Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods  on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes’ selective footprint in crops.Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, The online version contains supplementary material available at 10.1186/s12284-023-00633-4. Climate change is affecting agricultural productivity and its effects may limit global crop production by at least 10% in 2050  the list of known regulators of flowering time (termed heading date) includes some 53 genes involved in at least three pathways: photoperiod and circadian clock, chromatin-related pathway, and hormones pathway  and of the African rice (Oryza glaberrima) sampled across time. Third, we implemented two genome-scan methods on those populations and detected several selection footprints. Finally, we were able to connect the loci under selection to known genes and QTLs involved in reproductive development. Our results provide new insight into mechanisms of adaptation of self-fertilizing plant meta-populations, under environmental and human selection. To our best knowledge, this is the first study dealing with climate-changes’ selective footprint in crops.Here we present an analysis of the genetic bases of adaptation to climate changes based on sampling across time, in an autogamous crop species, rice, of major significance for the world food security. Our study place was the tropical forest and the Sudanian savannah areas of Guinea in West Africa, not much affected by the Green Revolution. The interval between the two sampling times was approximately 30 years. First, using local historical meteorological data we analysed and confirmed the reality of climate changes in the target area. Second, we analysed and confirmed significant phenological differences between the populations of the Asian rice (https://www.cirad.fr/) and IRAG (https://irag-guinee.org/). The collect area stretched from tropical forest to Sudanian savannah agro-ecological regions of Conakry Guinea: latitude 7°34′19.96″ N–12°29′1.50″ N; longitude 8°25′0.0″ O-13°17′59.17″ O  took place in 1979 and 1982  and, occasionally, the rice growing ecosystem  and the type of collect . Approximately 40% of the accessions were collected in the field.The collect strategy was to drive along major roads and other practicable trails, stop in villages without prior notice, conduct a quick inventory of the rice varieties and collect a sample of each of the identified varieties, in the field or from the granary. The passport data for Collect-1 samples included the village name, the variety name, the species . The Collect-2 campaign yielded 776 accessions.For Collect-1, 442 accessions were retrieved from the long-term conservation facilities of the Institute de Recherche pour le Development , (ii) detect accessions that could be considered as redundant , (iii) assess the pattern of genetic diversity within each genetic group, for each collect. Based on such information and logistic issues, 600 accessions were selected for genotyping by sequencing (GBS). DNA libraries were prepared at the Regional Genotyping Technology Platform (http://www.gptr-lr-genotypage.com), using the MATAB method for DNA extraction and the ApekI enzyme for DNA digestion. The libraries were single-end sequenced using Illumina HiSeq™2000  at the Regional Genotyping Platform (http://get.genotoul.fr/). The Fastq sequences were aligned to the rice reference genome, Os-Nipponbare-Reference-IRGSP-1.0 with Bowtie2 (default parameters). Non-aligning sequences and sequences with multiple positions were discarded. Single nucleotide polymorphisms (SNP) were called using Tassel GBS pipeline v5.2.29  ascertain the membership of accessions to one of the three genetic groups , O. sativa tropical japonica (Osj) and O. glaberrima (Og) accessions. An unweighted neighbour-joining tree was constructed based on this dissimilarity matrix, using DARwin.6  and the population parameter Population parameters were assessed for each genetic group subdivided into two subpopulations representing Collect-1 and Collect-2. This is 2 between pairs of markers on a chromosome basis, using the “full matrix” option of Tassel 5.2.6  in each subpopulation was estimated by computing rFST statistic, is significantly higher than the expected FST values under neutrality hypothesis, for a given average heterozygosity (h0) between populations and for a given demographic model  and on the effective population size (Ne). Loci under directional selection or linked to such loci are expected to exhibit larger differentiation values than expected under the neutral hypothesis. In order to account for the mainly selfing reproduction system, Navascués et al.  frequency. Indeed, in a mainly selfing species, allele copies within an individual are not independent samples from the population, while genotypes are independent samples. Moreover, in order to account for uncertainty of the initial genotype frequency, assuming the same prior probability for the three genotype frequencies, genotype frequencies in the population are sampled from the posterior probability distribution with Dir(K0 + 1), where K0 is the observed genotype counts in the sample of the focal locus at time The Navascués et al.  method , that iss et al.  developeFSTi are computed with the Weir and Cockerham  drawing the initial genotype frequency K0 of the locus, conditional on data, (ii) simulating allele frequency change for τ generations, based on p value for the test. In order to account for multiple tests across the genome, false discovery rates  are computed from the distribution of the p value. Genotype counts observed in the simulated sample of n0 individuals are modelled as coming from a multinomial distribution Mult frequencies in the populations as a function of the allele frequency Locus-by-locus differentiation ockerham  method. ockerham . Then, tOsi group was excluded from search for selection footprint given the small number of accessions available (70) and given the important disequilibrium in the number of accessions in Collect-1 and (15) and Collect-2 (55).The https://rapdb.dna.affrc.go.jp/index.html). The corresponding MSU7.0 gene identity (TIGR) was retrieved using gene-ID converter tool proposed by RAP-DB. The window size of 250 kb was chosen to represent approximately half the distance at which LD decayed to half its initial level, for both Og and Osj groups, estimated at 450 kb on average across all chromosomes.Genes located within an interval of 250 kb on both sides of independent loci detected to be under selection, were determined using the RAP-DB annotation of rice genome (http://bioinfo.cau.edu.cn/agriGO/) and Panther-GO , that use RAP and MSU gene identity, respectively, as input.Enrichment analysis of genes within the chromosomic segments bearing loci under selection was performed using two gene ontology tools: Agri-GO . Likewise, chromosomic segments bearing loci under selection were investigated for enrichment in quantitative trait loci (QTL) involved in DTHD, using the Gramene QTL database (http://www.gramene.org/).The chromosomic segments bearing loci under selection were also investigated for genes known to be involved in reproductive development processes, using available literature , Climatological data  of the 1961–2010 period were extracted from the archives of Guinea National Weather Service for a weather station in tropical forest area  and a second station in the Sudanian savannah  of the study region. Evolution of the annual rainfall and of the annual crops’ growth season rainfall was characterised using the Lamb index Lamb : \documetion WMO . The perPatterns of deviation from the normal reference (1960–1990 period), of the annual rainfall total (ART) and of the annual rainfall total during the crops growing season (GSART) along the period 1961–2010, in our two study areas, are given in Fig. Regarding the temperatures, patterns of the annual average minimum (T-Min) and maximum (T-Max) in the tropical forest area showed a systematic positive deviation from the normal reference from 1987 on Fig. . The aveOg, Osi and Osj, respectively). No significant relationship was found between the accessions’ DTHD and the latitudinal coordinate of their place of collect (R < 0.15) in both Collect-1 and Collect-2 subpopulations of each genetic group, suggesting homogenous environmental selective pressure across our study areas stretching between 7°34′19.96″ N and 12°29′1.50″ N.A large variability of day to heading (DTHD) was observed among the 651 accessions phenotyped (77 < DTHD < 161 days) and between the three genetic groups  and 3.4 days between Osj-1 and Osj-2 (p < 0.002)  was, on average, 4.3 days longer than the DTHD of Osi-1 accessions (114.67 ± 2.97 days). However, in both Osi-1 and Osi-2 the distribution of DTHD did not satisfy the normality (Shapiro–Wilk test) conditions needed for ANOVA  that included a larger number of old photosensitive landraces. Indeed, the maximum DTHD reached 161 days in Collect-2, versus 143 in Collect-1 , low for Osj-1 and Osj-2 (> 0.09), and of intermediate level (> 0.21) for Osi-1 and Osi-2 , the intermediate values for Osj-1 and Osj-2 (Mean θπ = 798) and the highest values for Osi-1 and Osi-2 (Mean θπ = 2867) , almost significant deviation in Osj-1 and Osj-2 , and non-significant deviation in Osi-1 and Osi-2  and 0.0303 (for Og-2), suggesting a random union of gametes within each population.Nucleotide