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

BACKGROUND: 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. RESULTS: 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) applied to 44,960 GBS loci, we estimated µ to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. CONCLUSIONS: Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

Adding Authenticity to Inquiry in a First-Year, Research-Based, Biology Laboratory Course.

Course-based undergraduate research experiences (CUREs) are an effective way to integrate research into an undergraduate science curriculum and extend research experiences to a large, diverse group of early-career students. We developed a biology CURE at the University of Miami (UM) called the UM Authentic Research Laboratories (UMARL), in which groups of first-year students investigated novel questions and conducted projects of their own design related to the research themes of the faculty instructors. Herein, we describe the implementation and student outcomes of this long-running CURE. Using a national survey of student learning through research experiences in courses, we found that UMARL led to high student self-reported learning gains in research skills such as data analysis and science communication, as well as personal development skills such as self-confidence and self-efficacy. Our analysis of academic outcomes revealed that the odds of students who took UMARL engaging in individual research, graduating with a degree in science, technology, engineering, or mathematics (STEM) within 4 years, and graduating with honors were 1.5-1.7 times greater than the odds for a matched group of students from UM's traditional biology labs. The authenticity of UMARL may have fostered students' confidence that they can do real research, reinforcing their persistence in STEM.