Evolutionary history of alpine and subalpine Daphnia in western North America

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Evolution and diversity of two cisco forms in an outlet of glacial Lake Algonquin

The diversity of Laurentian Great Lakes ciscoes (Coregonus artedi, sensu lato) arose via repeated local adaptive divergence including deepwater ciscoes that are now extirpated or threatened. The nigripinnis form, or Blackfin Cisco, is extirpated from the Great Lakes and remains only in Lake Nipigon. Putative nigripinnis populations were recently discovered in sympatry with artedi in a historical drainage system of glacial Lake Algonquin, the precursor of lakes Michigan and Huron. Given the apparent convergence on Great Lakes form, we labeled this form blackfin. Here, we test the hypothesis that nigripinnis may have colonized this area from the Great Lakes as a distinct lineage. It would then represent a relict occurrence of the historical diversity of Great Lakes ciscoes. Alternatively, blackfin could have evolved in situ in several lakes. We captured more than 600 individuals in the benthic or pelagic habitat in 14 lakes in or near Algonquin Provincial Park (Ontario, Canada). Fish were compared based on habitat, morphology, and genetic variation at 6,676 SNPs. Contrary to our expectations, both cisco and blackfin belonged to an Atlantic lineage that colonized the area from the east, not from the Great Lakes. Sympatric cisco and blackfin were closely related while fish from different lakes were genetically differentiated, strongly suggesting the repeated in situ origin of each form. Across lakes, there was a continuum of ecological, morphological, and genetic differentiation that could be associated with alternative resources and lake characteristics. This study uncovers a new component of cisco diversity in inland lakes of Canada that evolved independently from ciscoes of the Laurentian Great lakes. The diversity of cisco revealed in this study and across their Canadian range presents a challenge for designating conservation units at the intraspecific level within the framework of the Committee on the Status of Endangered Wildlife in Canada (COSEWIC).     

Specificity of root microbiomes in native‐grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization

Plants recruit microbial communities from the soil in which they germinate. Our understanding of the recruitment process and the factors affecting it is still limited for most microbial taxa. We analysed several factors potentially affecting root microbiome structure – the importance of geographic location of natural populations, the microbiome of native seeds as putative source of colonization and the effect of a plant's response to UVB exposure on root colonization of highly abundant species. The microbiome of Nicotiana attenuata seeds was determined by a culture‐dependent and culture‐independent approach, and the root microbiome of natural N. attenuata populations from five different locations was analysed using 454‐pyrosequencing. To specifically address the influence of UVB light on root colonization by Deinococcus, a genus abundant and consistently present in N. attenuata roots, transgenic lines impaired in UVB perception (irUVR8) and response (irCHAL) were investigated in a microcosm experiment with/without UVB supplementation using a synthetic bacterial community. The seed microbiome analysis indicated that N. attenuata seeds are sterile. Alpha and beta diversities of native root bacterial communities differed significantly between soil and root, while location had only a significant effect on the fungal but not the bacterial root communities. With UVB supplementation, root colonization of Deinococcus increased in wild type, but decreased in irUVR8 and irCHAL plants compared to nontreated plants. Our results suggest that N. attenuata recruits a core root microbiome exclusively from soil, with fungal root colonization being less selective than bacterial colonization. Root colonization by Deinococcus depends on the plant's response to UVB.     