diversity was very low for FST = 0.00014 between Og-1 and Og-2, FST = 0.00004 between Osj-1 and Osj-2, and FST < 0.00001 between Osi-1 and Osi-2), suggesting random distribution of genotypes across populations  molecular variance computed by AMOVA was extremely small (< 1%) and the “among individuals within populations” variance did not exceed 2.5%. The remaining large share of molecular variance was attributed to “within individuals” variance  was too small to provide a good estimate of LD. The three groups also differed for the subsequent decay of LD , i.e. distance between adjacent SNP loci below 250 kb and strong LD . Among the latter 54 SNP, 21 clustered with five of 14 previously defined IL. The remaining 33 SNP formed 16 additional independent loci composed of one to 14 SNP ; it exceeded 0.2 in 13% cases out of the 242 possible combinations of IL but never reached 0.5 ; the r2 value exceeded 0.2 in 17% cases out of the 125 possible combinations of independent loci and exceeded 0.5 in two combinations  or P <  = 0.05 (10 loci) with the heterozygosity-based detection method. Likewise, among the Osj 9282 SNP loci, 30 showed FST with q value < 0.05  or P <  = 0.05 (17 loci) with the heterozygosity-based detection method. Thus, the results of the drift-based method corroborate the results of heterozygosity-based method, especially for loci most significantly under selection.Search for selection footprint using the drift-based approach, among the 6250 ILUS) in Og and in Osj, belonging to the same chromosomes and within distance between the component SNP below 250 kb, were merged. The process reduced the total number of ILUS to 40, each composed of one to 45 individual SNP. Among these ILUS, nine, composed of one SNP and identified to be significantly under selection by one detection method only, were discarded from further analyses. The remaining 31 ILUS were divided into two categories: ILUS including at least one SNP identified to be significantly under selection by the two detection methods  and ILUS detected by one method only, namely the heterozygosity-based method , hereafter referred to as “M1 type”.Prior to functional characterisation, six independent loci under selection  did not markedly modify the pattern of gene enrichment  , were similar to that reported for the entire West Africa  was on the lowest side of the reported flowering time advancement.The extent of the heading date advance (10.3 days on average) in our Og-2 and Osj-2 subpopulations most probably corresponds to this process, helping the sensitive reproductive phases escape0 the higher drought risk of the end of the rainy season. This hypothesis is also supported by the fact that the shorter DTHD were observed in the two subpopulations Og-2 and Osj-2, almost exclusively cultivated in the drought-prone upland or hydromorphic ecosystems, and not in the Osi-2 subpopulation, cultivated in the lowland ecosystem, less prone to the effects of changes in rainfall regime. Unfortunately, the adaptive process of shorter growth cycle might have come to the detriment of grain yield potential, due to negative correlation between crop duration and biomass production  adaptation through phenotypic plasticity and less reversible genetic adaptation (Franks and Hoffmann Og-1 and Osj-1 subpopulations) by new exogenous rice varieties of shorter DTHD (Og-2 and Osj-2 subpopulations). (i) Penetration of improved O. sativa varieties, with shorter duration, in the slash-and-burn based upland rice cropping system of our study area was reported to be extremely limited  Distance based neighbour-joining tree did not show any structuring in relation with collect time. (iii) Genetic differentiation between Og-1 and Og-2 and between Osj-1 and Osj-2 was very low (FST < 0.001). (iv) The genetic diversity (nucleotide diversity and θ parameter) of the Collect-1 and Collect-2 subpopulations had the same order of magnitude. The two latter observations also argue for the fact that the combined human and environmental selection pressure has not given rise to the emergence of a few well-adapted individuals (i.e. shorter DTHD) colonizing the entire area of cultivation of O. glaberrima and O. sativa japonica. A more subtle selection/genetic adaptation process seems to have been at work, preserving the overall neutral genetic diversity.In our case, several facts argue against the hypothesis of replacement of the old rice landraces of long DTHD (O. sativa and O. glaberrima subpopulations is unlikely given the length of generation in rice (one year), the rather short interval (31 years) separating our two collect times and the rather low rate of outcrossing in rice. Indeed, the highest natural outcrossing rate reported is 6.8% in O. sativa  within-farm genetic diversity was high, i.e., up to 50% of total genetic diversity observed at the village level; (iv) each village pooled more than half of the regional allelic diversity; (v) regional allelic diversity was comparable to that noted worldwide for the Asian rice (O. sativa), but not as high for the African rice (O. glaberrima). Thus, one can consider that the O. sativa and O. glaberrima rice populations of our study area had had the adaptive evolution potential needed to face the environmental and human selection pressure over the last 30 years. More generally, one can assume that Og-1 – Og-2 and Osj-1 – Osj-2 subpopulations are independent replicates of the evolutionary process, where migration had a negligible role.According to the theory of genetic adaptation Orr , when a O. glaberrima (25 independent loci distributed on 11 chromosomes) and O. sativa  groups, and all the loci, identified by the latter method to be under selection, were also identified as such by the former method, assuming random mating. These results suggest that gene flow and recombination were not the main genetic processes underlying the observed phenotypic adaptation, i.e. earlier flowering time. In other words, the outlier values of change in allele frequency in some loci, detected from the comparison of the observed and expected temporal genetic differentiation (FST), were mainly the result of selection among the pre-existing allelic combinations. The above-described multiline genetic structure of rice landraces and the rather large and imbricated genetic diversity of rice at the farm, village and region levels , like all other loci not under selection. This adaptive process resembles the “evolutionary rescue” process in selfing plants described by Uecker , save one case on chromosome 6 of y Uecker . HoweverILUS, a relatively small share (13% in Og and 17% in Osj) were in LD above r2 > 0.2. This limited long-distance LD between the independent loci, on each chromosome and across chromosomes, testifies that, though polygenic, the adaptive process involved in Og and Osj did not translate into predominance of multilocus genotypes, as is often the case in selfing plants  involved in DHTD.Among the OsGI, the orthologue of GIGANTEA in A. thaliana, is strongly involved in the circadian clock system and Hd1, the orthologue of CONSTANCE in A. thaliana, is a major photosensitivity gene in rice. Over-expression of GI triggers higher expression of Hd1 and rapid flowering under any day length  gene belongs to the polycomb group proteins that play important roles in the epigenetic regulation of gene expression. Alteration of OsEMF2 has pleiotropic phenotypic consequences including early flowering time (and even skipping the vegetative phase) even under long-day conditions, and abnormal flower organs .Additional file 2: Fig. 2. Pattern of deviation of the monthly rainfall during crop growing season (June–October), from the normal reference, during the 1961–2010 period, in Kankan  and N’Zérekoré  sites of Guinea.Additional file 3: Table S2. Summary statistics and ANOVA of days to heading (DTHD) of rice accessions collected in 1980 (Collect-1) and in 2011 (Collect-2) and phenotyped in 2012 (Year-1) or 2013 (Year-2).Additional file 4: Fig. S3. Unweighted neighbor-joining tree of simple matching distances constructed from genotypes at 1.130 SNP loci, for O. glaberrima (Og) O. sativa indica (Osi) and O. sativa japonica (Osj) groups. Accessions from the first collect time  are shown in black.Additional file 5: Table S3. Molecular diversity and population parameters and relative importance of different diversity compartments revealed by AMOVA.Additional file 6: Table S4. Variability of decay of pairwise linkage disequilibrium with distance between markers among the 12 chromosomes in five rice populations.Additional file7: Table S5. Loci under selection detected by heterozygosity-base method  and by drift-based method , in O. glaberrima (Og) and O. sativa japonica groups.Additional file 8: Figure S4. Linkage disequilibrium between SNP loci under selection in O. glaberrima and O. sativa japonica (74 and 110 SNP loci respectively). Triangle above and below the bisectrix represent the r² and the r² p value respectively.Additional file 9: Table S6. Detailed results of gene enrichment analyses using Agri-Go  and Panther-GO  enrichment analysis tools.Additional file 10: Table S7. Presence of QTL and genes involved in days to heading (DTHD), on 31 chromosomic segments bearing the 31 independent loci under selection.Additional file 11: Table S1. Passport data of the 530 rice accessions from the collected campaigns of 1979-82 and 2011, genotyped for the present study.


