Lab exercise week Monday February 28, 2022 The Antillean manatee (Trichechus manatus) is a large marine mammal historically distributed across the Caribbean islands and coastal waters of Gulf of Mexico. Little is known about the extent of connectivity across the main remaining populations. Recent report of manatees moving between Florida and Cuba suggest that they may cross open water. However, a comprehensive picture of connectivity and population structure is lacking. The best-studied population include the large Florida population, Puerto Rico and Belize. Recent data has been collected on Cuban manatees as well. A recent graduate student from UF (Dr. Anmari Alvarez) added genetic data from Cuban manatees to assess the extent of overall connectivity across the Caribbean. As you can see on the map, Cuba may play a predominant role as a stepping-stone, facilitating connectivity across the region. The data you will be using includes two types of markers: 1) a microsatellite dataset consisting of 12 loci, and 2) a single nucleotide polymorphism dataset with > 1000 loci. Much of this exercise will reinforce last week’s but you will also be incorporating a PCA to qualitatively assess the extent of genetic substructure, and you will be contrasting patterns between the two marker types. The assignment will include working through the script to assess genetic structure based on the microsatellite data, then duplicating the script for the SNP data and changing the necessary variables within the code itself. General research question you will explore this week (actual assignment questions are listed in Canvas quiz): 1)
How genetically diverse are manatees? 2)
Is genetic structure more or less pronounced when assessed using microsatellites or SNPs? 3)
What type of population genetic model (i.e., island, stepping stone, isolation by distance) would best describe the pattern of variation seen amongst manatee populations? Figure 1. Mother with nursing calf
Figure 2. Map of Caribbean illustrating the geographic representation of Manatee genotypes represented in this project (purple lines).
