Data from: Bayesian divergence-time estimation with genome-wide SNP data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian isthmus

The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multi-species coalescent model, we here develop a new method combining the SNP-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the multi-species coalescent model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new RAD-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

长期以来，巴拿马地峡（Isthmus of Panama）的闭合被认为是分子分化时间估计领域最明确的生物地理校准点之一。然而，近期的地质与生物学证据对学界普遍认为的巴拿马地峡初始闭合发生于约3 Ma的时间提出了质疑，反而表明早在中新世中期或晚期就存在临时性陆桥。支撑这些更早陆桥存在的生物学证据，要么仅基于少量分子标记，要么采用了全基因组序列串联分析的方法——而该方法已知可能会产生具有误导性的分支长度与分化时间估计结果，进而损害此类证据的可靠性。为了借助更适宜的多物种溯祖模型（multi-species coalescent model）开展基因组数据的分化时间估计，本文开发了一种全新方法：将软件SNAPP基于单核苷酸多态性（SNP, single nucleotide polymorphism）的贝叶斯物种树推断，与可通过化石或生物地理约束进行校准的分子钟模型相结合。我们通过模拟实验验证了该方法的有效性，并将其用于重新分析新热带行军蚁（Dorylinae亚科）的基因组数据——此前这类数据支持中美洲与南美洲种群的分化时间早于约3 Ma的地峡闭合事件。基于多物种溯祖模型的重新分析将所有此类分化时间修正至3 Ma以内，这表明此前支持临时性陆桥更早存在的估算结果，至少部分是由串联分析方法所导致的人为假象。随后，我们将该方法应用于一套全新的新热带海鲶（海鲶科Ariidae）限制性位点关联DNA测序（RAD-seq, restriction-site associated DNA sequencing）数据集，并利用大量化石记录信息对其物种树进行校准。我们在加勒比海与太平洋海鲶类群之间发现了一系列发生于约10 Ma的分化事件，这表明与地峡形成相关的过程早在中新世晚期——即巴拿马地峡最终闭合数百万年前——就已引发了异域成种作用。