Molecular identification and characterization of partial COX1 gene from caecal worm (Aulonocephalus pennula) in Northern bobwhite (Colinus virginianus) from the Rolling Plains Ecoregion of Texas.
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ABSTRACT:
SUBMITTER: Kalyanasundaram A
PROVIDER: S-EPMC5526437 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Over the last few decades, there has been a decline in Northern bobwhite quail (Colinus virginianus) throughout their native range. While there are various factors that may be influencing this decline, it is suggested that parasites should be taken into consideration as a potential contributor in the Rolling Plains Ecoregion. High prevalence of the eyeworm (Oxyspirura petrowi) and caecal worm (Aulonocephalus pennula) in bobwhite of this region, coupled with a continuous decline, creates a need to assess infection through alternative methods for regional surveillance. Previous studies have developed a qPCR method and mobile research laboratory as an option for nonlethal procedures. However, there is still a need for standardization of these techniques. Therefore, this study builds on previous protocols to develop an application that considers factors that may influence qPCR results. In this study, cloacal swabs are collected from bobwhite in three locations throughout the Rolling Plains and scaled based on amount of feces present on the swab. This data is compared to qPCR standards as a limit of quantification for both eyeworm and caecal worm to define parasitic infection levels. Binary logistic regressions confirm that the probability of detection increases for both eyeworm (Odds Ratio: 2.3738; 95% Confidence Interval: [1.7804, 3.1649]) and caecal worm (Odds Ratio: 2.8516; 95% Confidence Interval: [2.2235, 3.6570]) as swab score increases. Infection levels for eyeworm and caecal worm are based on the generated cycle threshold value averages of qPCR standards. Based on the results of this study, this method can be applied in the mobile research laboratory to quantitatively assess regional parasitic infection in bobwhite throughout the Rolling Plains.
| S-EPMC6732722 | biostudies-literature
Project description:The widespread use of neonicotinoid insecticides in recent years has led to increasing environmental concern, including impacts to avian populations. In Texas and across their range, Northern bobwhite (Colinus virginianus) habitat frequently overlaps cultivated cropland protected by neonicotinoids. To address the effects of neonicotinoid use on bobwhites in Texas, we conducted a historical analysis from 1978-2012 in Texas' ecological regions using quail count data collected from North American Breeding Bird Survey and Texas Parks and Wildlife Department, and neonicotinoid use data from the U.S. Geological Survey. We considered bobwhite abundance, neonicotinoid use, climate, and land-use variables in our analysis. Neonicotinoid use was significantly (p<0.05) negatively associated with bobwhite abundance in the High Plains, Rolling Plains, Gulf Coast Prairies & Marshes, Edwards Plateau, and South Texas Plains ecological regions in the time periods following neonicotinoid introduction (1994-2003) or after their widespread use (2004-2012). Our analyses suggest that the use of neonicotinoid insecticides may negatively affect bobwhite populations in crop-producing regions of Texas.
| S-EPMC5764362 | biostudies-literature
Project description:Northern bobwhites (Colinus virginianus) are small quails in the New World Quail family (Odontophoridae) and are one of the most phenotypically diverse avian species. Despite extensive research on bobwhite ecology, genomic studies investigating the evolution of phenotypic diversity in this species are lacking. Here, we present a new, highly contiguous assembly for bobwhites using tissue samples from a vouchered, wild, female bird collected in Louisiana. By performing a de novo assembly and scaffolding the assembly with Dovetail Chicago and HiC libraries and the HiRise pipeline, we produced an 866.8 Mb assembly including 1,512 scaffolds with a scaffold N50 of 66.8 Mb, a scaffold L90 of 17, and a BUSCO completeness score of 90.8%. This new assembly represents approximately 96% of the non-repetitive and 84% of the entire bobwhite genome size, greatly improves scaffold lengths and contiguity compared to an existing draft bobwhite genome, and provides an important tool for future studies of evolutionary and functional genomics in bobwhites.
| S-EPMC6893191 | biostudies-literature
Project description:The avian haemosporidian parasites (phylum Apicomplexa) are taxonomically diverse and cosmopolitan in distribution; infecting most bird families. Sources of concern are reports of clinical haemosporidian infections in birds kept as part of zoo and aviary collections. Recently, severe and acute mortality episodes have been reported in masked bobwhite quail (Colinus virginianus ridgwayi), an endangered subspecies from the American Southwest. Two hundred and five eggs of the captive flock held in Arivaca, Arizona, were hatched at a zoo in the American Southwest. Thirty-four sub-adult or adult animals had lesions associated with tissue phases of haemoparasites, especially vasculitis, ventricular leiomyositis and ulcerative pododermatitis. Molecular techniques applied to blood collected from the zoo's last twelve remaining animals resulted in the detection of a Plasmodium juxtanucleare-like and Haemoproteus sp. parasites. A Raven (Corvus corax), in a contiguous exhibit, was positive for the same P. juxtanucleare-like parasite, but remained asymptomatic for three years following detection. These findings indicate that other birds in the exhibit within the zoo premises could act as reservoirs. We conclude that haemosporidian infections could be a factor in the demise of the captive masked bobwhite quails housed at the zoo. We suggest that active surveillance for haemoporidian parasites should be incorporated as a precaution to ex situ conservation efforts of susceptible endangered species.
