Genome Sequencing as an Alternative to Cytogenetic Analysis in Myeloid Cancers.

BACKGROUND: Genomic analysis is essential for risk stratification in patients with acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS). Whole-genome sequencing is a potential replacement for conventional cytogenetic and sequencing approaches, but its accuracy, feasibility, and clinical utility have not been demonstrated. METHODS: We used a streamlined whole-genome sequencing approach to obtain genomic profiles for 263 patients with myeloid cancers, including 235 patients who had undergone successful cytogenetic analysis. We adapted sample preparation, sequencing, and analysis to detect mutations for risk stratification using existing European Leukemia Network (ELN) guidelines and to minimize turnaround time. We analyzed the performance of whole-genome sequencing by comparing our results with findings from cytogenetic analysis and targeted sequencing. RESULTS: Whole-genome sequencing detected all 40 recurrent translocations and 91 copy-number alterations that had been identified by cytogenetic analysis. In addition, we identified new clinically reportable genomic events in 40 of 235 patients (17.0%). Prospective sequencing of samples obtained from 117 consecutive patients was performed in a median of 5 days and provided new genetic information in 29 patients (24.8%), which changed the risk category for 19 patients (16.2%). Standard AML risk groups, as defined by sequencing results instead of cytogenetic analysis, correlated with clinical outcomes. Whole-genome sequencing was also used to stratify patients who had inconclusive results by cytogenetic analysis into risk groups in which clinical outcomes were measurably different. CONCLUSIONS: In our study, we found that whole-genome sequencing provided rapid and accurate genomic profiling in patients with AML or MDS. Such sequencing also provided a greater diagnostic yield than conventional cytogenetic analysis and more efficient risk stratification on the basis of standard risk categories. (Funded by the Siteman Cancer Research Fund and others.).

Correction: Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon.

[This corrects the article DOI: 10.1371/journal.pgen.1008348.].

Ancestry and genetic structure of resident and anadromous rainbow trout (Oncorhynchus mykiss) in Argentina.

Since the first introduction from North America more than a century ago, rainbow trout (Oncorhynchus mykiss) have rapidly established self-sustaining populations in major river basins of Patagonia. Many generations later, only the freshwater resident life history is expressed in the Chubut and Negro rivers of northern Argentinian Patagonia, whereas both the resident and anadromous life histories are found in the Santa Cruz River of southern Argentina. Despite previous studies that have tried to identify the sources of these introduced populations, uncertainty still exists. Here we combined data from many single-nucleotide polymorphisms and microsatellite loci in O. mykiss populations from Argentina and North America to evaluate putative source populations, gene flow between Argentinian river basins, and genetic diversity differences between Argentinian and North American populations. We found that populations from northern and southern Patagonia are highly differentiated and have limited gene flow between them. Phylogeographic analysis also confirmed that they have separate origins, with the northern populations most closely related to the domesticated rainbow trout strains that are raised worldwide and the Santa Cruz River populations most closely related to North American populations from California and Oregon that have an anadromous component. In addition, fish with different life histories in the Santa Cruz River were found to constitute a single interbreeding population. No evidence was found of reduced genetic variation in introduced rainbow trout, suggesting multiple contributing sources. In spite of these advances in understanding, significant questions remain regarding the origins and evolution of the introduced O. mykiss in Patagonia.

Distinct patterns of inheritance shape life-history traits in steelhead trout.

Life-history variation is the raw material of adaptation, and understanding its genetic and environmental underpinnings is key to designing effective conservation strategies. We used large-scale genetic pedigree reconstruction of anadromous steelhead trout (Oncorhynchus mykiss) from the Russian River, CA, USA, to elucidate sex-specific patterns of life-history traits and their heritability. SNP data from adults returning from sea over a 14-year period were used to identify 13,474 parent-offspring trios. These pedigrees were used to determine age structure, size distributions and family sizes for these fish, as well as to estimate the heritability of two key life-history traits, spawn date and age at maturity (first reproduction). Spawn date was highly heritable (h2 = 0.73) and had a cross-sex genetic correlation near unity. We provide the first estimate of heritability for age at maturity in ocean-going fish from this species and found it to be highly heritable (h2 from 0.29 to 0.62, depending on sex and method), with a much lower genetic correlation across sexes. We also evaluated genotypes at a migration-associated inversion polymorphism and found sex-specific correlations with age at maturity. The significant heritability of these two key reproductive traits in these imperiled fish, and their patterns of inheritance in the two sexes, is consistent with predictions of both natural and sexually antagonistic selection (sexes experience opposing selection pressures). This emphasizes the importance of anthropogenic factors, including hatchery practices and ecosystem modifications, in shaping the fitness of this species, thus providing important guidance for management and conservation efforts.

Long-distance migration is a major factor driving local adaptation at continental scale in Coho salmon.

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river.

Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as 1 of 10 hybrid classes using 30 "diagnostic" single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e. jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon.