Macrocystis pyrifera) is explained by past climate changes occurring across the two hemispheres. We compared the species’ population genetic diversity and structure inferred with microsatellite markers, with range shifts and long-term refugial regions predicted with species distribution modelling (SDM) from the last glacial maximum (LGM) to the present. The broad antitropical distribution of Macrocystis pyrifera is composed by six significantly differentiated genetic groups, for which current genetic diversity levels match the expectations of past climate changes. Range shifts from the LGM to the present structured low latitude refugial regions where genetic relics with higher and unique diversity were found , while post-glacial expansions following ~ 40% range contraction explained extensive regions with homogenous reduced diversity. The estimated effect of past climate-driven range shifts was comparable between hemispheres, largely demonstrating that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. Additionally, the differentiation and endemicity of regional genetic groups, confers high conservation value to these localized intraspecific biodiversity hotspots of giant kelp forests.The paradigm of past climate-driven range shifts structuring the distribution of marine intraspecific biodiversity lacks replication in biological models exposed to comparable limiting conditions in independent regions. This may lead to confounding effects unlinked to climate drivers. We aim to fill in this gap by asking whether the global distribution of intraspecific biodiversity of giant kelp ( Particularly well reported are range shifts of low dispersive or sessile species driven by glacial-interglacial cycles of the Quaternary (c. 2.6 Myr to the present). The advance of ice sheets and compression of isotherms during glacial periods 5 caused poleward range contractions and lower latitude expansions9, while the opposite trend would have happened during interglacials 13. Behind such range-edge extinction-recolonization regions, climatic refugia are expected, where populations could have persisted for sufficient time to enable the evolution of genetic hotspots and endemic lineages7. In contrast, where extinctions/recolonizations occurred, populations tend to be genetically depauperate and highly homogeneous due to genetic bottlenecks along colonization fronts17. Despite the paradigm of past climate-driven range shifts in structuring intraspecific biodiversity, biological models exposed to comparable conditions in independent geographic regions are rarely available to allow for independent replicated assessment.The distribution of cold and temperate marine biodiversity at the infraspecific level often carries the footprints of past climate-driven range shifts18. The Northern hemisphere was buried under thick layers of permanent ice down to the latitudes matching Brittany (France) and Maine (USA) in the Atlantic Ocean, and Vancouver Island (Canada) in the Pacific Ocean5. In the Southern hemisphere, besides Antarctica and its surrounding islands, only Patagonia was severely affected18, thus providing additional opportunities for population persistence. However, a large portion of the Southern Hemisphere’s coasts are distributed in tropical areas, potentially providing less suitable habitat for cold-temperate species than in the Northern Hemisphere, where the coastline is more continuous from equatorial to Arctic regions. Major shifts in southern oceanic circulation, led by the intensification of the Circumpolar Antarctic Current (ACC) during LGM, likely added complexity to the glacial seascape, even in regions not affected by ice cover. For instance, the strong cooling of the Humboldt Current may have provided suitable habitat even in the inter-tropical zone19. Another peculiarity of the Southern hemisphere is the role of trans-oceanic dispersal at the end of LGM, leading to eastward , instead of southward recolonization of many species in Patagonia and other sub-Antarctic regions22. Numerous studies across the globe have shown the genetic effects of past climate changes24, but comparisons between hemispheres are lacking. Additionally, while the role of refugia as sources for poleward expansions is well‐documented, the effect of past genetic bottlenecks at lower latitudes is insufficiently understood8. Testing the drivers of intraspecific biodiversity on a single model species distributed in both hemispheres reduces potential confounding effects linked to comparing species’ specific responses to climate changes, which can largely result from interspecific niche differentiation26.The higher latitude regions of the Northern vs. Southern hemispheres provided contrasting evolutionary conditions for marine coastal species, particularly considering the differences in ice extent and shoreline morphology during glacial periodsMacrocystis pyrifera represents an ideal model to address the topic owing to its broad antitropical distribution27, with past distributional edges exposed to replicate conditions of higher (cold) and lower (warm) latitudes of both hemispheres. Additionally, its limited spore dispersal and ability to promote density barriers by local saturation of available habitats28 may allow retaining the signatures left by past demographic changes10. Giant kelp can further perform long‐distance dispersal events by rafting29, potentially extending distributional ranges and following climate velocity changes across whole biogeographic regions. Most importantly, while describing the drivers of intraspecific biodiversity, the identification of endemic genetic lineages for giant kelp is timely, as regional persistence might be currently threatened by ongoing and projected climate changes31. The recent increase in frequency and intensity of marine heat wave events has been linked to regional losses of the species in both hemispheres33, which can erode global diversity levels and shift genetic baselines34. These losses can also threaten the multiple ecosystem services provided, such as the role in blue carbon sequestration and coastal protection, as well as the nursery effect for numerous economically important species37.The giant kelp Macrocystis pyrifera were mostly performed without broadscale replication across the hemispheres. These aimed to explore the patterns of the species’ genetic structure41, disentangle the effect of quaternary climate change fluctuations in the distribution and productivity of the species42, the role of seascape drivers mediating genetic differentiation, by testing the role of isolation by habitat continuity, environment and ocean transport44 , as well as the vulnerability of populations to ongoing climatic stress45. Three studies sampling populations across the two hemispheres47 showed (1) Macrocystis as a monospecific genus based on two genetically distinguishable ecomorphs, M. pyrifera and M. integrifolia, (2) the northern48 hemisphere distribution as the potential ancestral origin of the genus, with consequently reduced genetic diversity in the southern hemisphere, and (3) highlighted the potential role of ice advances in structuring the distribution of genetic diversity. Yet, studies lacked independent estimates of past climate oscillations , were mostly performed with traditional mtDNA markers, typically prone to selection and poor resolution48, and were limited in sampling design. These together might have limited conclusions on how climate-driven range shifts structured the species’ intraspecific biodiversity of giant kelp.Previous genetic studies with Macrocystis pyrifera, estimated across the species’ entire distributional range, with independent Species Distribution Modelling (SDM) predicting past range shifts and long-term refugial regions from the last glacial maximum to the present. Overall, we hypothesize that the exposure to comparable past climate changes in the two hemispheres structured disjunct long-term refugial regions currently displaying higher and unique gene pools, relative to regions more recently colonized .In this study, we asked whether the distribution of intraspecific marine biodiversity is explained by past climate‐driven range shifts across the hemispheres. We compared the genetic variability of Macrocystis pyrifera, from Alaska to Baja California Sur (Mexico) in the northeast hemisphere, and from Peru to Tierra del Fuego (Argentina), as well as South Africa, Australia, New Zealand and sub-Antarctic Islands in the southern hemisphere.The study area comprised the entire distributional range of M. pyrifera might have occurred for the long-term. This approach used Boosted Regression Tress (BRT), a machine learning algorithm with high predictive performance, able to fit non-linear relationships and complex interactions, while strongly reducing overfitting through hyper-parametrization and