Variation in chronic radiation exposure does not drive life history divergence among Daphnia populations across the Chernobyl Exclusion Zone

Ionizing radiation is a mutagen with known negative impacts on individual fitness. However, much less is known about how these individual fitness effects translate into population‐level variation in natural environments that have experienced varying levels of radiation exposure. In this study, we sampled genotypes of the freshwater crustacean, Daphnia pulex, from the eight inhabited lakes across the Chernobyl Exclusion Zone (CEZ). Each lake has experienced very different levels of chronic radiation exposure since a nuclear power reactor exploded there over thirty years ago. The sampled Daphnia genotypes represent genetic snapshots of current populations and allowed us to examine fitness‐related traits under controlled laboratory conditions at UK background dose rates. We found that whilst there was variation in survival and schedules of reproduction among populations, there was no compelling evidence that this was driven by variation in exposure to radiation. Previous studies have shown that controlled exposure to radiation at dose rates included in the range measured in the current study reduce survival, or fecundity, or both. One limitation of this study is the lack of available sites at high dose rates, and future work could test life history variation in various organisms at other high radiation areas. Our results are nevertheless consistent with the idea that other ecological factors, for example competition, predation or parasitism, are likely to play a much bigger role in driving variation among populations than exposure to the high radiation dose rates found in the CEZ. These findings clearly demonstrate that it is important to examine the potential negative effects of radiation across wild populations that are subject to many and varied selection pressures as a result of complex ecological interactions.     

Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

Successful urban colonization by formerly rural species represents an ideal situation in which to study adaptation to novel environments. We address this issue using candidate genes for behavioural traits that are expected to play a role in such colonization events. We identified and genotyped 16 polymorphisms in candidate genes for circadian rhythms, harm avoidance and migratory and exploratory behaviour in 12 paired urban and rural populations of the blackbird Turdus merula across the Western Palaearctic. An exonic microsatellite in the SERT gene, a candidate gene for harm avoidance behaviour, exhibited a highly significant association with habitat type in an analysis conducted across all populations. Genetic divergence at this locus was consistent in 10 of the 12 population pairs; this contrasts with previously reported stochastic genetic divergence between these populations at random markers. Our results indicate that behavioural traits related to harm avoidance and associated with the SERT polymorphism experience selection pressures during most blackbird urbanization events. These events thus appear to be influenced by homogeneous adaptive processes in addition to previously reported demographic founder events.     

Increases in crop pests caused by Wasmannia auropunctata in Solomon Islands subsistence gardens

The impacts of Wasmannia auropunctata (the little fire ant) on the native biota and subsistence agriculture in the Solomon Islands are poorly understood. This species was originally introduced as a biological control against nut‐fall bugs (Amblypelta sp.) around 30 years ago and in the intervening time has spread throughout the Solomon Islands, aided movement of produce and planting material. It is now itself a major pest of coconut, cocoa and subsistence agriculture. In this study, we show the negative effects of this invasive ant on subsistence agriculture in the Solomon Islands. We do this by (i) assessing the presence of insect pests that develop a mutual relationship with W. auropunctata on four common subsistence crops; and (ii) measuring the impact of a significant pest (Tarophagus sp.) and its natural predator the bug Cyrtohinus fulvus, in the presence and absence of W. auropunctata on taro crops. The existence of insect pests that form a mutual relationship with W. auropunctata was measured in a total of 36 gardens of the four subsistence crops. This was conducted through standardized visual searches, plus identification and collecting from randomly selected plants within the gardens. A number of additional insect pests causing major problems to subsistence crops have also developed mutual relationships with W. auropunctata. Infested taro gardens have more Tarophagus sp. compared with taro plants that are free of the little fire ant. The presence and abundance of Wasmannia therefore has the potential to inflict considerable crop loss in rural subsistence gardens in the Solomon Islands.     

