Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

Abstract

Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri , a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

“…Higher temperatures can serve as a proxy for shallower depths, and therefore more incoming radiation. This may explain why our dataset shows enrichment of phototransduction genes as a response to temperature while previous studies have observed phototransduction gene enrichment in response to kairomones [31].…”

“…This study and Tams et al explicitly avoided the addition of conspecific alarm cues in our kairomone mixture as to measure only the effect of predator odors [73]. Other studies, such as [30, 31], tested responses to a mixture of predator-specific odors and alarm cues released by consumed conspecifics. Mitchell et al call for the separation of nomenclature between cues released from the predator regardless of diet and diet-specific cues [32], so that researchers can more accurately discern the independent effects of these different kairomone compounds.…”

“…D. pulicaria predation by O. mykiss in artificially stocked lakes is well established, specifically predation by juvenile rainbow trout [27,28], O. mykiss is one of the most abundant species for stocking previously fishless lakes in the Sierra Nevada mountains, the source of our Daphnia samples [29]. O. mykiss were fed TetraMin Tropical Flakes (Tetra, Blacksburg, Virginia, USA) prior to kairomone collection, rather than juvenile conspecific daphniids as in some other studies [30,31]. We selected this method to 8 minimize the presence of conspecific alarm cues in the isolated kairomone media, so that we could measure the phenotypic and genetic responses to only predator-released, diet agnostic kairomone cues.…”

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

“…O . mykiss were fed TetraMin Tropical Flakes (Tetra, Blacksburg, Virginia, USA) prior to kairomone collection, rather than juvenile conspecific daphniids as in some other studies [ 27 , 28 ]. We selected this method to minimize the presence of conspecific alarm cues in the isolated kairomone media, so that we could measure the phenotypic and genetic responses to only predator-released, diet agnostic kairomone cues.…”

Adaptive variation in homologue number within transcript families promotes expression divergence in reef‐building coral

“…This type of rapid gene evolution is particularly common in gene families involved in arms races such as immune genes (Machado & Ottolini, 2015; Malmstrøm et al, 2016). However, other types of ecologically relevant adaptation have been shown to follow this pattern of rapid changes in copy number such as expansions in hypoxia‐related genes in high‐altitude yaks (Qiu et al, 2012) and chemoreception and vision genes for predator responses in Daphnia (Zhang et al, 2021).…”