Basin-scale patterns of common carp physiological condition associated with EDC exposure in a large Anthropocene river

Environmental Biology of Fishes - Common carp (Cyprinus carpio) is a commercially and recreationally important species that has declined by > 80% across the Illinois River basin since the...     

Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes

The migration-selection balance often governs the evolution of lineages, and speciation with gene flow is now considered common across the tree of life. Ecological speciation is a process that can facilitate divergence despite gene flow due to strong selective pressures caused by ecological differences; however, the exact traits under selection are often unknown. The transition from freshwater to saltwater habitats provides strong selection targeting traits with osmoregulatory function. Several lineages of North American watersnakes (Nerodia spp.) are known to occur in saltwater habitat and represent a useful system for studying speciation by providing an opportunity to investigate gene flow and evaluate how species boundaries are maintained or degraded. We use double digest restriction-site associated DNA sequencing to characterize the migration-selection balance and test for evidence of ecological divergence within the Nerodia fasciata-clarkii complex in Florida. We find evidence of high intraspecific gene flow with a pattern of isolation-by-distance underlying subspecific lineages. However, we identify genetic structure indicative of reduced gene flow between inland and coastal lineages suggesting divergence due to isolation-by-environment. This pattern is consistent with observed environmental differences where the amount of admixture decreases with increased salinity. Furthermore, we identify significantly enriched terms related to osmoregulatory function among a set of candidate loci, including several genes that have been previously implicated in adaptation to salinity stress. Collectively, our results demonstrate that ecological differences, likely driven by salinity, cause strong divergent selection which promotes divergence in the N. fasciata-clarkii complex despite significant gene flow.     

Genetic evidence for seasonal consumption of monkfish (Lophius spp.) and salmonids (Salmo spp.) by gray seals

Recoveries of gray seal (Halichoerus grypus) populations across their eastern Atlantic distribution have led to a steady increase in seal-fishery interactions. Fishers have estimated depredation of salmonids (Salmo spp.) and monkfish (Lophius spp.) as high as 40% and 59% respectively in Ireland. However, empirical evidence for the consumption of these species has been extremely limited due to diagnostic hard part remains not being found in scats or stomach samples. We applied species-specific primers and tested for the presence of monkfish and salmonids in gray seal diet genetically using quantitative polymerase chain reaction (qPCR) on scats. Monkfish occurred in 29.7% of sampled scats, while salmonids occurred in 12.7%. Seasonal and regional variability in occurrence were noted for both species, likely related to the migratory behavior of the prey species and proximity of seal haul-outs to aquaculture sites. Traditional hard part analysis of scats, including scats that tested positive for monkfish and salmonid DNA, failed to find any evidence of either species. This study provides important empirical evidence for the consumption of these species in Ireland that can inform management.     

Unexpected larval habit of Listronotus bonariensis (Coleoptera: Curculionidae) raises questions about population dynamics analysis and management

Listronotus bonariensis (Kuschel) is a pest of agriculturally important graminaceous species, with mining larvae that kill the stems of the host plants. In this study, larval populations were measured in spring and summer in irrigated dairy grassland comprising Lolium perenne L. (cv. Nui) with and without the endophyte Epichloë festucae var. lolii Latch, M.J. Chr. and Samuels and Poa annua L.. Larvae were extracted from tillers taken from the swards of these two grass species and extracted from turves, and L. bonariensis population densities were estimated from tiller and turf larval counts on a m⁻² basis. Over the study period, the total number of larvae and larval densities extracted from turves was on average 2× greater than indicated from tillers. In most seasons, larval densities from turves were significantly higher than those from the tillers, though there was no correlation between tiller and turf larval densities. Mean head capsule widths of larvae emerging from turf samples showed significant seasonal effects compared with tillers, while mean head capsule widths of all four instars were significantly greater when extracted from tillers compared with turves. There was a significant endophyte effect on head capsule widths of larvae collected in summer, but the effect was not consistent across instars or source. Conversely, no significant endophyte effect on head capsule width was found in spring populations from either tillers or turves. This study shows that in irrigated dairy pasture, a high proportion of L. bonariensis larvae can live externally of tillers, presumably among the organic matter around the base of grasses in irrigated dairy pasture, and that density estimates based only on tiller populations will have significantly underestimated actual numbers. Having a precise indication of larval population densities is essential when developing life tables or determining economic damage threshold levels.     

A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.)

The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997–2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01–3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype–phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.