ABSTRACT Hybrids with different combinations of traits can be used to identify genomic regions that underlie phenotypic characters important to species identity and recognition. Here, we explore links between genomic and plumage variation in Blue-winged Warbler x Golden-winged Warbler (Vermivora cyanoptera x V. chrysoptera) hybrids, which have traditionally been categorized into 2 discrete types. “Lawrence's” hybrids are yellow overall, similar to Blue-winged Warblers, but exhibit the black throat patch and face mask of Golden-winged Warblers. “Brewster's” hybrids are similar to Golden-winged Warblers, but lack the black throat patch and face mask, and sometimes have yellow on their underparts. Previous studies hypothesized that (1) first generation hybrids are of the Brewster's type and can be distinguished by the amount of yellow on their underparts, and that (2) the throat patch/mask phenotype is consistent with Mendelian inheritance and controlled by variation in a locus near the Agouti-signaling protein (ASIP) gene. We addressed these hypotheses using whole genome re-sequencing of parental and hybrid individuals. We found that Brewster's hybrids had genomic hybrid index scores indicating this phenotype can arise by majority ancestry from either parental species, that their plumage varied in levels of carotenoid pigmentation, and individuals captured in multiple years grew consistently less yellow over time. Variation in carotenoid pigmentation showed little relationship with genomic hybrid index score and is thus inconsistent with previous hypotheses that first generation hybrids can be distinguished by the amount of yellow in their plumage. Our results also confirm that variation near ASIP underlies the throat patch phenotype, which we refined to an ∼10–15 Kb region upstream of the coding sequence. Overall, our results support the notion that traditional categorization of hybrids as either Lawrence's or Brewster's oversimplifies continuous variation in carotenoid pigmentation, and its inferred underlying genetic basis, and is based primarily on one discrete trait, which is the throat patch/mask phenotype. LAY SUMMARY We used whole genome sequences of hybrid Vermivora warblers to examine the genetic basis and inheritance of plumage pigmentation. Yellow carotenoid pigmentation varied among hybrids, decreased between years, and showed no clear relationship with degree of admixture, suggesting a complex genetic basis. The ASIP gene was previously linked to melanic (black) throat pigmentation and we refined the causal region to ∼10–15 Kb upstream of the coding sequence. We conclude that first generation hybrids in this system may not be readily distinguished by their degree of carotenoid pigmentation.

中文翻译：

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Vermivora 杂种的基因组和羽毛变异

摘要 具有不同性状组合的杂种可用于识别基因组区域，这些区域是对物种身份和识别很重要的表型特征的基础。在这里，我们探索了蓝翅莺 x 金翅莺 (Vermivora cyanoptera x V. chrysoptera) 杂交种中基因组和羽毛变异之间的联系，传统上将其分为 2 种离散类型。“劳伦斯”杂种整体呈黄色，与蓝翅莺相似，但具有金翅莺的黑色喉部斑块和面罩。“布鲁斯特”杂种类似于金翅莺，但没有黑色的喉部贴片和面罩，有时下体呈黄色。以前的研究假设 (1) 第一代杂种是布鲁斯特的 s 型，可以通过其下体的黄色量来区分，并且 (2) 喉咙贴片/面罩表型与孟德尔遗传一致，并受 Agouti 信号蛋白 (ASIP) 基因附近基因座的变异控制。我们使用亲本和杂种个体的全基因组重新测序来解决这些假设。我们发现布鲁斯特杂种的基因组杂种指数分数表明这种表型可以由任一亲本物种的多数血统产生，它们的羽毛在类胡萝卜素色素沉着水平上有所不同，并且多年捕获的个体随着时间的推移始终不那么黄。类胡萝卜素色素沉着的变化与基因组杂种指数得分几乎没有关系，因此与先前的假设不一致，即第一代杂种可以通过其羽毛中的黄色量来区分。我们的结果还证实了 ASIP 附近的变异是喉咙斑块表型的基础，我们将其细化到编码序列上游的 ~10-15 Kb 区域。总的来说，我们的结果支持这样一种观点，即传统的将杂种归类为劳伦斯或布鲁斯特的分类过度简化了类胡萝卜素色素沉着的连续变化及其推断的潜在遗传基础，并且主要基于一个离散特征，即喉咙贴片/面具表型。概述 我们使用杂种 Vermivora 莺的全基因组序列来检查羽毛色素沉着的遗传基础和遗传。黄色类胡萝卜素色素沉着因杂交种而异，年间减少，与混合程度无明显关系，表明其遗传基础复杂。ASIP 基因以前与黑色（黑色）喉咙色素沉着相关，我们将因果区域细化到编码序列上游的~10-15 Kb。我们得出的结论是，该系统中的第一代杂种可能不容易通过它们的类胡萝卜素色素沉着程度来区分。ASIP 基因以前与黑色（黑色）喉咙色素沉着相关，我们将因果区域细化到编码序列上游的~10-15 Kb。我们得出的结论是，该系统中的第一代杂种可能不容易通过它们的类胡萝卜素色素沉着程度来区分。ASIP 基因以前与黑色（黑色）喉咙色素沉着相关，我们将因果区域细化到编码序列上游的~10-15 Kb。我们得出的结论是，该系统中的第一代杂种可能不容易通过它们的类胡萝卜素色素沉着程度来区分。