The challenges associated with sampling rare species or populations can limit our ability to make accurate and informed estimates of biodiversity for clades or ecosystems. This may be particularly true for tropical trees, which tend to be poorly sampled, and are thought to harbor extensive cryptic diversity. Here, we integrate genomics, morphology, and geography to estimate the number of species in a clade of dioecious tropical trees (Canarium L.; Burseraceae) endemic to Madagascar, for which previous taxonomic treatments have recognized between one and 33 species. By sampling genomic data from even a limited number of individuals per taxon, we were able to clearly reject both previous hypotheses, and support instead an intermediate number of taxa. We recognize at least six distinct clades based on genetic structure and species delimitation analyses that correspond clearly with geographic and discrete morphological differences. Two widespread clades co-occur broadly throughout eastern wet forests, one clade is endemic to western dry forests, and several slightly admixed clades are more narrowly distributed in mountainous regions in the north. Multiple previously described taxa were recovered as paraphyletic in our analyses, some of which were associated with admixed individuals, suggesting that hybridization contributes to taxonomic difficulties in Canarium. An improved understanding of Canarium species diversity has important implications for conservation efforts and understanding the origins of diversity in Madagascar. Our study shows that even limited genomic sampling, when combined with geography and morphology, can greatly improve estimates of species diversity for difficult tropical clades.

与稀有物种或种群采样有关的挑战可能会限制我们对进化枝或生态系统的生物多样性做出准确而明智的估计的能力。对于热带树木来说尤其如此，因为热带树木往往采样较差，并且被认为具有广泛的神秘多样性。在这里，我们结合了基因组学，形态学和地理学，以估计一棵雌雄异株的热带树木（CanariumL .; Burseraceae）是马达加斯加特有的，以前的分类学处理已经认识到其中的一种至33种。通过从每个分类单元中抽取有限数量的个体的基因组数据，我们能够清楚地拒绝先前的两个假设，而支持中等数量的分类单元。根据遗传结构和物种定界分析，我们至少识别出六个不同的进化枝，它们清楚地对应于地理和离散的形态学差异。在东部的湿润森林中，广泛分布着两个进化枝，一个进化枝是西部干旱森林特有的，而在北部山区，一些稍微混合的进化枝则分布较窄。在我们的分析中，发现多个先前描述的分类单元是共生的，其中一些与混合个体相关，天竺葵。更好地了解天竺葵的物种多样性，对保护工作和了解马达加斯加的物种多样性具有重要意义。我们的研究表明，即使将有限的基因组采样与地理和形态相结合，也可以大大提高对困难热带进化枝物种多样性的估计。