Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from tissue collections, or are unavailable for molecular analysis for other reasons such as restrictive biological sample export laws. Other species went extinct recently and are only available in formalin museum preparations or perhaps even as sub-fossils. In this brief communication we present a new method for placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny of extant taxa using continuous character data. This method is based on a relatively simple modification of an established Maximum Likelihood (ML) method for phylogeny inference from continuous traits. We show that the method works well on simulated trees and data. We then apply it to the case of placing the Culebra Island Giant Anole (Anolis roosevelti) into a phylogeny of Caribbean anoles. Anolis roosevelti is a ‘crown-giant’ ecomorph anole hypothesized to have once been found throughout the Spanish, U.S., and British Virgin Islands, but that has not been encountered or collected since the 1930s. Although this species is widely thought to be closely related to the Puerto Rican giant anole, A. cuvieri, our ML method actually places A. roosevelti in a different part of the tree and closely related to a clade of morphologically similar species. We are unable, however, to reject a phylogenetic position for A. roosevelti that places it as sister taxon to A. cuvieri; although close relationship with the remainder of Puerto Rican anole species is strongly rejected by our method.近年来，学界投入了巨大的精力与资源以构建生命之树（tree of life）——即地球上所有物种的系统发育历史。绝大多数情况下，构建愈发完整的生物系统发育树的进展，均通过对分子数据的精细化分析得以实现。进入现代基因组学时代后，获取多数物种的分子遗传数据已变得极为便捷且成本低廉。然而，部分类群在组织样本库中代表性不足甚至完全缺失，或是受限于诸如严格的生物样本出口法规等其他原因，无法进行分子分析。另有一些物种已在近期灭绝，仅能通过福尔马林固定的博物馆标本，甚至亚化石获取其相关材料。在这篇简短的通讯中，我们提出了一种全新方法，可利用连续性状数据，将隐秘类群、近期灭绝类群或假想类群置入现生类群的超度量系统发育树（ultrametric phylogeny）中。该方法基于对现有连续性状系统发育推断的最大似然（Maximum Likelihood，ML）方法进行适度简化的修改。我们通过模拟树与模拟数据验证了该方法的有效性。随后，我们将其应用于将库莱布拉岛巨型安乐蜥（Anolis roosevelti）置入加勒比安乐蜥系统发育树的案例中。Anolis roosevelti是一种‘冠巨型’生态型安乐蜥，据推测曾广泛分布于西班牙、美国及英属维尔京群岛，但自1930年代起便未再有发现或采集记录。尽管学界普遍认为其与波多黎各巨型安乐蜥A. cuvieri亲缘关系密切，但我们的ML方法实际将A. roosevelti置于系统发育树的另一分支，且其与一类形态相似的物种构成的演化支亲缘关系紧密。不过，我们无法拒绝A. roosevelti作为A. cuvieri姊妹群的系统发育位置；尽管我们的方法强烈排除了其与波多黎各其余安乐蜥类群存在近缘关系的可能性。