DISSERTATION RESEARCH: Assessing Homology of Hoofed Mammal Cranial Appendages with 3D Morphometrics and Next-Generation Transcriptomics

论文研究：利用 3D 形态计量学和下一代转录组学评估有蹄哺乳动物颅附属物的同源性

• 批准号: 1601299
• 负责人: John Flynn
• 金额: $ 1.93万
• 依托单位: American Museum Natural History
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2017-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1601299&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Assessing; Homology; Hoofed

The horns, antlers, and other bony structures (cranial appendages) growing from the skulls of even-toed, hoofed mammals like deer, antelopes, and giraffes (the group of hoofed mammals called Pecora) are an evolutionary mystery. Cranial appendages are often used to determine how species are related to the different families of Pecora, because each family is distinguished by the presence of a specific type of appendage. When fossil species lack cranial appendages, it is difficult to assign them reliably to any particular family. These appendage-less fossil species could provide necessary information about the ancestral origins of cranial appendages in each family, but the inability to confidently place them in the context of pecoran evolutionary relationships precludes their use in studies of cranial appendage evolution. Prior studies have shown that variation in the way structures change as an animal grows can result in the origination of totally new structures. A better understanding of cranial appendage development will therefore provide much-needed context for hoofed mammal cranial appendage evolution and help resolve the question of their origins. It will also contribute to research on how skin and connective tissues contribute to bone growth and have implications for understanding pathways and patterns of skull development, with methods and results that are broadly applicable to skull and bone growth research in all vertebrates, including humans. This research will form the basis of a curriculum on genomic analyses and genetics for middle school students in the American Museum of Natural History's Lang Science Program, piloted with diverse groups of New York schoolchildren and available to teachers and schools across the country. This project will test two competing hypotheses: 1) the broad range of distinctive cranial appendages observed in fossil and extant pecoran artiodactyls do not share a common evolutionary origin, 2) portions of cranial appendages, such as the permanent bone pedicles of antlers and the bone cores of horns, may be homologous across some or all of the appendage types in this clade. Samples will be collected from the cranial appendage forming tissues of at least three individuals each from the four extant cranial-appendage-bearing families of Pecora (Bovidae, Cervidae, Giraffidae, and Antilocapridae) and an appendage-less outgroup taxon from Tragulidae, at 3 developmental stages: birth, one month, and two months old. RNA will be isolated from these tissues and sequenced using next-generation sequencing technologies. Gene expression profiles sequenced from tissues at a second location on the body of each individual will provide a somatic control to estimate gene expression specifically related to cranial appendage growth (the cranial appendage transcriptome). These transcriptomes will be optimized onto a phylogeny to test for homology of the genes responsible for cranial appendage growth across and within age groups.

角，鹿角和其他骨骼结构（颅附属物）从偶数趾的有蹄哺乳动物的头骨上生长出来，如鹿，羚羊和长颈鹿（有蹄哺乳动物的一组称为Pecora）是一个进化之谜。颅附器常被用来确定物种与不同的皮科拉科的关系，因为每个科都有一种特定类型的附器。当化石物种缺乏颅附器时，很难将它们可靠地分配给任何特定的科。这些无附属物的化石物种可以提供必要的信息，在每个家庭的颅附属物的祖先起源，但不能自信地把它们的背景下，皮科动物的进化关系排除了他们在颅附属物进化的研究使用。先前的研究表明，随着动物生长，结构变化的方式发生变化，可能导致全新结构的起源。因此，更好地了解颅附器的发展将提供急需的有蹄类哺乳动物颅附器的进化背景，并帮助解决他们的起源问题。它还将有助于研究皮肤和结缔组织如何促进骨骼生长，并对理解颅骨发育的途径和模式产生影响，其方法和结果广泛适用于包括人类在内的所有脊椎动物的颅骨和骨骼生长研究。这项研究将成为美国自然历史博物馆郎科学项目中学生基因组分析和遗传学课程的基础，该项目将在不同的纽约学童群体中进行试点，并提供给全国各地的教师和学校。该项目将测试两个相互竞争的假设：1）在化石和现存的偶蹄美洲虎中观察到的广泛的独特的颅附属物并不具有共同的进化起源，2）颅附属物的部分，如鹿角的永久骨蒂和角的骨芯，可能在这个分支中的一些或所有附属物类型中是同源的。将在出生、1个月和2个月大的3个发育阶段，从Pecora的4个现存的带颅附器家族（牛科、鹿科、长颈鹿科和Antilocapridae）和Tragulidae的无附器外群分类群中的至少3个个体的颅附器形成组织中采集样本。将从这些组织中分离RNA，并使用下一代测序技术进行测序。从每个个体身体上第二位置的组织测序的基因表达谱将提供体细胞对照以估计与颅附件生长特异性相关的基因表达（颅附件转录组）。这些转录组将被优化到一个基因组上，以测试负责颅附件生长的基因在不同年龄组之间和年龄组内的同源性。