Ionizing radiation causes increased tau phosphorylation in primary neurons

Radiotherapy is the major treatment modality for primary and metastatic brain tumors which involves the exposure of brain to ionizing radiation. Ionizing radiation can induce various detrimental pathophysiological effects in the adult brain, and Alzheimer's disease and related neurodegenerative disorders are considered to be late effects of radiation. In this study, we investigated whether ionizing radiation causes changes in tau phosphorylation in cultured primary neurons similar to that in Alzheimer's disease. We demonstrated that exposure to 0.5 or 2 Gy γ rays causes increased phosphorylation of tau protein at several phosphorylation sites in a time‐ and dose‐dependent manner. Consistently, we also found ionizing radiation causes increased activation of GSK3β, c‐Jun N‐terminal kinase and extracellular signal‐regulated kinase before radiation‐induced increase in tau phosphorylation. Specific inhibitors of these kinases almost fully blocked radiation‐induced tau phosphorylation. Our studies further revealed that oxidative stress plays an important role in ionizing radiation‐induced tau phosphorylation, likely through the activation of c‐Jun N‐terminal kinase and extracellular signal‐regulated kinase, but not GSK3β. Overall, our studies suggest that ionizing radiation may cause increased risk for development of Alzheimer's disease by promoting abnormal tau phosphorylation.

     

Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds

The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome‐wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.     

High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment

Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (F_ST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.     

High acclimation potential in floating Macrocystis pyrifera to abiotic conditions even under grazing pressure – a field study

The persistence of floating seaweeds, which depends on abiotic conditions but also herbivory, had previously been mostly tested in outdoor mesocosm experiments. In order to investigate if the obtained mesocosm results of high seaweed persistence under natural environmental conditions and under grazing pressure can be extrapolated to field situations, we conducted in situ experiments. During two summers (2007 and 2008), Macrocystis pyrifera was tethered (for 14 d) to lines in the presence and absence of the amphipod Peramphithoe femorata at three sites (Iquique, Coquimbo, Calfuco). We hypothesized that grazing damage and seaweed persistence vary among sites due to different abiotic factors. By incubating the sporophytes in mesh bags, we were either able to isolate (grazing) or exclude (control) amphipods. To test for a mesh bag artifact, a set of sporophytes was incubated without mesh bags (natural). Mesh bags used to exclude herbivores influenced sporophyte growth and physiological performance. The chlorophyll a (Chl a) content depended largely on grazers and grazed sporophytes grew less than natural and control sporophytes within the two summers. A decrease in Chl a content was found for the sites with the highest prevailing irradiances and temperatures, suggesting an efficient acclimation to these sea surface conditions. Our field‐based results of sporophyte acclimation ability even under grazing pressure widely align with previous mesocosm results. We conclude that M. pyrifera and other temperate floating seaweeds can function as long‐distance dispersal vectors even with hitchhiking mesoherbivores.     

AUXIN RESPONSE FACTOR 3 integrates the functions of AGAMOUS and APETALA2 in floral meristem determinacy

In Arabidopsis, AUXIN RESPONSE FACTOR 3 (ARF3) belongs to the auxin response factor (ARF) family that regulates the expression of auxin‐responsive genes. ARF3 is known to function in leaf polarity specification and gynoecium patterning. In this study, we discovered a previously unknown role for ARF3 in floral meristem (FM) determinacy through the isolation and characterization of a mutant of ARF3 that enhanced the FM determinacy defects of agamous (ag)‐10, a weak ag allele. Central players in FM determinacy include WUSCHEL (WUS), a gene critical for FM maintenance, and AG and APETALA2 (AP2), which regulate FM determinacy by repression and promotion of WUS expression, respectively. We showed that ARF3 confers FM determinacy through repression of WUS expression, and associates with the WUS locus in part in an AG‐dependent manner. We demonstrated that ARF3 is a direct target of AP2 and partially mediates AP2's function in FM determinacy. ARF3 exhibits dynamic and complex expression patterns in floral organ primordia; altering the patterns spatially compromised FM determinacy. This study uncovered a role for ARF3 in FM determinacy and revealed relationships among genes in the genetic network governing FM determinacy.     

