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

鹿、羚羊和长颈鹿（一种有蹄哺乳动物）等偶趾有蹄哺乳动物的头骨上长出的角、角和其他骨骼结构（颅骨附属物）是一个进化之谜。颅骨附属物经常被用来确定不同科的物种之间的关系，因为每个科的存在都是通过一种特定类型的附属物来区分的。当化石物种缺乏颅骨附属物时，很难将它们可靠地归属于任何特定的科。这些没有附属物的化石物种可以为每个家族的颅附属物的祖先起源提供必要的信息，但无法自信地将它们置于pecoran进化关系的背景下，这妨碍了它们在颅附属物进化研究中的应用。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产生。因此，更好地了解颅附属物的发育将为有蹄哺乳动物颅附属物的进化提供急需的背景，并有助于解决其起源问题。它还将有助于研究皮肤和结缔组织如何促进骨骼生长，并对理解头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头骨和骨骼生长研究。这项研究将成为美国自然历史博物馆朗科学项目中学生基因组分析和遗传学课程的基础，在纽约不同群体的学童中进行试点，并向全国各地的教师和学校开放。该项目将检验两个相互竞争的假设：1)在化石和现存的pecoran偶蹄动物中观察到的大量独特的颅骨附属物并不具有共同的进化起源；2)部分颅骨附属物，如鹿角的永久骨蒂和角的骨核，可能在该分支的某些或所有附属物类型中是同源的。在出生、1个月大和2个月大的3个发育阶段，将从现存的4个有颅附件的皮科（牛科、鹿科、长颈鹿科和Antilocapridae）和一个无附件的外群分类群（Tragulidae）中至少3个个体的颅附件形成组织中收集样本。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位置的组织中测序的基因表达谱将提供一个体细胞控制来估计与颅附属物生长特异性相关的基因表达（颅附属物转录组）。这些转录组将被优化到一个系统发育上，以测试负责颅附件生长的基因在不同年龄组和年龄组内的同源性。

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.