forcing of monotonic responses50.Species distribution modelling (SDM) estimated past distributional shifts and potential refugial regions where 29 were developed52 for the present-day and the LGM conditions using the computation pipelines of Bio-ORACLE51. These reflected essential resources (nutrients as Phosphate and Nitrate), disturbance (ice thickness) and factors affecting physiology . Predictors were clipped to 30 m depth, the typical maximum depth distribution of the species52. The LGM predictors considered sea level and shoreline displacements by placing the isobath of − 120 m below current sea level53. Presence records were extracted from the fine-tuned dataset of marine forest species54. The same number of pseudo-absences as presences were randomly generated in sites where no presences were recorded55. To reduce the negative effect of autocorrelation in the models, the correlation of predictors within the range of occurrence records (presence and pseudo-absences) was tested as a function of geographic distance. For this purpose, a correlogram was built to pinpoint the minimum distance at which predictors were significantly correlated. Records were pruned by randomly selecting one record from the pool found within such distance56.Biologically meaningful benthic predictors  for the species57. A tenfold cross-validation framework using independent latitudinal bands7 was implemented to find the optimal hyperparameter combination of number of trees , tree complexity (1–6) and learning rate . This approach also inferred the performance of models58 by using the area under the curve (AUC) of the receiver operating characteristic curve and sensitivity59. To reduce overfitting, models were forced to fit negative monotonic responses for maximum temperature and ice thickness, and positive responses for nutrients, salinity and minimum temperature60. The relative contribution of predictors to the models was determined by computing the increase in deviance explained  when each predictor was added to its alternative model. Physiological tolerance limits  were estimated from individual response functions produced for each predictor, while fixing all alternative predictors to their averages62.Considering the general pattern found in the species’ genetic structure see “”, models63 were built using a stepwise approach by fitting a full model  and interactively removing predictors one at the time, from the least to the higher contributive, until the difference of deviance explained between the full model and the reduced model was higher than zero64. Maps reflecting the potential distribution of the species for present-day conditions and the LGM were developed with the parsimonious models fitting the optimal hyperparameters. These maps were reclassified to binomial surfaces, reflecting presence and absence of Macrocystis pyrifera, by applying a threshold maximizing both specificity (true negative rate) and sensitivity65. Range shifts were determined in terms of area by comparing the LGM and present modelled distributions for the regions where genetic sampling took place  with higher potential for transferabilityace see “” below. 66 and39.Approximately 30 individuals were sampled per site  for genetic analysis, by removing a piece of the blade and preserving it in silica drying crystals. Genomic DNA extraction was performed with the NucleoSpin 96 Plant Kit II  and standard protocols. Microsatellite amplification and scoring was performed for 6 polymorphic loci using PCR conditions and methods described in67 without a priori population assignment, allowing admixture, using the model of correlated allele frequencies for a range of K clusters between 1 and 10, a burn-in time of 2 × 105 repetitions and 1 × 106 iterations. The potential number of clusters was inferred with the DeltaK criterion68, which identifies the “best” K value as the one maximizing the rate of change in the log probability of the data (ΔK). The analysis was performed under two hierarchical steps8: the first aimed to discover the main genetic groups when considering the entire distribution, and the second aimed to reveal the regional levels of genetic structure within each of the main genetic groups that resulted from the first step. This approach allows the analysis of regional genetic differentiation within the main genetic groups independently of their differences in allelic richness. Two sites showing signs of admixture in the first hierarchal step  to the nodes based on the edge’s distance. The significance of this process was inferred by testing the proportion of 104 random membership assignments retrieving higher Modularity than observed. Network eigenvector centrality was also determined to identify sites serving as hubs to gene flow69.Genetic structure was also inferred with a network analysis, with nodes defined by the sampled sites and edges by their relative number of shared allelesFST because it is more suitable for comparisons with contrasting levels of diversity71, as in this case .The distribution models included multiple predictors, from which temperatures (maximum and minimum) had a prominent role in explaining the distribution of both northern and southern genetic groups  showed disjunct potential distributions between the northern and southern hemispheres during the LGM and the present. Throughout the Southern Ocean, models showed broad suitable conditions for rafting with present-day conditions, while during the LGM, a discontinuity might have occurred along southern Chile and Tierra del Fuego (Argentina).A total of 156 alleles were amplified across 3872 genotyped specimens . The Evanno criteria applied to the first hierarchal level of Structure revealed 2 genetic clusters associated to the northern and southern hemispheres, and 4 clusters dividing the northern hemisphere in (1) Alaska to Point San Luis, (2) Point Conception region and (3) Channel Islands to Mexico Figs. . This leThe two main clusters associated with the northern and southern hemispheres showed high differentiation  and in Peru , potentially involved in the ancestral radiation of lineages, are suggested here as priority conservation areas under Climate Change Integrated Conservation Strategies for potentially endangered phylogeographic lineages72. The distribution of 6 distinct clusters, with strong genetic discontinuities corresponding to previously described phylogeographic breaks of additional species and well-known oceanographic barriers shaped by ocean currents and habitat discontinuities, allow making broad generalizations about the process driving marine phylogeography, particularly important for ecosystems structuring species.The rare opportunity to study a biological model with replication of postglacial expansions in both northern and southern hemispheres allowed us to demonstrate that the distribution of intraspecific marine biodiversity can be structured by comparable evolutionary forces across the global ocean. By combining independent theoretical distribution modelling with empirical genetic data, we show how past range shifts (c. 20 Kyr ago to the present) shaped refugial regions in both hemispheres, where Macrocystis pyrifera  mainly driven by thermal conditions , which is typical for marine forest species modelled at the scales of our study7. The estimated thermal tolerance of the species between approx. 2 and 24 °C largely agreed with empirical physiological studies74, which together with the evidence found of niche conservatism between hemispheres  provided strong support for the models, particularly important when performing temporal transferability to estimate demographic changes75. The high performance shown by our SDM approach is expected when using machine learning algorithms with proper hyper-parameterization and monotonicity constrains49, fitting biologically meaningful predictors against comprehensive datasets of distribution records76. Despite the general agreement found between predicted suitable habitats and reported occurrence records , overprediction was found in Alaska, Chile, and Southwestern Africa, and, to a lower extent, in Western and Southern Australia52, and along the coastlines of Washington and Oregon states (USA). While the models predicted favorable conditions, additional predictor variables not considered might be preventing its occurrence. Specifically, the lack of rocky substrate43, interspecific competition77, limited light conditions78, and restricted dispersal potential29 can be excluding the species from such areas predicted as suitable.The SDM approach showed the potential distribution of 14, but were never addressed before with the same biological model exposed to the LGM conditions of both hemispheres in a SDM framework. This allowed identifying multiple mid- to low latitude refugia at global scales, for which peri-glacial margins