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，学界已投入大量精力与资源，以构建地球所有物种的系统发育生命之树。时至今日，构建愈发完整的生物系统发育树的核心进展，几乎均通过分子数据的精密分析得以实现。在当代基因组学时代，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，部分演化支在组织样本库中的占比极低，甚至完全缺失；或是受限于生物样本出口管制法规等因素，无法开展分子分析。另有部分物种已在近期灭绝，仅能通过博物馆的福尔马林固定标本获取其遗存，甚至仅存亚化石样本。
本研究简报提出了一种全新方法，可借助连续性状数据，将隐存类群、近期灭绝类群或假说类群嵌入现存类群的超度量系统发育树中。该方法基于对现有基于连续性状构建系统发育树的最大似然（Maximum Likelihood, ML）法的简易改进。研究表明，该方法在模拟演化树与模拟数据上均表现优异。
随后，我们将该方法应用于将库莱布拉岛巨型安乐蜥（Anolis roosevelti）嵌入加勒比安乐蜥系统发育树的案例中。Anolis roosevelti属于‘冠层巨型’生态型安乐蜥，被认为曾广泛分布于西属、美属及英属维尔京群岛，但自20世纪30年代起便未再有目击或采集记录。尽管学界普遍认为该物种与波多黎各巨型安乐蜥（A. cuvieri）亲缘关系紧密，但我们的最大似然法分析结果显示，Anolis roosevelti实则位于演化树的另一分支，与一组形态相似的物种构成演化支。不过，我们无法否定Anolis roosevelti作为A. cuvieri姊妹分类群的系统发育位置；但该物种与波多黎各其余安乐蜥类群存在紧密亲缘关系的假设，已被本方法显著排除。