Understanding the cryptic introgression and mixed ancestry of Red Junglefowl in India.
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ABSTRACT:
SUBMITTER: Thakur M
PROVIDER: S-EPMC6188471 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110-150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral-wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.
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Project description:BackgroundChicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens.ResultsWe successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.ConclusionsIn summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.
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Project description:Contact seeking with humans is documented in some domestic animals, mainly dogs, which have advanced communication skills. Domestication as a companion animal is thought to underlie this ability. However, also domesticated horses and goats display similar human-directed behaviors. This suggests either a broader effect of domestication on contact-seeking behavior, or alternatively, that social interactions with humans can result in the development of human contact seeking. As part of another study, we observed contact-seeking behavior in juvenile red junglefowl (Gallus gallus) chicks exposed to behavioral training since hatching, during a foraging task, where chicks were singly required to collect food rewards in a familiar arena using odor cues. If chicks left the arena, we recorded if they approached and looked up at the experimenter, or if they approached other objects (including another human). Chicks approached the experimenter significantly more often than they approached other objects. This behavior was not linked to a fast performance in the test arena, which gave some birds more time to explore the surroundings, or to learning ability measured in a cognitive task. Yet, the preference for the experimenter was lower for chicks that were handled more prior to the experiment. Also, approach probability was positively correlated with escape attempts in a novel arena test. The observed variation in approach behavior suggests a link to aspects of personality, and exposure to human interactions and experimental procedures. Our observations suggest that, although neither domesticated nor selectively bred, red junglefowl that are socialized with humans can potentially develop behavior used to describe contact seeking. Together with evidence from cognitive and behavioral studies, our results suggest that social experiences, not only domestication, can affect human-animal interactions. We propose how interactions between behavior, cognition and handling could be studied further in controlled settings to validate the preliminary findings of our study and uncover the underlying mechanisms.
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Project description:Natural selection can act on between-individual variation in cognitive abilities, yet evolutionary responses depend on the presence of underlying genetic variation. It is, therefore, crucial to determine the relative extent of genetic versus environmental control of these among-individual differences in cognitive traits to understand their causes and evolutionary potential. We investigated heritability of associative learning performance and of a cognitive judgement bias (optimism), as well as their covariation, in a captive pedigree-bred population of red junglefowl (Gallus gallus, n > 300 chicks over 5 years). We analysed performance in discriminative and reversal learning (two facets of associative learning), and cognitive judgement bias, by conducting animal models to disentangle genetic from environmental contributions. We demonstrate moderate heritability for reversal learning, and weak to no heritability for optimism and discriminative learning, respectively. The two facets of associative learning were weakly negatively correlated, consistent with hypothesized trade-offs underpinning individual cognitive styles. Reversal, but not discriminative learning performance, was associated with judgement bias; less optimistic individuals reversed a previously learnt association faster. Together these results indicate that genetic and environmental contributions differ among traits. While modular models of cognitive abilities predict a lack of common genetic control for different cognitive traits, further investigation is required to fully ascertain the degree of covariation between a broader range of cognitive traits and the extent of any shared genetic control.This article is part of the theme issue 'Causes and consequences of individual differences in cognitive abilities'.
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Project description:Early animal domestication may have been driven by selection on tameness. Selection on only tameness can bring about correlated selection responses in other traits, not intentionally selected upon, which may be one cause of the domesticated phenotype. We predicted that genetically reduced fear towards humans in Red Junglefowl, ancestors of domesticated chickens, would be correlated to other traits included in the domesticated phenotype. Fear level was determined by a standardised behaviour test, where the reaction towards an approaching human was recorded. We first selected birds for eight generations for either high or low fear levels in this test, to create two divergent selection lines. An F3 intercross, with birds from the eighth generation as parentals, was generated to study correlations between fear-of-human scores and other unselected phenotypes, possibly caused by pleiotropy or linkage. Low fear-of-human scores were associated with higher body weight and growth rates, and with increased activity in an open field test, indicating less general fearfulness. In females, low fear-of-human scores were also associated with more efficient fear habituation and in males with an increased tendency to emit food calls in a mirror test, indicating increased social dominance. Low fear-of-human scores were also associated with smaller brain relative to body weight, and with larger cerebrum relative to total brain weight in females. All these effects are in line with the changes observed in domesticated chickens compared to their ancestors, and we conclude that tameness may have been a driving factor underlying some aspects of the domesticated phenotype.
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Project description:Illumina Miseq paired-end sequencing (2x250 or 2x75) of 550 pb fragment from the genome of one red junglefowl
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Project description:We genotyped 45 new samples from 4 populations of Northwest India and combined it with previously published data to characterize the population structure of modern Northwest Indian populations in the context of their geographic neighbors across South Asia and West Eurasia.
2018-12-05 | GSE119653 | GEO
Project description:The relationship between animal cognition and consistent among-individual behavioral differences (i.e., behavioral types, animal personality, or coping styles), has recently received increased research attention. Focus has mainly been on linking different behavioral types to performance in learning tasks. It has been suggested that behavioral differences could influence also how individuals use previously learnt information to generalize about new stimuli with similar properties. Nonetheless, this has rarely been empirically tested. Here, we therefore explore the possibility that individual variation in generalization is related to variation in behavioral types in red junglefowl chicks (Gallus gallus). We show that more behaviorally flexible chicks have a stronger preference for a novel stimulus that is intermediate between 2 learnt positive stimuli compared to more inflexible chicks. Thus, more flexible and inflexible chicks differ in how they generalize. Further, behavioral flexibility correlates with fearfulness, suggesting a coping style, supporting that variation in generalization is related to variation in behavioral types. How individuals generalize affects decision making and responses to novel situations or objects, and can thus have a broad influence on the life of an individual. Our results add to the growing body of evidence linking cognition to consistent behavioral differences.
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Project description:Substantial concentrations of testosterone are not only present in a male's circulation, but also in its ejaculate. Surprisingly, the regulation of ejaculate T and its effects on females and their offspring, potentially a cryptic paternal trait, are not known. We found lower circulating and higher ejaculate T concentrations in subordinate red junglefowl (Gallus gallus gallus) males compared to dominant males, suggestive of an adaptive trade-off in T allocation to circulation and their ejaculate. Subsequently, we artificially inseminated females with either testosterone enriched (TE) or control ejaculates (CE) in a cross-over design. TE females produced heavier eggs than CE females. Offspring growth and tonic immobility were affected in a sex-specific way by TE. TE sons were heavier with shorter TI duration than CE sons, and TE daughters were lighter than CE daughters but daughters did not differ in TI score. However, the chicks competitiveness was not influenced by the TE nor CE. This indicates a previously unknown function of ejaculate testosterone as well as a new form of interaction between a cryptic paternal trait and a maternal effect that may be widespread in the animal kingdom.
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Project description:We characterized the SF proteome of the polyandrous Red junglefowl, Gallus gallus, the wild species that gave rise to the domestic chicken. We identify 1,141 SFPs, including proteins involved in immunity and antimicrobial defences, sperm maturation, and fertilisation, revealing a functionally complex SF proteome. This includes a predominant contribution of blood plasma proteins that is conserved with human SF. By comparing the proteome of young and old males with fast or slow sperm velocity in a balanced design, we identify proteins associated with ageing and sperm velocity, and show that old males that retain high sperm velocity have distinct proteome characteristics. SFP comparisons with domestic chickens revealed both qualitative and quantitative differences likely associated with domestication and artificial selection. Collectively, these results shed light onto the functional complexity of avian SF, and provide a platform for molecular studies of fertility, reproductive ageing, and domestication.
2016-12-23 | PXD005160 | Pride