 morphologically unique bacterial colonies were selected from nonselective aerobic and anaerobic cultures, as well as selective and enrichment cultures. Analysis of the first 500-bp 16S rRNA gene sequences in conjunction with biochemical identifications revealed 190 non-redundant species-level taxonomic units, representing 160 known bacterial species and 30 novel species. The bacterial species were classified into 4 phyla, 14 orders, 37 families, and 59 or more genera. Firmicutes was the most commonly encountered phylum (57%) followed by Actinobacteria (24%), Proteobacteria (17%) and Bacteroidetes (0.02%). Extensive diversity in the species composition of quail microbiota was observed among individual birds and anatomical locations. Quail microbiota harbored several opportunistic pathogens, such as E. coli and Ps. aeruginosa, as well as human commensal organisms, including Neisseria species. Phenotypic characterization of selected bacterial species demonstrated a high prevalence of resistance to the following classes of antimicrobials: phenicol, macrolide, lincosamide, quinolone, and sulphate. Data from the current investigation warrant further investigation on the source, transmission, pathology, and control of antimicrobial resistance in wild quail populations.

Parrot Behavior at a Peruvian Clay Lick

Abstract We documented the behavior of 13 parrot species at a geophagy site along the Tambopata River in southeastern Peru. These species use the lick in one or more multi-species aggregations composed predominantly of (1) large parrots and small macaws (81% of lick use), (2) large macaws (5%), or (3) parakeets and small parrots (5%). Monospecific flocks accounted for only 8% of lick use and lone individuals <1% of lick use. The multi-species aggregations sorted by body size and were generally composed of species with similar coloration suggesting that group composition was driven by a mix of competition and predation. Three species regularly used the lick in monospecific groups and these had the largest group sizes away from the lick, suggesting a causal relationship between intraspecific sociality and lick use in monospecific groups. All groups were wary when approaching the lick, probably due to the risk from landslides and predators. We suggest that clay lick use strategies are molded by predation risk and competition acting on a suite of species with varying body size, coloration, and gregariousness.