largely match additional genetic studies; for instance, Vancouver Island adjacent to the Laurentide Ice sheet in the northern hemisphere79 and Patagonia and the Falkland Islands in the southern hemisphere24. As anticipated, populations within refugia showed higher and unique genetic diversity levels, as long-term persistence rendered the possibility of population to accumulate and retain regional diversity levels80. Outside refugia, where range shifts might have occurred, diversity levels were always lower regardless the hemisphere, with private alleles reduced to negligible values < 1 at distances > 55 km of refugia, and to 0 at distances > 150 km. This skewed pattern of diversity occurring at such short distances of closest refugia  might have provided suitable habitats from the LGM to the present. The rate and magnitude of these changes are not uncommon for cold-temperate species11. In particular, the genetic hotspot found from Channel Islands to Mexico, with striking higher diversity compared to anywhere else, was the only sampled region that increased suitable habitats during the LGM. An additional study shows this region with even larger habitats (up to threefold) from the LGM to the mid-Holocene42. Large and stable habitats can potentially maintain population sizes large enough to counteract the genetic effects of inbreeding depression and drift over time84. This contrasts with regions like Patagonia and sub-Antarctic islands that might have experienced severe population reductions, while not complete extinct (up to 56% LGM contraction), and today show reduced diversity. But comparing diversity levels between sites / genetic groups must consider additional drivers beyond potential habitat changes through time. For instance, the major genetic bottleneck during the colonization of the southern hemisphere46  as a proxy of effective population size changes through timee46 see “” may hav85. In the present study, Mexico (northern hemisphere) and Peru (southern hemisphere) can represent such cases. Despite being predicted within refugia, considering their high private diversity levels and SDM estimates, both regions show low allelic richness. There, studies following demographic changes of giant kelp have recurrently linked the extreme conditions of El Niño events to local population extinctions86, which might have produced bottlenecks and shifted genetic baselines34. Cryptic persistence in deep colder waters or microscopic gametophyte stages, as suggested elsewhere88, could have counteracted complete genetic losses and safeguarded the observed unique diversity. In this context, climate change scenarios are projected to shift the 24 °C isotherm matching the species’ thermal tolerance to more poleward regions, hundreds of km beyond these sites, particularly in the no mitigation scenarios overlooking the Paris Agreement initiative89. The complete loss of unique genes, as recently reported for the Ecklonia forests of Oman90, is of particular concern30, calling for considering both warm range edges of M. pyrifera as priority for conservation in light of Climate Change Integrated Conservation Strategies for potentially endangered phylogeographic lineages72.Genetic erosion within refugia can further occur due to the exposure of individuals to peripheral niche conditions at low latitude range margins, typically characterized by nutrient-deprived warmer watersM. pyrifera composed by two main genetic clusters, which coincide with the division of both hemispheres, followed by a second and more complex level of structure comprising six clusters. All clusters showed significant pairwise differentiation levels, largely suggesting the effect of genetic drift, not compensated by regular gene flow. Compared to the southern hemisphere, the northern hemisphere showed significantly higher genetic diversity and up to fourfold more private alleles , rendering it the potential ancient origin of the species. This is supported by previous studies also hypothesizing the southern hemisphere distribution of M. pyrifera and additional cold-temperate species of macroalgae resulting from northward introductions91. The centrality patterns found in both genetic structure and network analyses point to Catalina Island bridging the hemispheres through the region sampled in Peru, a hypothesis raised elsewhere46. This process can explain the admixture levels found in Peru, and may have occurred by stepping-stone through unsampled tropical regions where the species occurred, or still occurs in elusive habitats 92, yet in a distant past beyond the LGM, as SDM does not suggest the possibility of rafting between the hemispheres. Additional temperature reconstructions for this tropical area match the sea surface temperature anomaly of our data during the LGM of approx. − 2 °C, reinforcing a plausible long-term barrier for rafting. Earlier periods like the pre- or mid-Pleistocene climate transition (620–435 Kyr ago and 870–620 Kyr ago) could have provided suitable conditions for the stepping-stone process, as suggested for the red algae Callophyllis variegata91.Results showed 93; this contrasts with additional persistent areas  from which dispersal might have been hindered by the major discontinuity for rafting occurring along southern Chile and Tierra del Fuego, as suggested by the SDM.Marked genetic structure hinders the inference of other colonization pathways, with the exception for the regions more recently colonized . Structure and network analyses  suggest Alaska and Canada potentially originating from Monterey Bay, and the sub-Antarctic Islands being colonized by Tierra del Fuego or a neighboring persistent location , where the species could have dispersedM. pyrifera46, and reinforce the role of oceanographic currents and habitat discontinuity shaping the genetic structure of the species, as previously studied along the Californian coastline44. In the northern hemisphere, the deflection of the Alaska and California currents94 can explain the division between G1  and G2 (Santa Cruz to Point San Luis), while the well-known biogeographic barrier of Point Conception95 defines a genetic cluster per se. In the southern hemisphere, the split of the Antarctic Circumpolar Current into the northward Humboldt current and the southward Cape Horn current shapes a barrier at − 42° latitude matching the observed division between Patagonia and N. Chile (G5 and G6). The genetic discontinuities in this region were also associated with founder effects during post-glacial colonization of Patagonia for other macroalgae species, as well as for invertebrates and vertebrates99. The subdivision of Peru can result from habitat discontinuity shaped by extensive sandy beaches, or by the highly advective Humboldt Current System, which promotes off-shore transport, therefore generating a connectivity barrier to coastal populations. Lastly, the Tasman Sea, identified as a major biogeographical barrier for marine biodiversity100, explains the additional separation of G5 and G6, from Australia to New Zealand.The genetic divisions observed in both hemispheres are corroborated by previous studies of 98. In contrast, long-distance dispersal by rafting must be a rare process29, but crucial to the colonization of unoccupied suitable habitats following glacial events. Together, these processes shaped disjunct genetic lineages at short distances , rendering them of higher conservation value in the face of future climate changes, particularly if one considers the potential loss of unique alleles at low latitude range margins, and the multiple ecological, and socioeconomic services provided by giant kelp forests27. The insights provided with replication across hemispheres, contribute to a better understanding of the genetic effects of past climate changes, and may be generalizable to additional cold-temperate species, particularly for other important ecosystem-structuring species.Overall, the present study with replication along the northern and southern hemisphere, highlights the role of past climate changes at global scales in structuring refugial regions where populations may display higher and unique genetic diversity, compared to more recent populations resulting from post-glacial expansions. Additional drivers such as regional population size changes, genetic bottlenecks produced by major phylogeographic events  and the exposure to peripheral niche conditions in warm range edges might have further been key to structuring global diversity levels. The study also highlights the role of major oceanographic currents and habitat discontinuities, coupled with the density barrier effects of previously established populations, restricting the homogenization of distinct genetic lineages over time, as suggested for other kelp speciesSupplementary Table 1.Supplementary Information.Supplementary Figures.


