Most of the knowledge generated to bridge the research-practice gap has been derived from experimental studies implementing specific treatment models. Alternatively, this study uses observational methods to generate knowledge about community-based treatment processes and outcomes. Aims are to (a) describe outcome trajectories for children with disruptive behavior problems (DBPs), and (b) test how observed delivery of a benchmark set of practice elements common in evidence-based treatments may be associated with outcome change while accounting for potential confounding variables. Participants included 190 children ages 4 to 13 with DBPs and their caregivers, plus 85 psychotherapists, recruited from six clinics. All treatment sessions were videotaped and a random sample of 4 sessions in the first 4 months of treatment was reliably coded for intensity on 27 practice elements (benchmark set and others). Three outcomes (child symptom severity, parent discipline, and family functioning) were assessed by parent report at intake, 4, and 8 months. Data were collected on several potential covariates including child, parent, therapist, and service use characteristics. Multilevel modeling was used to assess relationships between observed practice and outcome slopes while accounting for covariates. Children and families demonstrated improvements in all 3 outcomes, but few significant associations between treatment processes and outcome change were identified. Families receiving greater intensity on the benchmark practice elements did demonstrate greater improvement in the parental discipline outcome. Observed changes in outcomes for families in community care were generally not strongly associated with the type or amount of treatment received.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Background

Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.

Results

We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.

Conclusion

This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.