Evolutionary Genomics of a Subdivided Species

Abstract

The ways in which genetic variation is distributed within and among populations is a key determinant of the evolutionary features of a species. However, most comprehensive studies of these features have been restricted to studies of subdivision in settings known to have been driven by local adaptation, leaving our understanding of the natural dispersion of allelic variation less than ideal. Here, we present a geographic population-genomic analysis of ten populations of the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics. These populations exhibit a pattern of moderate isolation by distance, with an average migration rate of 0.6 individuals per generation, and average effective population sizes of ∼ 650, 000 individuals. Most populations contain numerous private alleles, and genomic scans highlight the presence of islands of excessively high population subdivision for more common alleles. A large fraction of such islands of population divergence likely reflect historical neutral changes, including rare stochastic migration and hybridization events. The data do point to local adaptive divergence, although the precise nature of the relevant variation is diffuse and cannot be associated with particular loci, despite the very large sample sizes involved in this study. In contrast, an analysis of between-species divergence highlights positive selection operating on a large set of genes with functions nearly nonoverlapping with those involved in local adaptation, in particular ribosome structure, mitochondrial bioenergetics, light reception and response, detoxification, and gene regulation. These results set the stage for using D. pulex as a model for understanding the relationship between molecular and cellular evolution in the context of natural environments.

The Genome-wide Signature of Short-term Temporal Selection

“…Generally, the population enters a phase of sexual reproduction and resting egg production by June, as the pond dries up and remains so until the following spring. Genotype frequencies at the time of sampling closely adhere to Hardy-Weinberg expectations, as is true for most other temporary-pond populations of D. pulex (Maruki et al 2022).…”

“…After extraction of DNA, the clonal samples were barcoded, multiplexed, and sequenced to an average of 9× coverage per clone to generate 100 to 150-bp paired-end reads, which were then mapped to the high-quality reference assembly for a clone taken from an adjacent population (Supplemental Text). Following various filters for quality control (Maruki et al 2022), allelefrequency estimates were obtained with a maximum-likelihood procedure (Maruki and Lynch 2015).…”

“…Thee inferred N e estimates are inconsistent with standing-levels of variation. Based on levels of silent-site diversity, the PA population is estimated to have a long-term effective population size of ∼ 600, 000, and studies of nine other populations in the same geographic region and with similar ecologies have long-term N e in the range of 430,000 to 750,000 (Lynch et al 2020;Maruki et al 2022). Thus, given the major disparity between the temporal estimates of N e noted above and those based on standing levels of variation, we conclude that the vast majority of observed temporal changes in allele frequencies reported on below are too large to be reasonably attributable to random genetic drift.…”

“…However, given the > 2, 000, 000 informative sites in the study, it remains possible to estimate the average intensity and variance of selection operating on sites of specific functional significance and in particular chromosomal locations. Nearly all polymorphic sites in the study population contain just two alleles (> 97%; Maruki et al 2022), but as we cannot yet be certain of the ancestral states at individual sites, the following analyses are oriented on minor alleles at biallelic sites (i.e., those with average frequencies across all years < 0.5); the estimated selection coefficients for major alleles have identical absolute values and simply differ in sign.…”

Analysis of genetic relationship and inbreeding coefficient of Hetian Qing donkey based on simplified genome sequencing

“…For most species, due to human activities and environmental factors, it is easy to lead to changes in gene flow among species, resulting in genetic differentiation of different degrees among populations in the region and changing the genetic structure of species. Therefore, species genomics has become an important means of species research [7]. According to the different methods of constructing a genome library, simplified genome sequencing technology can be divided into reduced representation library sequencing (RRLs), restriction site-associated DNA (RAD), and Genotyping by Sequencing (GBS).…”