Public health genomics prioritizes effective and ethical translation of genomic science into population health precision medicine. With the rapid development of cost-effective, next-generation genome sequencing, calls are growing for greater inclusion of Black people in genomic research, policy, and practice. Genetic testing is often the first step in precision medicine. This study explores racial differences in patient concerns about genetic testing for hereditary breast cancer. Employing a community-based participatory mixed methods research design, we developed a semi-structured survey that was shared broadly. There were 81 survey respondents, of which, forty-nine (60%) self-identified as Black, twenty-six (32%) indicated they had a history of a breast cancer diagnosis, or had received BRCA genetic testing. Black participants who expressed concerns about genetic testing were fairly equally distributed between concerns that could be addressed with genetic counseling (24%) and concerns about the subsequent use of their genetic data (27%). The concerns expressed by the participants in our study underscore a need for transparent disclosures and assurances regarding the use and handling of genetic data. These findings should be viewed in context with patient-led efforts to overcome systemic inequities in cancer care, as Black cancer patients have joined forces with advocates and researchers to develop protective health data initiatives and to improve their representation in genomic datasets. Future research should prioritize the information needs and concerns of Black cancer patients. Interventions should be developed to support their hidden work as a means to reduce barriers and improve representation in precision medicine. Public health genomics prioritizes the effective and ethical translation of genomic science into population health benefits and personalized health care. Genetic testing is often the first step in the process to personalize medicine. However, many cancer patients face barriers to accessing genetic testing and counseling services , and BlaGenetic testing has been available for many hereditary cancers since the 1990s. For Black patients in the United States, hereditary breast, ovarian, and colorectal cancers highlight stark disparities. Hereditary breast cancer and ovarian cancer (HBOC) incidence rates tend to be higher among younger (< 45 years old) Black women than among white women and mortality from breast cancer is 42% higher in Black patients than in white patients. Similarly, hereditary colorectal cancer tends to present earlier in Black patients than in white patients and Lynch syndrome is the most common colorectal cancer syndrome among high-risk Black patients . Black hRacial disparities in precision medicine often are a result of limited access to and awareness of clinical genetic evaluation services . Many inInitiatives to engage underrepresented populations in cancer clinical trials and genomic research are growing . AlthougThis study employed a community-based participatory mixed methods research design. It was conducted in partnership with three breast cancer advocacy groups My Breast Years Ahead, a support group created by Black women to support others with breast cancer and affiliated with My Style Matters; Brave Bosom, a citizen data science organization affiliated with The Light Collective; and Facing Our Risk of Cancer Empowered (FORCE), a nonprofit organization for people with hereditary breast, ovarian, and other cancers. The first author conducted extensive pre-study fieldwork by attending meetings held by the advocacy groups and volunteering locally at events hosted by the Florida Breast Cancer Foundation (FBCF). Two other authors hold leadership roles within breast cancer advocacy groups [TT and JH] and were a critical bridge to understanding concerns of HBOC patients throughout the study. As a result of the fieldwork, we determined our research priority would be to better understand racial differences in concerns about genetic testing for hereditary breast and ovarian cancer (HBOC). The research was conducted in Tallahassee, Florida, as part of a PhD dissertation in Information Science. The study procedures were approved by the Florida State University Institutional Review Board.Adult participants, aged 18 or older, were recruited through snowball sampling. An invitation to participate in the study, including an anonymous link to the Qualtrics secure online survey software, was distributed on social media outlets and online via cancer advocacy groups’ web posts or newsletters, was posted on social media sites with messaging to encourage readers to share the invitation with others. Cancer advocacy groups organized around inherited cancer risk constituted a natural constituency. Surveys were considered complete if more than 80% of the eligible questions were answered. For their time and effort, all participants who completed the survey received a $10 Amazon gift card.Out of 102 surveys submitted, 81 were complete. The respondents ranged in age from 24 to 76 years. All resided in North America. The sample was stratified by race . Black women with breast cancer were deliberately targeted for recruitment. Forty-nine respondents (60%) self-identified as Black. Twenty-six (32%) indicated they had a history of a breast cancer diagnosis.The data were collected using a secure online survey, which included structured items and unstructured free text questions, adapted from validated measures in the Health Information National Trends Survey (HINTS) . The NatWe collected the following socio-demographic information: self-reported race, ethnicity, age, education, income, marital status, insurance, and geographic region. Cities where the participants currently reside were grouped into geographic regions. Questions to capture a brief health history were included self-reported history of a breast cancer diagnosis and family cancer history were included. We collected information about the participants’ awareness of genetic tests in general and their past experience with genetic testing. In addition, participants were asked about their willingness to take a genetic test and we captured information about genetic counseling. Genetic testing concerns were captured as an unstructured field, in which participants were asked to type a response to the question “Do you have any concerns about genetic testing? Please describe.”Prior to analysis, all responses were deidentified and assigned a unique participant number. We conducted a complete case analysis to screen for errors, determine frequencies, and identify normality of distribution patterns in the data to assess its overall quality. We used R to conduct exploratory data analysis and preprocess the data.Descriptive statistics were calculated for all variables of interest. Continuous measures were summarized using means, standard deviations, and ranges. Categorical measures were summarized using counts and percentages.We created a preliminary unstructured coding guide based on constructs of Dervin’s Sensemaking Theory . SensemaAll participants identified their gender as female or gender nonconforming. The study population was educationally diverse, with higher educational achievement than the general population . The study population reported 28.4% below $60,000, 34.6% between $60,000 and $99,000, and 27.2% with $100,000 or more annual household income. Most had insurance (93.8%), were married (48.1%), and had children (76.5%). Only 8.6% indicated Latinx or Hispanic ethnicity. Black participants represented 60.5% of the study population.The frequency of the two themes  between Black participants and non-Black participants showed interesting differences . Nearly Non-Black participants shared more concerns that could be addressed with genetic counseling (47%) than concerns related to the subsequent use of their genetic test data (25%). Both Black and non-Black participants expressed similar concerns that are described in the following passages, which include exemplar quotations.There were five unique concerns expressed by participants that traditionally have been addressed by Genetic Counselors: validity of results, medical decisions, education, insurance considerations and family communications.Participants reported concerns about the“possibilities of inaccuracies”(P03)in the test results. This implies that patients prefer certainty in the results. Black breast cancer patients who have undergone genetic testing often receive uncertain results or VUS (variants of uncertain significance) results, which reflects an ever-evolving need for research and discovery related to the classification of variants. Populations with African ancestry are underrepresented in genetic databases that classify variants and genetic testing results can vary in clinical validity.Genetic testing results are important tools for making medical decisions. At various stages along the breast cancer care continuum, patients can feel unsure how to make decisions based upon the results of the genetic test.“My concern is when they find an anomaly and there isn’t any information in how to deal with it.”(P50)Some may opt to be tested before breast cancer is suspected because they have a family history of HBOC or perhaps they engaged in recreational testing purely for the knowledge. Others may be recently diagnosed and need to use the information to make surgical decisions to prevent the progression of the disease. While others may have survived breast cancer and have incorporated genetic testing as a means of surveillance in case of recurrence. In each of these situations, the genetic testing would address different types of medical decisions.Patients expressed a need to be educated about the process and what to expect after the testing has been completed.“Honestly I probably don’t know enough about the testing to really know if I should be concerned.”(P65)Patients may need information in order to raise questions and self-advocate.Insurance concerns were expressed by the participants. They worried about“Insurance ramifications”(P08)The Genetic Information Nondiscrimination Act of 2008 helps to prevent health insurance plans discriminating against patients with genetic susceptibility for diseases and disorders. However, these types of concerns may be extremely important for marginalized groups due to increased likelihood of encountering structural barriers to care and limited insurance benefits. Some patients may be reluctant to agree to genetic testing due to perceived changes in medical costs or reduced insurance coverage.When patients receive the news that they have a hereditary cancer syndrome, it can impact the entire family. Patients who have a pathogenic variant often carry the primary responsibility to communicate directly with relatives, which can be especially difficult for parents.