A role for differential gene regulation in the rapid diversification of melanic plumage coloration in the dark-eyed junco (<i>Junco hyemalis</i>)

Āboliņš-Ābols, Mikus; Kornobis, Étienne; Ribeca, Paolo; Wakamatsu, Kazumasa; Mp, Peterson; Ketterson, Ellen D.; Milá, Borja

doi:10.1101/315762

Cited by 5 publications

(5 citation statements)

References 80 publications

(16 reference statements)

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“…The study of epistasis can be interesting because epistatic interactions aid understanding of the functional relations of genes involved in the trait under study and sometimes can compensate for a lack of additive genome-wide studies in quantitative traits (Visscher et al 2012(Visscher et al , 2017Lee et al 2016). Distinct genes in chickens control plumage color traits (Li et al 2019a,b) and the genes associated with plumage pigmentation, such as melanocortin 1 receptor (MC1R; Kerje et al 2003;Hoque et al 2013;Zhang et al 2013;Ran et al 2016;Tu et al 2019;Yang et al 2019), tyrosinase (TYR;Yang et al 2019;Zheng et al 2020), premelanosome protein (PMEL; Kerje et al 2004;Abolins-Abols et al 2018;Zheng et al 2020), melanophilin (MLPH;Vaez et al 2008;Bed'hom et al 2012), Agouti signaling protein (ASIP; Robic et al 2019;Yang et al 2019), SRY-box (SOX families; Harris et al 2010;Gunnarsson et al 2011), solute carrier family member 2 (SLC45A2; Gunnarsson et al 2007;Zheng et al 2020) and endothelin B2 receptor (EDNRB2; Kinoshita et al 2014;Li et al 2015;Wu et al 2017;Xi et al 2020), are well known. Accordingly, multiple responsible genes have been reported for plumage color variation, but studies have focused on single loci with a major effect, rather than effective modifier loci with small or epistatic effects that influence plumage color more delicately.…”

Section: Introductionmentioning

confidence: 99%

New insights into genetics underlying of plumage color

et al. 2021

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Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10 −6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B,

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Section: Introductionmentioning

confidence: 99%

New insights into genetics underlying of plumage color

et al. 2021

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“…Altogether, these results demonstrate that the diversity in plumage patterns observed in the southern capuchinos has been shaped by mutations and subsequent selection in the different genes involved in the melanogenesis pathway, and is likely the result of the epistatic interactions between these gene products. Subsets of these genes have also been implicated in shaping coloration in other avian radiations [14,16,29]. We also identified GPR161, TBX19, DIO2 and AHCY as new pigmentation genes related to coloration differences in capuchinos [28].…”

Section: Discussionmentioning

confidence: 65%

“…The candidate regions depended on the specific colour determined by the pigment content of each patch, with black throats likely controlled by changes in TYRP1 and OCA2, two melanogenesis genes connected to variation in shades of brown, grey and black in mammals and birds [28]. The white throat in S. palustris was associated with changes in MLANA, a gene implicated in melanosome biosynthesis and known to be differentially expressed in white feathers in dark-eyed juncos (Junco hyemalis) [29] and rock pigeons (Columba livia) [32].…”

Section: Discussionmentioning

confidence: 99%

Concerted variation in melanogenesis genes underlies emergent patterning of plumage in capuchino seedeaters

et al. 2022

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Coloration traits are central to animal communication; they often govern mate choice, promote reproductive isolation and catalyse speciation. Specific genetic changes can cause variation in coloration, yet far less is known about how overall coloration patterns—which involve combinations of multiple colour patches across the body—can arise and are genomically controlled. We performed genome-wide association analyses to link genomic changes to variation in melanin (eumelanin and pheomelanin) concentration in feathers from different body parts in the capuchino seedeaters, an avian radiation with diverse colour patterns despite remarkably low genetic differentiation across species. Cross-species colour variation in each plumage patch is associated with unique combinations of variants at a few genomic regions, which include mostly non-coding (presumably regulatory) areas close to known pigmentation genes. Genotype–phenotype associations can vary depending on patch colour and are stronger for eumelanin pigmentation, suggesting eumelanin production is tightly regulated. Although some genes are involved in colour variation in multiple patches, in some cases, the SNPs associated with colour changes in different patches segregate spatially. These results suggest that coloration patterning in capuchinos is generated by the modular combination of variants that regulate multiple melanogenesis genes, a mechanism that may have promoted this rapid radiation.

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“…These regions may be developmentally linked, under similar selective regimes, or the result of differential regulation of separate genes across patches or patch regions [50]. Regulatory controls on feather color may work at patch-level, feather tract-level, or whole bird-level scales [48,49,51,52], and understanding how these pathways are connected will elucidate how complex plumage colors and patterns evolve. For example, most lorikeets have all-green wings with black-tipped primaries, and our ancestral reconstruction analysis indicates that the ancestor to all lories had green wings, but some Eos taxa have evolved red wings with black barring and UV coloration on some wing patches, demonstrating a clear interplay between region-and patch-level pigment and structural color regulation.…”

Section: Independent or Correlated Patchesmentioning

confidence: 99%

Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds

2020

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Background: Bird plumage exhibits a diversity of colors that serve functional roles ranging from signaling to camouflage and thermoregulation. However, birds must maintain a balance between evolving colorful signals to attract mates, minimizing conspicuousness to predators, and optimizing adaptation to climate conditions. Examining plumage color macroevolution provides a framework for understanding this dynamic interplay over phylogenetic scales. Plumage evolution due to a single overarching process, such as selection, may generate the same macroevolutionary pattern of color variation across all body regions. In contrast, independent processes may partition plumage and produce region-specific patterns. To test these alternative scenarios, we collected color data from museum specimens of an ornate clade of birds, the Australasian lorikeets, using visible-light and UV-light photography, and comparative methods. We predicted that the diversification of homologous feather regions, i.e., patches, known to be involved in sexual signaling (e.g., face) would be less constrained than patches on the back and wings, where new color states may come at the cost of crypsis. Because environmental adaptation may drive evolution towards or away from color states, we tested whether climate more strongly covaried with plumage regions under greater or weaker macroevolutionary constraint. Results: We found that alternative macroevolutionary models and varying rates best describe color evolution, a pattern consistent with our prediction that different plumage regions evolved in response to independent processes. Modeling plumage regions independently, in functional groups, and all together showed that patches with similar macroevolutionary models clustered together into distinct regions (e.g., head, wing, belly), which suggests that plumage does not evolve as a single trait in this group. Wing patches, which were conserved on a macroevolutionary scale, covaried with climate more strongly than plumage regions (e.g., head), which diversified in a burst. Conclusions: Overall, our results support the hypothesis that the extraordinary color diversity in the lorikeets was generated by a mosaic of evolutionary processes acting on plumage region subsets. Partitioning of plumage regions in different parts of the body provides a mechanism that allows birds to evolve bright colors for signaling and remain hidden from predators or adapt to local climatic conditions.

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A role for differential gene regulation in the rapid diversification of melanic plumage coloration in the dark-eyed junco (Junco hyemalis)

Abstract: 21

Cited by 5 publications

References 80 publications

New insights into genetics underlying of plumage color

New insights into genetics underlying of plumage color

Concerted variation in melanogenesis genes underlies emergent patterning of plumage in capuchino seedeaters

Macroevolutionary bursts and constraints generate a rainbow in a clade of tropical birds

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