ABSTRACT
Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.
ABSTRACT
Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.
Subject(s)
Genetics, Population , Reproductive Isolation , Humans , Chromosome Inversion , Genome , Genomics , Hybridization, Genetic , Genetic SpeciationABSTRACT
Genotype-environment association (GEA) studies have the potential to identify the genetic basis of local adaptation in natural populations. Specifically, GEA approaches look for a correlation between allele frequencies and putatively selective features of the environment. Genetic markers with extreme evidence of correlation with the environment are presumed to be tagging the location of alleles that contribute to local adaptation. In this study, we propose a new method for GEA studies called the Weighted-Z Analysis (WZA) that combines information from closely linked sites into analysis windows in a way that was inspired by methods for calculating FST . Performing GEA methods in analysis windows has the advantage that it takes advantage of the increased linkage disequilibrium expected surrounding sites subject to local adaptation. We analyse simulations modelling local adaptation to heterogeneous environments to compare the WZA with existing methods. In the majority of cases we tested, the WZA either outperformed single-SNP (single nucleotide polymorphism)-based approaches or performed similarly. In particular, the WZA outperformed individual SNP approaches when a small number of individuals or demes were sampled. Particularly troubling, we found that some GEA methods exhibit very high false positive rates. We applied the WZA to previously published data from lodgepole pine and identified candidate loci that were identified in the original study alongside numerous loci that were not found in the original study.
Subject(s)
Adaptation, Physiological , Polymorphism, Single Nucleotide , Humans , Adaptation, Physiological/genetics , Gene Frequency , Genotype , Genetics, PopulationABSTRACT
The ability to navigate effectively in a rich and complex world is crucial for the survival of all animals. Specialist neural structures have evolved that are implicated in facilitating this ability, one such structure being the ring attractor network. In this study, we model a trio of Spiking Neural Network (SNN) ring attractors as part of a bio-inspired navigation system to maintain an internal estimate of planar translation of an artificial agent. This estimate is dynamically calibrated using a memory recall system of landmark-free allotheic multisensory experiences. We demonstrate that the SNN-based ring attractor system can accurately model motion through 2D space by integrating ideothetic velocity information and use recalled allothetic experiences as a positive corrective mechanism. This SNN based navigation system has potential for use in mobile robotics applications where power supply is limited and external sensory information is intermittent or unreliable.
ABSTRACT
OBJECTIVE: To assess the educational of value of teaching assistant (TA) cases from the perspectives of attending, chief resident, and junior resident. We hypothesized the greatest educational value of TA cases would be for chief residents more so than other team members. DESIGN: A prospective survey was designed and collected for TA cases separately from attendings, chief residents, and junior residents to assess operative details and educational value. The study period ran from August 2021 through December 2022. Qualitative and quantitative analysis was undertaken to compare answers and discover themes in the free-text responses of attendings and residents. SETTING: Single center, tertiary care institution, Maine Medical Center, Department of Surgery, Portland, ME PARTICIPANTS: Sixty-nine teaching assistant cases were captured from a total of 117 completed surveys that were completed by 44 chief residents, 49 junior residents, 22 attendings (nâ¯=â¯22) and 2 APPs. RESULTS: A wide variety of TA cases were included in the study with the most common reason for performing a TA case being resident request 68%. Operative complexity was most commonly rated easiest third (50%) and middle third (41%) of overall cases. Both junior and chief residents felt that compared to working with an attending alone, TA cases contributed more or much more to their procedural independence >80% of the time. Attendings reported learning something about the resident's skills that they were not expecting in 59% of the cases. Thematic analysis: attendings focused on the steps of the procedure, including the technical aspects, particularly regarding opening while residents largely focused on communication and preparation. CONCLUSIONS: Teaching assistant cases seem to have more educational value for chief and junior residents than attendings. Both junior and chief residents felt that compared to working with an attending alone, TA cases contributed more or much more to their procedural independence >80% of the time.