“I do [have concerns] for my own children - not sure when is too early.”(P43)Standard practice is for providers to support patients with “a family letter” to share the news of their genetic risk and to encourage them to seek genetic testing and counseling services as well.Concerns about how the genetic information would be stored, kept private, or destroyed after testing were described. Participants wanted to know who would have access to the information and whether it would be used to socially discriminate against them or to commit genocide.In addition to using genetic testing results to make medical decisions, patients would like to have agency in what happens to their genetic information.“After the testing what happens to my genetic samples? Will they be kept, disposed of, or returned to me? Am I able to make that decision?”(P39)Concerns about agency are related to protecting the privacy of such sensitive information. Truly protecting privacy can be a challenge with de-identification.“Information security, privacy, testing or any part of the data analysis being done outside the U.S.”(P56)Genetic data is unique to the individual and even if it has been separated from other personally identifiable information, genetic data is forever linked to the individual. People often view genetic information about themselves as private. Specific variants within an individual’s genome may be widely shared with biological relatives or even across the entire human population.Often laws limit how genetic data may be used or by whom the data may be accessed but patients are not aware of how their genetic data will be protected.“I learned after the test about potential problem of obtaining life insurance because of genetic testing regardless of the results. I feel those who are tested should be made aware of that fact.”(P29)Some marginalized communities have faced historic trauma related to discrimination and oppression, which bleeds into current day experiences with social discrimination.“My concern would be if my results could be used towards other testing or sold to outside companies.”(P47)Black breast cancer patients may experience disproportionate exposure to forensic surveillance and overrepresentation in law enforcement genetic databases. Consideration of the additional dimensions of discrimination may be a priority among Black patients.Genocide is the deliberate killing of people related by geographic region, ethnicity, religion, national origin, or other physical or genetic characteristic. This may sound like a farfetched concern but historically there have been a number of genocidal acts in the 20th century, including the Holocaust which is the largest and most well documented case of genocide in human history.“Just worry future Nazi genocidal maniacs will use the information against us.”(P79)The historical ties between human genome research and antiquated eugenics practices may foster additional concerns that extremist organizations will use genetic information to carry out genocide.This study demonstrates the value of partnership with underrepresented communities in public health genomics research and expands our awareness of breast cancer advocacy efforts. When one thinks about breast cancer advocacy, typically the efforts are seen through a lens of social support. Many advocates address barriers related to social determinants of health by providing transportation to appointments, raising funds for housing, and offering healthy meals. Yet there are additional collective advantages of having advocacy groups embedded within research teams. Advocacy extends beyond the clinical research settings into underrepresented communities. From the outset of this study, partners from underrepresented communities affected by cancer and specifically those that supported Black breast cancer patients were engaged. This aided in successfully representing Black women in our study population.Our study is novel in that nuances of medical mistrust have been unpacked as patient concerns specific to genetic testing. We discovered two categories of concerns expressed about genetic testing, one theme reflecting a need for genetic counseling prior to testing and the other reflecting issues specific to genetic data use after a test has been taken. Although Black participants in this study raised concerns about genetic testing that are similar to those raised by non-Black participants, their data use concerns may highlight an imminent need. We must increase access to genetic counseling services in parallel with more transparent disclosures and assurances about the use and handling of genetic data. These findings should be viewed in context with existing patient-led efforts to overcome systemic inequities in cancer care. Advocacy groups have become an ongoing source of emotional support and a bridge to activism and representation . Black bOur study shows that among Black participants who expressed concerns about genetic testing, nearly half of those concerns could be addressed by having access to genetic counseling services. Typically, genetic counseling helps patients make informed, autonomous choices about whether or not to undergo a genetic test, how to interpret the results, and weigh options related to the results. Medical decisions can be challenging and genetic testing can further the complexity of considerations. For example, advocates have developed extensive educational materials to describe the differences between direct-to-consumer genetic testing  and genetic testing provided by laboratories regulated by the Clinical Laboratory Improvement Amendments or CLIA . These educational materials are designed to help patients understand the differences in testing technologies, the limitations of the results, and the potential data risks related to the subsequent use of their genetic data. This work is significant for Black breast cancer patients, who may require CLIA-certified laboratory tests because to identify more than the three Ashkenazi Jewish founder variants. Also, relevant to patient concerns about data use, the CLIA-certified laboratories are not able to resell genetic testing data. Advocates make these types of educational materials accessible to supplement information from health care providers. This is an example of information that would be discussed as a part of genetic counseling.Unfortunately, there is a clear shortage of health professionals specifically trained to provide genetic counseling. Advocacy groups fill these voids and unmet needs of communities vulnerable to lacking access to genetic counseling. Without access to certified genetic counselors, many patients facing a hereditary cancer diagnosis seek information and decision support from trusted advocacy groups . Many adOur findings indicate that Black participants are interested in genetic testing but they have reservations about the misuse and abuse of genetic data. The technologies and data structures, which support clinical genetic services must be evaluated and updated often. Recent news headlines describing the racial inequities built into clinical algorithms used for monitoring and surveillance can erode trust in clinical technologies. “…we are in need of new analytic tools, forged by critical scholars of science and technology, that draw into view the mutual constitution of social and scientific practice”. We mustCommunities, patients, and advocates need to be embedded within interdisciplinary teams that identify variants and build systems that use their data. Co-creation of knowledge and systems is required to build and sustain trust with diverse communities. Data trusts may facilitate the use of data across organizational boundaries and protect the interests of multiple stakeholders  by empowRacial disparities in the uptake of genetic testing for breast cancer consists of many factors. The results of this study add to the literature that intersects precision medicine and sociotechnical systems to advance medical care and reduce health disparities. Although this study was limited in scope and a small convenience sample, the findings challenge us to engage in new ways with genetic data. Future research should be conducted with a larger, less homogenous sample to verify the types of concerns, document the frequency at which they are present and generalizable in the population, and identify discordance within and between groups.Concerted interdisciplinary actions by multiple stakeholders are required to translate results into clinical practice. Data security and privacy protections are a priority. Both traditional genetic counseling and protective data initiatives are required to educate and build trust with underrepresented communities. Fostering meaningful partnerships with breast cancer advocacy groups may be the key to achieving representative genomic datasets and more equitable access to precision medicine.