A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

Sex Differences in Comorbidities of Pediatric Craniosynostosis at Presentation.

INTRODUCTION: Craniosynostosis is a common pediatric presentation in which the premature fusion of one or more cranial sutures results in a misshapen skull. This birth defect is often associated with comorbidities due to structural impacts on nearby anatomical features. While there is some evidence for a male predominance among craniosynostosis patients, little has been investigated regarding sex differences in comorbidities of this condition. This study seeks to explore potential sexual dimorphisms in craniosynostosis patients at the time of presentation. METHODS: We conducted a retrospective, cross-sectional review of male and female non-syndromic craniosynostosis (NSC) patients between the ages of 1 month and 9 years that were evaluated at a 500-bed academic hospital or a 977-bed private hospital in Lubbock, TX, USA. Common comorbidities including ophthalmologic diagnoses, developmental delays, obstructive sleep apnea, chronic otitis media, hearing loss, chronic headaches, and seizure disorders were evaluated. The NSC cohort was compared to a similarly aged trauma group that represented the normal population. RESULTS: 175 NSC patients fit the inclusion criteria, of which 109 (62%) were male. A diagnosis of craniosynostosis was significantly associated with ophthalmological diagnoses (p < 0.0001), chronic otitis media (p < 0.0001), developmental delays (p < 0.0001), and hearing loss (p = 0.0047). Male NSC patients were less likely to present with ophthalmological diagnoses (p = 0.0010) or hearing loss (p = 0.0052) than females. CONCLUSIONS: Our findings expand on current literature evaluating possible comorbidities of NSC, particularly supporting the association with ophthalmological diagnoses, chronic otitis media, developmental delays, and hearing loss. We also report sex differences in ophthalmological diagnoses and hearing loss for NSC patients. These findings can serve to educate physicians of symptoms requiring prompt recognition and management in these patients.

Multiple-brooding rockfishes (Sebastes spp.) can utilize stored sperm from individual sires to fertilize consecutive broods.

Viviparous rockfishes (Sebastes spp., family Scorpaenidae) mate and store sperm in the ovaries for several months prior to fertilization, as oocytes develop for the parturition season. Although multiple paternity has been documented in single-brooding rockfishes, paternity in consecutive broods of multiple-brooding species has not been studied. Analyses of multilocus microsatellite genotypes in both residual larvae left in the ovary from a previous parturition and upcoming fertilized broods in the same ovary demonstrated evidence of the same sires in consecutive broods in chilipepper (Sebastes goodei) and speckled (Sebastes ovalis) rockfishes. One S. goodei mother showed evidence of multiple paternity from the same two sires in both consecutive broods. The ability to retain sperm, even after a parturition event, for use in subsequent broods, confers an advantage to ensure fertilization and allows for extension of the parturition season. This life-history strategy provides a bet-hedging advantage in the California Current system, an environmentally dynamic ecosystem where larval survivorship and subsequent recruitment to adult populations can vary temporally by orders of magnitude.

Organochlorine and Metal Contaminants in the Blood Plasma of Green Sturgeon Caught in Washington Coastal Estuaries.

Non-invasive monitoring was used to evaluate the concentrations of 40 contaminants in the blood plasma of the North American Green Sturgeon Acipenser medirostris caught and released from three estuaries in Washington State. The highest contaminant concentrations were found in fish caught in the most urbanized sites. Few statistical differences were found when evaluating contaminant levels according to sex, maturation stage, or distinct population segments of Green Sturgeon. The results indicate that recent exposure to legacy contaminants was reflected in Green Sturgeon plasma. Aldrin, 4,4-DDE, α-HCH, copper, and selenium were the most frequently detected contaminants. This study also explored the challenges of assessing toxicity in threatened species using non-lethal approaches. There is currently a lack of environmental contaminant monitoring data in estuaries frequented by Green Sturgeon and limited plasma to tissue toxicity correlations.

Heterogeneous genetic basis of age at maturity in salmonid fishes.

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.

Polygenic Basis and the Role of Genome Duplication in Adaptation to Similar Selective Environments.

Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and nonparallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while 3 of the 4 populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these 2 inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.

Dispersal of a nearshore marine fish connects marine reserves and adjacent fished areas along an open coast.

Marine species with pelagic larvae typically exhibit little population structure, suggesting long-distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for the design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current-dominated ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, because the distance between sedentary parents and their settled offspring is the lifetime dispersal distance. Large sample sizes and intensive sampling are critical for increasing the likelihood of detecting parent-offspring matches in such systems and we sampled more than 6,000 kelp rockfish and analysed them with a powerful set of 96 microhaplotype markers. We identified eight parent-offspring pairs with high confidence, including two juvenile fish that were born inside MPAs and dispersed to areas outside MPAs, and four fish born in MPAs that dispersed to nearby MPAs. Additionally, we identified 25 full-sibling pairs, which occurred throughout the sampling area and included all possible combinations of inferred dispersal trajectories. Intriguingly, these included two pairs of young-of-the-year siblings with one member each sampled in consecutive years. These sibling pairs suggest monogamy, either intentional or accidental, which has not been previously demonstrated in rockfishes. This study provides the first direct observation of larval dispersal events in a current-dominated ecosystem and direct evidence that larvae produced within MPAs are exported both to neighbouring MPAs and to proximate areas where harvest is allowed.