Subject(s)
General Surgery , Internship and Residency , Humans , Prospective Studies , Surveys and Questionnaires , Clinical Competence , Medical Staff, Hospital , General Surgery/education , TeachingABSTRACT
OBJECTIVE: The ongoing complexity of general surgery training has led to an increased focus on ensuring the competence of graduating residents. Entrustable professional activities (EPAs) are units of professional practice that provide an assessment framework to drive competency-based education. The American Board of Surgery convened a group from the American College of Surgeons, Accreditation Council for Graduate Medical Education (ACGME) Surgery Review Committee, and Association of Program Directors in Surgery to develop and implement EPAs in a pilot group of residency programs across the country. The objective of this pilot study was to determine the feasibility and utility of EPAs in general surgery resident training. METHODS: 5 EPAs were chosen based on the most common procedures reported in ACGME case logs and by practicing general surgeons (right lower quadrant pain, biliary disease, inguinal hernia), along with common activities covering additional ACGME milestones (performing a consult, care of a trauma patient). Levels of entrustment assigned (1 to 5) were observation only, direct supervision, indirect supervision, unsupervised, and teaching others. Participating in site recruitment and faculty development occurred from 2017 to 2018. EPA implementation at individual residency programs began on July 1, 2018, and was completed on June 30, 2020. Each site was assigned 2 EPAs to implement and collected EPA microassessments on residents for those EPAs. The site clinical competency committees (CCC) used these microassessments to make summative entrustment decisions. Data submitted to the independent deidentified data repository every 6 months included the number of microassessments collected per resident per EPA and CCC summative entrustment decisions. RESULTS: Twenty-eight sites were selected to participate in the program and represented geographic and size variability, community, and university-based programs. Over the course of the 2-year pilot programs reported on 14 to 180 residents. Overall, 6,272 formative microassessments were collected (range, 0 to 1144 per site). Each resident had between 0 and 184 microassessments. The mean number of microassessments per resident was 5.6 (SD = 13.4) with a median of 1 [interquartile range (IQR) = 6]. There were 1,763 summative entrustment ratings assigned to 497 unique residents. The average number of observations for entrustment was 3.24 (SD 3.61) with a median of 2 (IQR 3). In general, PGY1 residents were entrusted at the level of direct supervision and PGY5 residents were entrusted at unsupervised practice or teaching others. For each EPA other than the consult EPA, the degree of entrustment reported by the CCC increased by resident level. CONCLUSIONS: These data provide evidence that widespread implementation of EPAs across general surgery programs is possible, but variable. They provide meaningful data that graduating chief residents are entrusted by their faculty to perform without supervision for several common general surgical procedures and highlight areas to target for the successful widespread implementation of EPAs.
Subject(s)
Internship and Residency , Humans , Pilot Projects , Education, Medical, Graduate , Competency-Based Education/methods , Clinical CompetenceABSTRACT
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
ABSTRACT
BACKGROUND: Poor personal financial health has been linked to key components of health including burnout, substance abuse, and worsening personal relationships. Understanding the state of resident financial health is key to improving their overall well-being. STUDY DESIGN: A secondary analysis of a survey of New England general surgery residents was performed to understand their financial well-being. Questions from the National Financial Capability Study were used to compare to an age-matched and regionally matched cohort. RESULTS: Overall, 44% (250 of 570) of surveyed residents responded. Residents more frequently reported spending less than their income each year compared to the control cohort (54% vs 34%, p < 0.01). However, 17% (39 of 234) of residents reported spending more than their income each year. A total of 65% of residents (152 of 234), found it "not at all difficult" to pay monthly bills vs 17% (76 of 445) of the control cohort (p < 0.01). However, 32% (75 of 234) of residents reported it was "somewhat" or "very" difficult to pay monthly bills. Residents more frequently reported they "certainly" or "probably" could "come up with" $2,000 in a month compared to the control cohort (85% vs 62% p < 0.01), but 16% (37 of 234) of residents reported they could not. In this survey, 21% (50 of 234) of residents reported having a personal life insurance policy, 25% (59 of 234) had disability insurance, 6% (15 of 234) had a will, and 27% (63 of 234) had >$300,000 worth of student loans. CONCLUSIONS: Surgical residents have better financial well-being than an age-matched and regionally matched cohort, but there is still a large proportion who suffer from financial difficulties.