Wheat's wild relatives vary in their response to nitrogen and ozone

The wild relatives of bread wheat ( Triticum aestivum ) are valued by plant breeders for their genetic diversity. However, increasing levels of nitrogen (N) deposition and ground‐level ozone (O₃) threaten plant biodiversity in the Mediterranean and Near‐East, a hotspot for many crop wild relatives. Knowledge of the effect of these air pollutants in combination is still limited, but early indications are that effects vary depending on the level of pollutants, and on the sensitivity of the species to N and O₃. This study examined the responses of four important wheat wild relatives ( Aegilops tauschii , Aegilops speltoides , Triticum dicoccoides and Triticum monococcum ) and one modern wheat cultivar ( T. aestivum ‘Cadenza’) to treatments of N (equivalent to 50 kg ha^?1 year^?1 ammonium nitrate) and O₃ (100 ppb for 21 days), alone and in combination. Measurements included root, shoot and seed biomass, and electrolyte ratios. The O₃ sensitivity of A. tauschii and T. aestivum ‘Cadenza’ were exacerbated by the addition of N, while A. speltoides was found to be nitrophilous, with N ameliorating the negative effect of O_3. Both T. aestivum ‘Cadenza’ and T. dicoccoides produced immature seed heads, with the cultivar's seed head biomass reduced in response to O₃ and N + O₃ while that of T. dicoccoides was largely unaffected. These data suggest that all four wild relatives are likely to be affected when N and O₃ air pollutants co‐occur, and there in situ populations may therefore be at risk. Equally, the results of this study can inform use of their beneficial traits by wheat breeders, and alert them to the inadvertent inclusion of N and O₃ sensitivity.     

Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae)

Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata , ‘Hishou’, has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip‐like organs. Here, we isolated four DEFICIENS ‐ like and two AGL 6 ‐like genes from H. radiata , and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the ‘Hishou’ cultivar, except Hr DEF ‐C3. The Hr DEF ‐C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in ‘Hishou’. Sequence analysis of the Hr DEF ‐C3 loci revealed that the ‘Hishou’ genome harbored two types of Hr DEF ‐C3 genes: one identical to wild‐type Hr DEF ‐C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between ‘Hishou’ and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the Hr DEF ‐C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the Hr DEF ‐C3 promoter, resulting in the ectopic expression of Hr DEF ‐C3 . As the expression of Hr AGL 6‐C2 was limited to lateral sepals and lip, the overlapping expression of Hr DEF ‐C3 and Hr AGL 6‐C2 is likely to be responsible for the sepal to lip‐like identity in the lateral sepals of the ‘Hishou’ cultivar.     

Leaf surface wax is a source of plant methane formation under UV radiation and in the presence of oxygen

The terrestrial vegetation is a source of UV radiation‐induced aerobic methane (CH₄) release to the atmosphere. Hitherto pectin, a plant structural component, has been considered as the most likely precursor for this CH₄ release. However, most of the leaf pectin is situated below the surface wax layer, and UV transmittance of the cuticle differs among plant species. In some species, the cuticle effectively absorbs and/or reflects UV radiation. Thus, pectin may not necessarily contribute substantially to the UV radiation‐induced CH₄ emission measured at surface level in all species. Here, we investigated the potential of the leaf surface wax itself as a source of UV radiation‐induced leaf aerobic CH₄ formation. Isolated leaf surface wax emitted CH₄ at substantial rates in response to UV radiation. This discovery has implications for how the phenomenon should be scaled to global levels. In relation to this, we demonstrated that the UV radiation‐induced CH₄ emission is independent of leaf area index above unity. Further, we observed that the presence of O₂ in the atmosphere was necessary for achieving the highest rates of CH₄ emission. Methane formation from leaf surface wax is supposedly a two‐step process initiated by a photolytic rearrangement reaction of the major component followed by an α‐cleavage of the generated ketone.     

