Novel Procedures for Simulating Phylogenetic Trees and Speciation

生物多样性正在减少，保护在当今社会变得越来越重要。物种形成的过程，即新物种是如何进化的，是维持生物多样性的基础，但人们还没有完全了解。系统发育树显示了当今物种多样性的起源，准确地指出了物种进化的时间，并描述了它们之间的亲缘关系。它们也被用来模拟不同类型的疾病，如流感。为了通过评估各种模型来解释物种形成和系统发育树，已经进行了大量的研究。在这个项目中，我们使用中性模型，该模型提出了一个有争议的假设，即所有个人以相同的方式与系统交互，而不考虑他们的物种。尽管这些模型做出了假设，但它们以惊人的精度匹配生态数据，吸引了许多研究人员的注意。对于系统发育树的建模，中性模型对许多早期模型进行了改进，因为物种灭绝的概率与代表性个体的数量成正比。点突变是这些模型中经常使用的三种物种形成模式之一。它指出，每个新出生的个体都有恒定的可能性成为新物种。一种基于融合的强大计算方法可以在时间上追溯个体的祖先。这解决了与替代远期模拟相关的等待均衡和限制模拟大小的问题。点突变创造了许多只有一个成员的物种，这在现实中是没有观察到的。因此，它生成的系统发育树看起来不切实际，许多经过的突变被算作新物种。另外两种机制是随机分裂和外围隔离物种形成，即新物种作为一个小的创始种群到来。这种方法很有希望，但聚结模拟不能用于这些形态形成模式。这是非常严格的，阻碍了详细的研究。我们将开发新的聚结修饰，使其适用于研究物种形成的随机裂变和外围隔离模式。自然界中的物种形成是一个渐进的过程，但现有的三种机制都假定物种形成事件是突然发生的。我们提出了一种新的物种形成机制，即每个个体都有一个包含两个基因的简单基因组。这解决了以不同方式传递突变的问题；它们存在，但永远不会被定义为一个不同的物种，因为传递的突变只会影响两个基因中的一个。这种物种形成的机制是渐进的，因为第一个基因的突变和第二个基因的突变之间经过了一段时间。正是第二个基因的突变完成了物种形成过程。我们将充分研究这种物种形成模式及其产生的系统发育树。我们对这些新方法有许多令人兴奋的应用，每一种方法都需要模型中不同的空间显式结构。该模型的二维空间显式版本适合与合作者斯蒂芬·哈贝尔的经验系统学进行比较。我们有权获得在降雨梯度上收集的进一步数据集。这将使我们有机会测试包含栖息地异质性的模型的一个版本。不同社区的网络对于包括群岛和疾病动态在内的许多应用来说是一个适当的空间结构。例如，我们的合作者卢克·哈蒙收集了从淡水湖中收集的浮游动物数据，与中性模型进行比较将是有洞察力的。还存在关于生物膜的医学应用。这些是粘连基质和感染，无法用抗生素治疗。最近的研究表明，这些生物膜的多样性速度极快。使用三维中性模型的测试将是在生物膜竞争中理解的有洞察力的研究。

Biodiversity is in decline and conservation is becoming increasingly important in today's society. The process of speciation, how new species evolve, is fundamental to biodiversity maintenance but is not fully understood. Phylogenetic trees show the origins of present day diversity, pinpointing when species evolved and describing their relatedness. They are also used in modeling the different strains of diseases such as flu. A lot of research has taken place with the aim of interpreting speciation and phylogenetic trees by evaluating various models. In this project, we use neutral models, which make the controversial assumption that all individuals interact with the system in an identical manner regardless of their species. Despite their assumptions, these models match ecological data with astounding precision, attracting a lot of research attention. For modeling phylogenetic trees, neutral models improve on many earlier models because the probability of a species becoming extinct becomes proportional to the number of representative individuals. Point mutation is one of three modes of speciation regularly used in these models. It states that every newborn individual has a constant probability being a new species. A powerful computational method based on coalescence traces the ancestry of individuals backwards in time. This solves the problems of waiting for equilibrium and restrictive simulation sizes associated with alternative forwards simulations. Point mutation creates a lot of species with only one member, which is not observed in reality. The phylogenetic trees it generates consequently appear unrealistic having many passing mutations counted as novel species. The other two mechanisms are random fission and peripheral isolate speciation where new species arrive as a small founding population. This approach is promising but the coalescence simulations cannot be used for these modes of speciation. This is extremely restrictive and prevents detailed studies. We will develop novel modification of coalescence to make it suitable for investigating the random fission and peripheral isolate modes of speciation. Speciation in nature is a gradual process but all three existing mechanisms assume a sudden speciation event. We propose a novel speciation mechanism where each individual has a simple genome including two genes. This solves the problem of passing mutations in a different way; they exist but would never be defined as a distinct species because the passing mutation would only influence one of the two genes. This mechanism of speciation is gradual because time passes between the mutation of the first gene and mutation of the second gene. It is mutation of the second gene that completes the speciation process. We will fully investigate this mode of speciation and the phylogenetic trees it generates. We have a number of exciting applications for these novel methods, each of which requires a different spatially explicit structure in the model. A two dimensional spatially explicit version of the model is suitable for comparison with empirical phylogenies from collaborator Stephen Hubbell. We have access to a further dataset collected across a rainfall gradient. This will give us the opportunity to test a version of the model that includes habitat heterogeneity. A network of distinct communities is an appropriate spatial structure for many applications including archipelagos and disease dynamics. For example, our collaborator Luke Harmon has zooplankton data collected from fresh water lakes, where a comparison with neutral models would be insightful. A medical application also exists regarding bioflms. These are adhesive matrices and infections that are untreatable with antibiotics. Recent research has shown an extreme rate of diversification in these biofilms. A test using a three dimensional neutral model would be insightful research in understanding within biofilm competition.