Subject(s)
Burnout, Professional , Internship and Residency , Humans , Income , New England , Surveys and Questionnaires , Burnout, Professional/epidemiologyABSTRACT
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
Subject(s)
Genome , Genomics , Animals , Phylogeny , Species Specificity , Birds/geneticsABSTRACT
BACKGROUND: Exploring the lived experiences of surgeons is necessary to understand the changing culture of surgery and the unique challenges of being a woman in surgery. Surgeons have significant experiences and observations best discovered through qualitative study. The purpose of this study is to identify the similarities and differences between the experiences of men and women surgeons after initiation of mandatory microaggression training. STUDY DESIGN: Qualitative semi-structured interviews with female and male surgeons and residents were done following a year-long series of training sessions on the detrimental effects of microaggression. Participants were selected using a convenience sampling method. MAXQDA coding software (Verbi) was used to evaluate interview transcripts with thematic analysis. RESULTS: Nineteen surgeons and surgical residents were interviewed. The participants were of equal gender identification, with the majority being attending surgeons. Multiple themes highlighted similarities and differences between male and female participants. Differences were noted in identification of a sensitive personality, family planning considerations, and experiences of bias. Similarities were related to the personality traits required to be successful in surgery, the sacrifice inherent to a surgical career, and the war rhetoric used to describe the comradery of residency. CONCLUSION: The challenges and rewards of surgery are similar for women and men, but women have additional stressors, including gender-based bias, microaggression, and family planning. These stressors take up energy, decreasing the mental space available for additional roles and affecting the work environment. Microaggression education can incite necessary discussions of bias and provide women with an opportunity to reflect on and share their experiences.
Subject(s)
Internship and Residency , Physicians, Women , Surgeons , Female , Humans , Male , Qualitative Research , SexismABSTRACT
BACKGROUND: Surgical culture has shifted to recognize the importance of resident well-being. This is the first study to longitudinally track regional surgical resident well-being over 5 years. STUDY DESIGN: An anonymous cross-sectional, multi-institutional survey of New England general surgery residents using novel and published instruments to create three domains: health maintenance, burnout, and work environment. RESULTS: Overall, 75% (15 of 20) of programs participated. The response rate was 44% (250 of 570), and 53% (133 of 250) were women, 94% (234 of 250) were 25 to 34 years old, and 71% (178 of 250) were in a relationship. For health maintenance, 57% (143 of 250) reported having a primary care provider, 26% (64 of 250) had not seen a primary care provider in 2 years, and 59% (147 of 250) endorsed being up to date with age-appropriate health screening, but only 44% (109 of 250) were found to actually be up to date. Only 14% (35 of 250) reported exercising more than 150 minutes/week. The burnout rate was 19% (47 of 250), with 32% (81 of 250) and 25% (63 of 250) reporting high levels of emotional exhaustion and depersonalization, respectively. For program directors and attendings, 90% of residents reported that they cared about resident well-being. Eighty-seven percent of residents believed that it was acceptable to take time off during the workday for a personal appointment, but only 49% reported that they would personally take the time. CONCLUSIONS: The personal health maintenance of general surgery residents has changed little over the past five years, despite an overwhelming majority of residents reporting that attendings and program directors care about their well-being. Further study is needed to understand the barriers to improvement of resident wellbeing.
Subject(s)
Burnout, Professional , Internship and Residency , Adult , Burnout, Professional/epidemiology , Burnout, Professional/psychology , Cross-Sectional Studies , Female , Humans , Male , New England , Surveys and QuestionnairesABSTRACT
Although rapid phenotypic evolution has been documented often, the genomic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that were transplanted from high-predation (HP) to low-predation (LP) environments have been shown to evolve toward the phenotypes of naturally colonized LP populations in as few as eight generations. These changes persist in common garden experiments, indicating that they have a genetic basis. Here, we report results of whole genome variation in four experimental populations colonizing LP sites along with the corresponding HP source population. We examined genome-wide patterns of genetic variation to estimate past demography and used a combination of genome scans, forward simulations, and a novel analysis of allele frequency change vectors to uncover the signature of selection. We detected clear signals of population growth and bottlenecks at the genome-wide level that matched the known history of population numbers. We found a region on chromosome 15 under strong selection in three of the four populations and with our multivariate approach revealing subtle parallel changes in allele frequency in all four populations across this region. Investigating patterns of genome-wide selection in this uniquely replicated experiment offers remarkable insight into the mechanisms underlying rapid adaptation, providing a basis for comparison with other species and populations experiencing rapidly changing environments.
ABSTRACT
Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a 'supergene' on the sex chromosome. Here, we phenotype and genotype four guppy 'Iso-Y lines', where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis.
