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1. Genome-Wide Allele-Specific Expression in Obligately Asexual Daphnia pulex and the Implications for the Genetic Basis of Asexuality

   https://doi.org/10.1093/gbe/evab243  

   Ye, Zhiqiang; Jiang, Xiaoqian; Pfrender, Michael E; Lynch, Michael (November 2021, Genome Biology and Evolution)

   Betancourt, Andrea (Ed.)

   Abstract Although obligately asexual lineages are thought to experience selective disadvantages associated with reduced efficiency of fixing beneficial mutations and purging deleterious mutations, such lineages are phylogenetically and geographically widespread. However, despite several genome-wide association studies, little is known about the genetic elements underlying the origin of obligate asexuality and how they spread. Because many obligately asexual lineages have hybrid origins, it has been suggested that asexuality is caused by the unbalanced expression of alleles from the hybridizing species. Here, we investigate this idea by identifying genes with allele-specific expression (ASE) in a Daphnia pulex population, in which obligate parthenogens (OP) and cyclical parthenogens (CP) coexist, with the OP clones having been originally derived from hybridization between CP D. pulex and its sister species, Daphnia pulicaria. OP D. pulex have significantly more ASE genes (ASEGs) than do CP D. pulex. Whole-genomic comparison of OP and CP clones revealed ∼15,000 OP-specific markers and 42 consistent ASEGs enriched in marker-defined regions. Ten of the 42 ASEGs have alleles coding for different protein sequences, suggesting functional differences between the products of the two parental alleles. At least three of these ten genes appear to be directly involved in meiosis-related processes, for example, RanBP2 can cause abnormal chromosome segregation in anaphase I, and the presence of Wee1 in immature oocytes leads to failure to enter meiosis II. These results provide a guide for future molecular resolution of the genetic basis of the transition to ameiotic parthenogenesis. 

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2. Evolutionary change in metabolic rate of Daphnia pulicaria following invasion by the predator Bythotrephes longimanus

   https://doi.org/10.1002/ece3.9003  

   Rani, Varsha; Burton, Tim; Walsh, Matthew; Einum, Sigurd (June 2022, Ecology and Evolution)

   Abstract Metabolic rate is a trait that may evolve in response to the direct and indirect effects of predator‐induced mortality. Predators may indirectly alter selection by lowering prey densities and increasing resource availability or by intensifying resource limitation through changes in prey behavior (e.g., use of less productive areas). In the current study, we quantify the evolution of metabolic rate in the zooplanktonDaphnia pulicariafollowing an invasive event by the predatorBythotrephes longimanusin Lake Mendota, Wisconsin, US. This invasion has been shown to dramatically impactD.pulicaria, causing a ~60% decline in their biomass. Using a resurrection ecology approach, we compared the metabolic rate ofD.pulicariaclones originating prior to theBythotrephesinvasion with that of clones having evolved in the presence ofBythotrephes. We observed a 7.4% reduction in metabolic rate among post‐invasive clones compared to pre‐invasive clones and discuss the potential roles of direct and indirect selection in driving this change. 

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3. Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation

   https://doi.org/10.1093/gbe/evaa182  

   Neupane, Swatantra; Xu, Sen (October 2020, Genome Biology and Evolution)

   Baer, Charles (Ed.)

   Abstract Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution. 

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4. Resurrection genomics provides molecular and phenotypic evidence of rapid adaptation to salinization in a keystone aquatic species

   https://doi.org/10.1073/pnas.2217276120  

   Wersebe, Matthew J.; Weider, Lawrence J. (February 2023, Proceedings of the National Academy of Sciences)

   Ecologists and evolutionary biologists are increasingly cognizant of rapid adaptation in wild populations. Rapid adaptation to anthropogenic environmental change is critical for maintaining biodiversity and ecosystems services into the future. Anthropogenic salinization of freshwater ecosystems is quickly emerging as a primary threat, which is well documented in the northern temperate ecoregion. Specifically, many northern temperate lakes have undergone extensive salinization because of urbanization and the associated increase in impervious surfaces causing runoff, and the extensive use of road deicing salts (e.g., NaCl). It remains unclear whether increasing salinization will lead to extirpation of species from these systems. Using a “resurrection genomics” approach, we investigated whether the keystone aquatic herbivore,Daphnia pulicaria,has evolved increased salinity tolerance in a severely salinized lake located in Minnesota, USA. Whole-genome resequencing of 54Daphniaclones from the lake and hatched from resting eggs that represent a 25-y temporal contrast demonstrates that many regions of the genome containing genes related to osmoregulation are under selection in the study population. Tolerance assays of clones revealed that the most recent clones are more tolerant to salinity than older clones; this pattern is concomitant with the temporal pattern of stabilizing salinity in this lake. Together, our results demonstrate that keystone species such asDaphniacan rapidly adapt to increasing freshwater salinization. Further, our results indicate that rapid adaptation to salinity may allow lakeDaphniapopulations to persist in the face of anthropogenic salinization maintaining the food webs and ecosystem services they support despite global environmental change. 

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5. Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

   https://doi.org/10.1093/gbe/evad202  

   Ye, Zhiqiang; Pfrender, Michael E; Lynch, Michael (November 2023, Genome Biology and Evolution)

   Abstract Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. In this study, we compared population-genomics data between Daphnia pulex and Daphnia pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. Daphnia pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, a higher incidence of private alleles, and a substantially more linkage disequilibrium than D. pulex. Positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended life span in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Additionally, we found that the two species have similar average evolutionary rates at the DNA-sequence level, although approximately 160 genes have significantly different rates in the two lineages. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats. 

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