Data from: Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time ...

• Main Authors: McComish, Bennet, Charleston, Michael, Parks, Matthew, Baroni, Carlo, Salvatore, Maria Cristina, Li, Ruiqiang, Zhang, Guojie, Millar, Craig, Holland, Barbara, Lambert, David
• Format: Dataset
• Language: English
• Published: Dryad 2019
• Subjects: Aptenodytes forsteri; Apaloderma vittatum; Egretta garzetta; Cariama cristata; Gavia stellata; Pterocles gutturalis; Takifugu rubripes; Haliaeetus albicilla; Picoides pubescens; Anolis carolinensis; Calypte anna; Cuculus canorus; Merops nubicus; Struthio camelus australis; Cavia porcellus; Manacus vitellinus; Xenopus tropicalis; Chaetura pelagica; Meleagris gallopavo; Gallus gallus; Pelecanus crispus; Branchiostoma floridae; Buceros rhinoceros silvestris; Homo Sapiens; Melopsittacus undulatus; Balearica regulorum gibbericeps; Nestor notabilis; Antrostomus carolinensis; Cathartes aura; Mesitornis unicolor; Opisthocomus hoazin; Phoenicopterus ruber ruber; Equus caballus; Mus musculus; Charadrius vociferus; Leptosomus discolor; Colius striatus; Rattus norvegicus; Danio rerio; Petromyzon marinus; Tauraco erythrolophus; Fulmarus glacialis; Corvus brachyrhynchos; Taeniopygia guttata; Nipponia nippon; Pongo abelii; Monodelphis domestica; Haliaeetus leucocephalus; Chlamydotis macqueenii; Eurypyga helias; Kya; Nestor
• Online Access: https://dx.doi.org/10.5061/dryad.7gt3rg2; https://datadryad.org/stash/dataset/doi:10.5061/dryad.7gt3rg2

Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over two time scales: one based on Adélie penguin samples dating to approximately 46.5 kya, the other dating to the diversification of chordates more than 500 Mya. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long time scales, particularly in ... : # Data from: Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time This file explains the code and data that accompany McComish et al (2024) Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time. For further information, please contact Bennet McComish at . Each step in the analysis is described below, with the names of relevant scripts and archives of output files. Please note that many of the scripts contain hard-coded file paths and will need to be modified to run on a different system. In some cases, example scripts for one species or sample are given, and scripts for other species/samples can be generated by substituting species/sample codes and names as appropriate. Scripts are bundled together in the file code.tar.gz. Reference genomes, annotations, and pairwise alignments can be found at (for the 48 bird species) and (for the other 15 vertebrates). Adélie penguin sample reads can be found at . Species codes used ...