Subject(s)
Poecilia , Animals , Female , Genotype , Haplotypes/genetics , Male , Phenotype , Poecilia/genetics , Sex ChromosomesABSTRACT
The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL crosses to examine the genetic basis of seven (five female, two male) guppy life history phenotypes and discuss how these genetic architectures may facilitate or constrain rapid adaptation and convergence. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many loci of small-effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid, repeatable phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but subsequent genetic redundancy may limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent analyses of wild guppies.
Subject(s)
Life History Traits , Poecilia , Animals , Chromosome Mapping , Female , Male , Multifactorial Inheritance , Phenotype , Poecilia/genetics , Quantitative Trait LociABSTRACT
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
Subject(s)
Evolution, Molecular , Genetic Variation , Genome/genetics , Poecilia/genetics , Predatory Behavior , Alleles , Animals , Chromosomes/genetics , Genetic Introgression , Genetics, Population , HaplotypesABSTRACT
OBJECTIVE: The interview process for applying to general surgery residency is burdened by a high volume of applicants, resulting in unprofessional behavior by both applicants and programs. Sharing more information regarding interview scheduling with applicants may limit fourth year medical student educational disruptions, minimized late cancellations to interview, and improve overall satisfaction with the process. Thus, we set out to determine what information is currently available to applicants. DESIGN: We used publicly accessible sources to determine what information was shared by US general surgery residency programs with applicants. Specifically, we looked at the deadline for applications, United States Medical Licensing Examination Step 1 and 2 score cutoffs, number of interview dates available, specific interview dates, a stated policy to not offering more interviews than slots, dates when applicants can expect to be notified of interview offers, notification of decision to decline, and International Medical Graduate and visa policies. SETTING: This study took place at Maine Medical Center in Portland, Maine, an academic medical center with a general surgery residency program. PARTICIPANTS: Not applicable. RESULTS: Three hundred seventeen programs were examined. Seventy-six percent of programs specified an application deadline, 65% of programs specified a Step 1 cut-off score, 50% of programs specified a Step 2 cut-off score, 61% of programs stated a visa policy, and 50% of programs stated an International Medical Graduate policy. Twenty-five percent of programs disclosed the number of interview dates, 23% disclosed what those interview dates were. About 3.4% of programs gave interview release dates, 2.8% of programs notify applicants of decline to interview, and 0.63% of programs explicitly describe a policy of offering only as many interviews as slots available. Thirty-two percent of programs provided conflicting information. CONCLUSIONS: The information available to applicants from public access sources regarding interview scheduling is minimal, unstandardized, and unreliable. Notably lacking were policies that only offer as many interviews as slots available, dates when applicants can expect to be notified of interview offers, and notification of declines. Providing such information to applicants in a standardized way may improve satisfaction with the interview scheduling process.
Subject(s)
Internship and Residency , Personnel Selection , Humans , United StatesABSTRACT
OBJECTIVE: Undergraduate and graduate education research has stratified study strategies from low-utility to high-utility with respect to durable learning. The purpose of this study was to determine the prevalence of these evidence-based learning strategies among surgery residents in preparation for the American Board of Surgery In-Training Examination (ABSITE). DESIGN: A 23-item survey was administered during individual interviews. It assessed whether they had a study plan, and the average length and frequency of their independent study, both during the year and the month prior to the ABSITE. Data were also collected on their primary resources and study strategies. Residents rated their usage of those strategies based on a 5-point Likert scale. SETTING: Maine Medical Center, an academic tertiary care center located in Portland, ME. PARTICIPANTS: All residents in the Department of Surgery. RESULTS: Residents (n= 23) intensified their preparation for the ABSITE in the month prior to the exam compared to the remainder of the year, adopting study plans (87% vs 61%, pâ¯=â¯0.53) and increasing the time spent studying (median, 420 vs 120 minutes per week, p < 0.001). Primary resources used were textbooks (65%), ABSITE review books (26%) and online question banks (9%). All residents (100%) often or always used testing, but fewer residents often or always used spacing (24%), both considered high-utility strategies. Most residents (60%) often or always used highlighting, considered a low-utility strategy. There were no relationships between study strategies and ABSITE scores. CONCLUSIONS: All residents use self-testing as a study strategy. Most underuse spacing and overuse highlighting. Further research is needed to establish the relationship between these study strategies and ABSITE scores.
Subject(s)
General Surgery , Internship and Residency , Clinical Competence , Curriculum , Education, Medical, Graduate , Educational Measurement , General Surgery/education , Humans , United StatesABSTRACT
Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.