Hand function, not proximity, biases visuotactile integration later in object processing: An ERP study.

Behavioral studies document a functional hand proximity effect: objects near the palm, but not the back of the hand, affect visual processing. Although visuotactile bimodal neurons integrate visual and haptic inputs, their receptive fields in monkey cortex encompass the whole hand, not just the palm. Using ERPs, we investigated whether hand function influenced the topology of integrated space around the hand. In a visual detection paradigm, target and non-target stimuli appeared equidistantly in front or in back of the hand. Equivalent N1 amplitudes were found for both conditions. P3 target versus non-target amplitude differences were greater for palm conditions. Hand proximity biased processing of visual targets equidistant from the hand early in processing. However, hand function biases emerged later when targets were selected for potential action. Thus, early hand proximity effects on object processing depend on sensory-reliant neural responses, whereas later multisensory integration depend more on the hand's functional expertise.

Attention orienting near the hand following performed and imagined actions.

Recent studies have documented that the hand's ability to perform actions affects the visual processing and attention for objects near the hand, suggesting that actions may have specific effects on visual orienting. However, most research on the relation between spatial attention and action focuses on actions as responses to visual attention manipulations. The current study examines visual attention immediately following an executed or imagined action. A modified spatial cuing paradigm tested whether a brief, lateralized hand-pinch performed by a visually hidden hand near the target location, facilitated or inhibited subsequent visual target detection. Conditions in which hand-pinches were fully executed (action) were compared to ones with no hand-pinch (inaction) in Experiment 1 and imagined pinches (imagine) in Experiment 2. Results from Experiment 1 indicated that performed hand pinches facilitated rather than inhibited subsequent detection responses to targets appearing near the pinch, but target detection was not affected by inaction. In Experiment 2, both action and imagined action conditions cued attention and facilitated responses, but along differing time courses. These results highlight the ongoing nature of visual attention and demonstrate how it is deployed to locations even following actions.

Feeling but not seeing the hand: Occluded hand position reduces the hand proximity effect in ERPs.

The hand proximity effect (nearby hands influence visual processing) reflects the integration of vision and proprioception for upcoming action; it is reduced when hand position is occluded. In an ERP study, we investigate whether hand proximity, without vision of the hand, accentuates the processing of stimuli requiring actions (targets) early (N1) and later (P3) in processing. In a go/no-go paradigm, participants viewed stimuli between two panels with hands placed near or far from stimuli. Occlusion of the hand eliminated near-hand target vs. non-target differentiation of the N1; amplification of near-hand target amplitudes emerged at the P3. Visual hand location appears necessary to draw visual attention to intended-action objects to integrate body and visual information early in processing. The integration of visual stimulus information and hand position from proprioception appears later in processing, indicating greater reliance on cognitive systems for discriminating the task-relevance of a stimulus.

Stronger effects of heterozygosity on survival in harsher environments.

The hypothesis that the effects of heterozygosity vary with environmental conditions was tested using six populations of marble trout Salmo marmoratus from western Slovenia as a model system. The hypotheses tested were: stronger effects of heterozygosity on survival in populations characterized by low average survival; no effects of heterozygosity on probability of surviving flash floods owing to their largely non-selective effects across traits; stronger effects of heterozygosity on survival for fish born after floods than fish born before. A significant effect of heterozygosity on survival was found in populations characterized by low average survival. There were no effects of heterozygosity on probability of surviving flash floods, but in one population a positive correlation between heterozygosity and survival for fish born after the extreme events was found, probably because crowding in a small section of the stream caused more intense competition for resources.

Genetic and life-history consequences of extreme climate events.

Climate change is predicted to increase the frequency and intensity of extreme climate events. Tests on empirical data of theory-based predictions on the consequences of extreme climate events are thus necessary to understand the adaptive potential of species and the overarching risks associated with all aspects of climate change. We tested predictions on the genetic and life-history consequences of extreme climate events in two populations of marble trout Salmo marmoratus that have experienced severe demographic bottlenecks due to flash floods. We combined long-term field and genotyping data with pedigree reconstruction in a theory-based framework. Our results show that after flash floods, reproduction occurred at a younger age in one population. In both populations, we found the highest reproductive variance in the first cohort born after the floods due to a combination of fewer parents and higher early survival of offspring. A small number of parents allowed for demographic recovery after the floods, but the genetic bottleneck further reduced genetic diversity in both populations. Our results also elucidate some of the mechanisms responsible for a greater prevalence of faster life histories after the extreme event.

Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris.

The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species.