Dataset Information

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus).

ABSTRACT: 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.

SUBMITTER: Salter JF

PROVIDER: S-EPMC6893191 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus).

Salter Jessie F JF Johnson Oscar O Stafford Norman J NJ Herrin William F WF Schilling Darren D Cedotal Cody C Brumfield Robb T RT Faircloth Brant C BC

G3 (Bethesda, Md.) 20191203 12

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 asse ...[more]

PMID: 31611345

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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.

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.

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.

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.

Dataset Information

A Highly Contiguous Reference Genome for Northern Bobwhite (Colinus virginianus).

Publications

A Highly Contiguous Reference Genome for Northern Bobwhite (<i>Colinus virginianus</i>).

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