The response regulator Npun_F1278 is essential for scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme ATCC 29133

Following exposure to long‐wavelength ultraviolet radiation (UVA), some cyanobacteria produce the indole‐alkaloid sunscreen scytonemin. The genomic region associated with scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme includes 18 cotranscribed genes. A two‐component regulatory system (Npun_F1277/Npun_F1278) directly upstream from the biosynthetic genes was identified through comparative genomics and is likely involved in scytonemin regulation. In this study, the response regulator (RR), Npun_F1278, was evaluated for its ability to regulate scytonemin biosynthesis using a mutant strain of N. punctiforme deficient in this gene, hereafter strain Δ1278. Following UVA radiation, the typical stimulus to initiate scytonemin biosynthesis, Δ1278 was incapable of producing scytonemin. A phenotypic characterization of Δ1278 suggests that aside from the ability to produce scytonemin, the deletion of the Npun_F1278 gene does not affect the cellular morphology, cellular differentiation capability, or lipid‐soluble pigment complement of Δ1278 compared to the wildtype. The mutant, however, had a slower specific growth rate under white light and produced ~2.5‐fold more phycocyanin per cell under UVA than the wildtype. Since Δ1278 does not produce scytonemin, this study demonstrates that the RR gene, Npun_F1278, is essential for scytonemin biosynthesis in N. punctiforme. While most of the evaluated effects of this gene appear to be specific for scytonemin, this regulator may also influence the overall health of the cell and phycobiliprotein synthesis, directly or indirectly. This is the first study to identify a regulatory gene involved in the biosynthesis of the sunscreen scytonemin and posits a link between cell growth, pigment synthesis, and sunscreen production.     

Morphological abnormalities in gall-forming aphids in a radiation-contaminated area near Fukushima Daiichi: selective impact of fallout?

To evaluate the impact of fallout from the Fukushima Daiichi Nuclear Power Plant accident on organisms, this study compared the morphology and viability of gall‐forming aphids between the Fukushima population and control populations from noncontaminated areas. This study, in particular, focused on the morphology of first‐instar gall formers derived from the first sexual reproduction after the accident. Of 164 first instars from Tetraneura sorini galls collected 32 km from Fukushima Daiichi in spring 2012, 13.2% exhibited morphological abnormalities, including four conspicuously malformed individuals (2.4%). In contrast, in seven control areas, first instars with abnormal morphology accounted for 0.0–5.1% (on average, 3.8%). The proportions of abnormalities and mortality were significantly higher in Fukushima than in the control areas. Similarly, of 134 first instars from T. nigriabdominalis galls, 5.9% exhibited morphological abnormalities, with one highly malformed individual. However, of 543 second‐generation larvae produced in T. sorini galls, only 0.37% had abnormalities, suggesting that abnormalities found in the first generation were not inherited by the next generation. Although investigation is limited to one study site, this result suggests that radioactive contamination had deleterious effects on embryogenesis in eggs deposited on the bark surface, but a negligible influence on the second generation produced in closed galls. Furthermore, analysis of both species samples collected in spring 2013 indicated that the viability and healthiness of the aphids were significantly improved compared to those in the 2012 samples. Thus, the results of this study suggest the possibility that a reduced level of radiation and/or selection for radiation tolerance may have led to the improved viability and healthiness of the Fukushima population.     

Genomic regions influencing coat color saturation and facial markings in Fleckvieh cattle

Genomic regions associated with coat color and pigmented areas of the head were identified for Fleckvieh (dual‐purpose Simmental), a red‐spotted and white‐headed cattle breed. Coat color was measured with a chromameter, implementing the CIELAB color space and resulting in numerical representation of lightness, color intensity, red/green and blue/yellow color components, rather than subjective classification. Single marker regression analyses with fixed effects of the sex and barn were applied, and significant regions were determined with the local false discovery rate methodology. The PMEL and ERBB3 genes on chromosome 5 were in the most significant region for the color measurements. In addition to the blue/yellow color component and color intensity, the AP3B2 gene on chromosome 21 was identified. Its function was confirmed for similar traits in a range of model species. The KIT gene on chromosome 6 was found to be strongly associated with the inhibition of circum‐ocular pigmentation and pigmented spots on the cheek.