| S-EPMC3742108 | biostudies-literature
Project description:Avian monitoring strategies are usually linked to bird singing or calling behavior. Individual availability for detection can change as a result of conspecific factors affecting bird behavior, though the magnitude of these effects is difficult to quantify. We evaluated behavioral and temporal factors affecting Northern Bobwhite (Colinus virginianus) breeding season individual availability for detection during three common survey times (3 min, 5 min, 10 min). We conducted 10-minute surveys associated with radio-collared male Northern Bobwhites on Peabody Wildlife Management Area, Kentucky, from 2010-2011. We homed to within 50 m of radio-collared males and recorded number of distinct Northern Bobwhite whistles (singing rate) per 1-minute interval, number of other males calling during the survey, minutes-since-sunrise, and day-of-season. We also recorded the number of minutes during a 10-minute survey that radio-collared male Northern Bobwhites called. We used logistic regression to estimate availability of radio-collared individuals for 3-minute, 5-minute, and 10-minute surveys. We also modeled number of minutes during 10-minute surveys that radio-collared Northern Bobwhites called, and we modeled singing rate. Individual availability for detection of radio-collared individuals during a 10-minute survey increased by 100% when at least 1 other Northern Bobwhite called during a survey (6.5% to 13.1%) and by 626% when 6 other Northern Bobwhites were calling (6.5% to 47.6%). Individual availability was 30% greater for 10-minute surveys than 5-minute surveys or 55% greater for 10-minute surveys than 3-minute surveys. Northern Bobwhite called most (2.8 ± 0.66 minutes/10-min survey) and at a greater rate (11.8 ± 1.3 calls/10-min period) when at least 5 other Northern Bobwhites called. Practitioners risk biasing population estimates low if individual availability is unaccounted for because species with low populations will not be stimulated by other calling males, are less likely to call, call less frequently, and call fewer times per minute, reducing their individual availability and likelihood to be counted on a survey even when they are present.
| S-EPMC5741256 | biostudies-literature
Project description: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.
| S-EPMC4061065 | biostudies-literature
Project description:Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.
| S-EPMC4699210 | biostudies-literature
Project description:Colinus virginianus strain:Texas Genome sequencing and assembly
| PRJNA188411 | ENA
Project description:BACKGROUND:Oxyspirura petrowi (Spirurida: Thelaziidae), a heteroxenous nematode of birds across the USA, may play a role in the decline of the northern bobwhite (Colinus virginianus) in the Rolling Plains Ecoregion of West Texas. Previous molecular studies suggest that crickets, grasshoppers and cockroaches serve as potential intermediate hosts of O. petrowi, although a complete study on the life-cycle of this nematode has not been conducted thus far. Consequently, this study aims to improve our understanding of the O. petrowi life-cycle by experimentally infecting house crickets (Acheta domesticus) with O. petrowi eggs, feeding infected crickets to bobwhite and assessing the life-cycle of this nematode in both the definitive and intermediate hosts. METHODS:Oxyspirura petrowi eggs were collected from gravid worms recovered from wild bobwhite and fed to house crickets. The development of O. petrowi within crickets was monitored by dissection of crickets at specified intervals. When infective larvae were found inside crickets, parasite-free pen-raised bobwhite were fed four infected crickets each. The maturation of O. petrowi in bobwhite was monitored through fecal floats and bobwhite necropsies at specified intervals. RESULTS:In this study, we were able to infect both crickets (n = 45) and bobwhite (n = 25) with O. petrowi at a rate of 96%. We successfully replicated and monitored the complete O. petrowi life-cycle in vivo, recovering embryonated O. petrowi eggs from the feces of bobwhite 51 days after consumption of infected crickets. All life-cycle stages of O. petrowi were confirmed in both the house cricket and the bobwhite using morphological and molecular techniques. CONCLUSIONS:This study provides a better understanding of the infection mechanism and life-cycle of O. petrowi by tracking the developmental progress within both the intermediate and definitive host. To our knowledge, this study is the first to fully monitor the complete life-cycle of O. petrowi and may allow for better estimates into the potential for future epizootics of O. petrowi in bobwhite. Finally, this study provides a model for experimental infection that may be used in research examining the effects of O. petrowi infection in bobwhite.
| S-EPMC6873741 | biostudies-literature
Project description:The potential of parasites to affect host abundance has been a topic of heated contention within the scientific community for some time, with many maintaining that issues such as habitat loss are more important in regulating wildlife populations than diseases. This is in part due to the difficulty in detecting and quantifying the consequences of disease, such as parasitic infection, within wild systems. An example of this is found in the Northern bobwhite quail (Colinus virginanus), an iconic game bird that is one of the most extensively studied vertebrates on the planet. Yet, despite countless volumes dedicated to the study and management of this bird, bobwhite continue to disappear from fields, forest margins, and grasslands across the United States in what some have referred to as “our greatest wildlife tragedy”. Here, we will discuss the history of disease and wildlife conservation, some of the challenges wildlife disease studies face in the ever-changing world, and how a “weight of evidence” approach has been invaluable to evaluating the impact of parasites on bobwhite in the Rolling Plains of Texas. Through this, we highlight the potential of using “weight of the evidence” to better understand the complex effects of diseases on wildlife and urge a greater consideration of the importance of disease in wildlife conservation. Graphical abstract Image 1 Highlights • Wildlife disease has gained increased recognition as a potentially significant mechanism affecting animal populations.• Global change associated with anthropogenic factors may increase the intensity and proliferation of wildlife diseases.• Disease effects may be discreet and contextually dependent, confounding efforts to quantify their impacts.• A weight of the evidence (WOE) approach evaluates and integrates multiple lines of evidence to identify causal factors.• WOE may provide an effective means to discern significant disease impacts, setting foundations for further empirical study.
| S-EPMC7415643 | biostudies-literature