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

角、鹿角和其他骨骼结构(颅骨附件)是从鹿、羚羊和长颈鹿(称为Pecora的有蹄哺乳动物群体)的双趾哺乳动物的头骨中生长出来的，这是一个进化之谜。颅骨附属物经常被用来确定物种与Pecora的不同科之间的关系，因为每个科都有一种特定类型的附属物。当化石物种缺乏颅骨附属物时，很难将它们可靠地归类于任何一个特定的科。这些没有附肢的化石物种可以提供有关每个科的头骨起源的必要信息，但无法确定它们与山核桃进化关系的背景，从而排除了它们在头骨进化研究中的应用。先前的研究表明，随着动物的成长，结构变化的方式可能会导致全新结构的起源。因此，更好地了解颅附件的发育将为有蹄哺乳动物的颅附件进化提供急需的背景，并有助于解决其起源的问题。它还将有助于研究皮肤和结缔组织如何促进骨骼生长，并有助于了解颅骨发育的途径和模式，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生长研究。这项研究将成为美国自然历史博物馆语言科学项目中学生基因组分析和遗传学课程的基础，该课程将在纽约不同群体的小学生中试行，并可供全国各地的教师和学校使用。该项目将检验两个相互竞争的假说：1)在化石中观察到的广泛的独特的头骨附肢与现存的山核偶指龙并不具有共同的进化起源；2)部分头骨附肢，如鹿角的永久骨蒂和角骨的骨核，可能在该分支的某些或所有附肢类型中是同源的。样本将从至少三个个体的颅附件形成组织中采集，每个个体来自Pecora的四个现存的有颅附件的科(牛科、鹿科、长颈鹿科和长颈鹿科)和来自Traguidae的一个无附属物的外群分类群，分别在出生、一个月和两个月大的发育阶段。RNA将从这些组织中分离出来，并使用下一代测序技术进行测序。从每个个体身体第二个位置的组织中测序的基因表达谱将提供一个体细胞对照，以估计与颅骨附件生长(颅骨附件转录组)特定相关的基因表达。这些转录本将被优化到系统发育图上，以测试负责跨年龄组和年龄组内颅骨附件生长的基因的同源性。

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.