Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applie...巴拿马地峡的形成与中美洲海道（Central American Seaway, CAS）的最终闭合，为检测DNA替换速率提供了独立的校准锚点。这一异域分隔事件已被广泛用于估算线粒体基因组的替换速率，并为其他类群的进化事件定年。在系统发育与进化研究中，核序列数据正日益被用于补充线粒体数据集；此类研究将得益于源自核基因组的DNA替换速率与模式相关信息。 为估算全基因组中性突变率（μ），研究人员为鼓虾属（Alpheus）的3个跨地峡物种对构建了基因型测序（genotype-by-sequencing, GBS）数据集。研究人员评估了一系列生物信息学过滤参数，以尽可能降低由单核苷酸多态性（Single Nucleotide Polymorphism, SNP）过滤所可能引发的突变率估算偏差。本研究采用贝叶斯溯祖分析方法（G-PhoCS）进行……