Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken

The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillating pattern as the host, but this association was not as strong as found in mammals. Finally, the fecal microbiota was found to be not representative of cecal microbiota membership and structure in young birds. This is one of the first studies to demonstrate the use of photoperiods to modulate microbiota acquisition in newly hatched chicks, and show their potential as a tool to promote the colonization of beneficial microorganisms

Effective population sizes and adaptive genetic variation in a captive bird population

Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations

Effective population size of Culex quinquefasciatus under insecticide-based vector management and following Hurricane Harvey in Harris County, Texas

Introduction:Culex quinquefasciatus is a mosquito species of significant public health importance due to its ability to transmit multiple pathogens that can cause mosquito-borne diseases, such as West Nile fever and St. Louis encephalitis. In Harris County, Texas, Cx. quinquefasciatus is a common vector species and is subjected to insecticide-based management by the Harris County Public Health Department. However, insecticide resistance in mosquitoes has increased rapidly worldwide and raises concerns about maintaining the effectiveness of vector control approaches. This concern is highly relevant in Texas, with its humid subtropical climate along the Gulf Coast that provides suitable habitat for Cx. quinquefasciatus and other mosquito species that are known disease vectors. Therefore, there is an urgent and ongoing need to monitor the effectiveness of current vector control programs.Methods: In this study, we evaluated the impact of vector control approaches by estimating the effective population size of Cx. quinquefasciatus in Harris County. We applied Approximate Bayesian Computation to microsatellite data to estimate effective population size. We collected Cx. quinquefasciatus samples from two mosquito control operation areas; 415 and 802, during routine vector monitoring in 2016 and 2017. No county mosquito control operations were applied at area 415 in 2016 and 2017, whereas extensive adulticide spraying operations were in effect at area 802 during the summer of 2016. We collected data for eighteen microsatellite markers for 713 and 723 mosquitoes at eight timepoints from 2016 to 2017 in areas 415 and 802, respectively. We also investigated the impact of Hurricane Harvey’s landfall in the Houston area in August of 2017 on Cx. quinquefasciatus population fluctuation.Results: We found that the bottleneck scenario was the most probable historical scenario describing the impact of the winter season at area 415 and area 802, with the highest posterior probability of 0.9167 and 0.4966, respectively. We also detected an expansion event following Hurricane Harvey at area 802, showing a 3.03-fold increase in 2017.Discussion: Although we did not detect significant effects of vector control interventions, we found considerable influences of the winter season and a major hurricane on the effective population size of Cx. quinquefasciatus. The fluctuations in effective population size in both areas showed a significant seasonal pattern. Additionally, the significant population expansion following Hurricane Harvey in 2017 supports the necessity for post-hurricane vector-control interventions

Whole-genome survey reveals extensive variation in genetic diversity and inbreeding levels among peregrine falcon subspecies

Article describes how, in efforts to prevent extinction, resource managers are often tasked with increasing genetic diversity in a population of concern to prevent inbreeding depression or improve adaptive potential in a changing environment. The authors used whole-genome resequencing to generate over two million single nucleotide polymorphisms (SNPs) from multiple individuals of all peregrine falcon subspecies

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Methods We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. Results We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. Conclusions We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats

Cloacal Swabs Are Unreliable Sources for Estimating Lower Gastro-Intestinal Tract Microbiota Membership and Structure in Broiler Chickens

The gastrointestinal microbiota of chickens plays a central role in health and performance. Cloacal swabs, due to their proximity to the ceca (a vital site of functional activity), are an alternative, non-invasive method used for assaying microbial communities and might be a viable option for longitudinal studies. In this study, the microbiota of twenty paired cecal content and cloacal swab samples representing two dietary treatments was assessed using 16S rRNA V4 hypervariable region sequencing and was analyzed using the MOTHUR pipeline, Phyloseq, and Vegan packages. Paired t-test and Wilcoxon signed-rank tests showed significant differences in the Chao1 index (p-value <0.0001 and p-value <0.0001, respectively) but not in the Inverse Simpson species diversity estimator (p-value = 0.06763 and p-value = 0.06021, respectively) between the cecal content and cloacal swabs. β-diversity between the cloacal swabs and cecal microbiota also showed significant differences using PERMANOVA, HOMOVA, and weighted UniFrac testing (p-values < 0.001). Based on a paired sample analysis, this study provided evidence of the high inter-individual variation and randomness of cloacal microbiota, in contrast to cecal microbiota. Our findings indicated that cloacal swabs do not approximate the α or β diversity of cecal samples and are not suitable for longitudinal studies of gut microbiota

Using Genealogical Mapping and Genetic Neighborhood Sizes to Quantify Dispersal Distances in the Neotropical Passerine, the Black-Capped Vireo.

Dispersal is a key demographic process, ultimately responsible for genetic connectivity among populations. Despite its importance, quantifying dispersal within and between populations has proven difficult for many taxa. Even in passerines, which are among the most intensely studied, individual movement and its relation to gene flow remains poorly understood. In this study we used two parallel genetic approaches to quantify natal dispersal distances in a Neotropical migratory passerine, the black-capped vireo. First, we employed a strategy of sampling evenly across the landscape coupled with parentage assignment to map the genealogical relationships of individuals across the landscape, and estimate dispersal distances; next, we calculated Wright's neighborhood size to estimate gene dispersal distances. We found that a high percentage of captured individuals were assigned at short distances within the natal population, and males were assigned to the natal population more often than females, confirming sex-biased dispersal. Parentage-based dispersal estimates averaged 2400m, whereas gene dispersal estimates indicated dispersal distances ranging from 1600-4200 m. Our study was successful in quantifying natal dispersal distances, linking individual movement to gene dispersal distances, while also providing a detailed look into the dispersal biology of Neotropical passerines. The high-resolution information was obtained with much reduced effort (sampling only 20% of breeding population) compared to mark-resight approaches, demonstrating the potential applicability of parentage-based approaches for quantifying dispersal in other vagile passerine species