The single amino acid substitution of lysine to methionine harbors a neoantigen that is presented in tumor tissue. The long peptide vaccine H3K27M-vac targeting this major histocompatibility complex class II (MHC class II)-restricted neoantigen induces mutation-specific immune responses that suppress the growth of H3K27MINTERCEPT H3 is a non-controlled open label, single arm, multicenter national phase 1 trial to assess safety, tolerability and immunogenicity of H3K27M-vac in combination with standard radiotherapy and the immune checkpoint inhibitor atezolizumab (ATE). 15 adult patients with newly diagnosed K27M-mutant histone-3.1 (H3.1K27M) or histone-3.3 (H3.3K27M) DMG will be enrolled in this trial. The 27mer peptide vaccine H3K27M-vac will be administered concomitantly to standard radiotherapy (RT) followed by combinatorial treatment with the programmed death‐ligand 1 (PD-L1) targeting antibody ATE. The first three vaccines will be administered bi-weekly (q2w) followed by a dose at the beginning of recovery after RT and six-weekly administrations of doses 5 to 11 thereafter. In a safety lead-in, the first three patients (pts. 1–3) will be enrolled sequentially.H3K27M-vac is a neoepitope targeting long peptide vaccine derived from the clonal driver mutation H3K27M in DMG. The INTERCEPT H3 trial aims at demonstrating (1) safety and (2) immunogenicity of repeated fixed dose vaccinations of H3K27M-vac administered with RT and ATE in adult patients with newly diagnosed H3K27M-mutant DMG.NCT04808245.The online version contains supplementary material available at 10.1186/s42466-023-00282-4. Diffuse midline gliomas (DMG) are universally lethal central nervous system tumors that occur predominantly in children and young adults. The vast majority of these tumors are characterized by a clonal driver mutation in canonical H3.1) or noncanonical (H3.3) histone-3 H3K27M) that causes widespread epigenomic changes and deregulated gene expression [ or nonca7M that c26–35 peptide vaccine has been shown to elicit CD8+ T cell responses against H3.3K27M in children with newly-diagnosed HLA-A*02:01+, H3.3K27M+ DMG [+ T cell remains controversial [Much like in other forms of malignant glioma , 7, immu27M+ DMG , the recoversial .+ T cell-mediated immune responses in MHC-humanized mice. Vaccinated mice with H3K27M-expressing flank tumors displayed effective tumor control and post-vaccine-tumors were infiltrated with H3K27M-reactive T cells [+ T cells that expanded in peripheral blood upon vaccination and were also detectable in the CSF  class II-restricted antigen presentation for effective cancer immunotherapy –19. A lo T cells . The adm T cells ). Furtheedicine, , Boscheredicine, ).INTERCEPT H3 assesses safety and immunogenicity of H3K27M-vac in combination with standard RT and with ATE in adult patients with newly diagnosed H3K27M-mutant DMG.The non-controlled open label, single arm, multicenter national phase 1 trial will enroll 15 patients with newly diagnosed H3.1K27M- or H3.3K27M-mutant DMG, WHO grade 4. Patients must not have received previous treatment except for surgery. The trial treatment consists of subcutaneous injections of the long peptide vaccine H3K27M-vac in addition to standard RT. Thereafter, patients will receive a combination of the human anti-PD-L1 antibody ATE and H3K27M-vac. The primary treatment phase comprises 50 weeks (last administration in week 47). Patients will receive eleven doses of H3K27M-vac. The first four vaccines will be administered bi-weekly (q2w) concomitant to and after RT. After a four-weeks recovery period, seven vaccinations are given in six-week intervals (q6w) in combination with 14 doses of ATE administered every three weeks (q3w)  peptide emulsified in Montanide (ISA50) to a total volume of 1 ml. The vaccine is injected subcutaneously in the thigh or abdomen followed by topical administration of imiquimod, a toll-like receptor 7/8 agonist  . A totalPrimary outcome measures will be safety and immunogenicity of H3K27M-vac in combination with RT and ATE assessed at the date of study termination.For safety assessment, patients will be medically reviewed at each visit including recording of concomitant medications and adverse events (AE). All AE will be graded according to National Cancer Institute Common Terminology Criteria for Adverse Events (CTCAE) version 5.0. The primary safety endpoint is the Regime Limiting Toxicity (RLT) until end of the recovery phase in week 10. RLT is defined as any of the following if considered related to the administration of H3K27M-vac: (1) any injection site reaction of CTCAE grade 4; (2) any injection site reaction ≥ CTCAE grade 3 that persists after four weeks; (3) any other hypersensitivity, anaphylaxis or local allergic reaction ≥ CTCAE grade 3; (4) brain edema of CTCAE grade 4; (5) autoimmunity ≥ CTCAE grade 3; (7) ≥ CTCAE grade 3 toxicity to organs other than the bone marrow, but excluding the following: transient (≤ 6 h) CTCAE grade 3 flu-like symptoms or fever, which are controlled with medical management, grade 3 nausea, grade 3 or 4 vomiting in patients who have not received optimal treatment with anti-emetics, grade 3 or 4 diarrhea in patients who have not received optimal treatment with anti-diarrheas, transient (≤ 24 h) grade 3 fatigue, local reactions, headache, nausea, emesis that resolves to grade ≤ 1, single laboratory values out of normal range (excluding grade ≥ 3 liver function test increase) that resolve to grade ≤ 1 within 7 days with adequate medical management, tumor flare phenomenon defined as local pain, irritation, or rash localized at sites of known or suspected tumor; and (8) death (including death due to disease progression). Dose de-escalation of the trial agents is not allowed, but administration may be skipped because of AE. Secondary safety endpoints include the frequency and severity of AE, occurrence of serious AE, their suspected relationship to the study medication, as well as changes in laboratory parameters.The primary immunogenicity endpoint is the presence of an H3K27M-specific T cell response at any time point during the trial. H3K27M-specific T cell responses are measured on Peripheral Blood Mononuclear Cells (PBMC) using IFN-gamma Enzyme-linked-immuno-Spot (ELISpot) assay  progression free survival (PFS), (2) overall response rate (ORR), defined as the proportion of patients showing complete response, partial response or stable disease at end of study compared to MRI at visit 1, (3) association between immunogenicity and ORR, (4) association between immunogenicity and PFS.To analyze biological activity in more detail, H3K27M-reactive T cell subtypes and H3K27M-reactive antibody subtypes in peripheral blood and CSF will be characterized. Immunogenicity will be related to the HLA-type and to the presence of H3K27M DNA in the peripheral circulation, furthermore clinical outcome to the presence of H3K27M-reactive T cells within the CSF as well as to the presence of H3K27M DNA in the peripheral circulation. In addition, H3K27M-specific antibody and B cell responses will be assessed at any time point during the trial measured by Enzyme-linked Immunosorbent Assay (ELISA) and patient-specific H3K27M-reactive T cell receptors will be characterized, benchmarked and functionally validated. Finally, functionality of vaccine-induced T cell receptors will be correlated with clinical outcome parameters.Translational research objectives of the trial comprise the assessment of H3K27M immunoreactivity, H3K27M peptide presentation and H3K27M-specific TCR repertoire and phenotype in recurrent tumors, if re-resection or biopsy is clinically indicated and tissue is available. Furthermore, H3K27M mutation status in recurrent tumors and H3K27M-reactive T cell receptors in recurrent tumors will be analyzed in that case.The main patient inclusion criteria are patient age ≥ 18 years, histologically confirmed diagnosis of an H3.1K27M or H3.3K27M-mutated diffuse midline glioma WHO grade 4 , no previous treatment except for surgery, availability of tumor tissue for translational analyses (FFPE bulk tissue or biopsy), Patients are scheduled to receive RT, Patients should be immunocompetent (steroid levels must not exceed 2 mg/day dexamethasone), Patients should have a Karnofsky Performance Status of at least 60.Sponsor: German Cancer Research Center, Im Neuenheimer Feld 280, 69,120 Heidelberg.Investigators: Michael Platten, Neurology Clinic, Medical Faculty Mannheim, University Heidelberg; Katharina Sahm, Neurology Clinic, Medical Faculty Mannheim, University Heidelberg.+ T cell dominated immune responses against the clonal driver mutation H3K27M in diffuse midline glioma and the first trial to investigate the combined treatment with H3K27M-specific peptide vaccine, RT and anti-PD-L1 therapy in DMG.The lysine to methionine substitution constitutes an attractive therapeutic target, because it is a clonal driver mutation. Preliminary data suggests that the H3K27M neoepitope can be safely targeted with H3K27M-vac following standard-of-care (SOC) treatment and that the vaccine induces peripheral mutation-specific T cell responses that translate into CNS-specific immunity . SimilaBelow is the link to the electronic supplementary material.Supplementary Material 1


Podarcis raffonei. Results indicate a current population size of about a hundred individuals, a body size of lizards significantly larger than previously known, and a complete lack of genetic diversity. Cephalic malformations observed on all captured individuals indicate the detrimental effect of inbreeding depression and represent a severe threat to the persistence of this population.Information about the status and trends of endangered species populations are vital for conservation actions, yet these data are often limited for those inhabiting remote and difficult-to-access areas. With the technical support of an alpine guide, I climbed on La Canna sea stack, a columnar volcanic pinnacle 70 m high, to gather information on the size, morphology, and genetic variability of the tiniest population of the critically endangered Aeolian wall lizard −2, twice of a previous estimate. Standard methods for estimating population size are unsuitable for La Canna. An educated guess of about a hundred individuals can be drawn, considering the extent of habitat available on the stack and the number of observed lizards. Lizards on La Canna were not fearless, despite what was reported by alpinists, possibly because of aggressive intraspecific interactions or high environmental temperatures during sampling. Biometric data significantly extend the body size of La Canna’s lizards and indicate that it is not smaller than other P. raffonei populations. A complete lack of genetic diversity was found at the mitochondrial nd4 gene, in line with previous allozyme data and with estimates on other microinsular Podarcis populations. The small size of the La Canna population implies severe genetic drift and an extremely high level of inbreeding, as supported by low heterozygosity found across the genome. Detrimental effects of inbreeding depression are evident as cephalic malformations observed in all captured lizards of La Canna and might represent the more immediate threat to the persistence of this population.Among the extant populations of the critically endangered Aeolian wall lizard, the most vulnerable is the one surviving on La Canna, a columnar volcanic stack off the Filicudi Island. Here, I report the results of the first climbing expedition by a biologist on La Canna, that contributed direct observations and updated information on the size, morphology, and genetic variability of this population. Lizard density at the sampling site  was 1.7 m The Aeolian wall lizard is perhaps the emblem of a species on the brink of extinction among European herps ,2. SurviPodarcis sicula cucchiarai [Podarcis raffonei [Among the extant populations of this lizard, one of the most vulnerable is the one surviving on La Canna, a columnar volcanic stack rising 71 m above sea level, 1.6 km off Filicudi Island in the N-W sector of the Aeolian archipelago. La Canna represents the remnant lava neck of an eruptive centre that has been almost totally eroded, and that was active from 40 ka until 29 ka . The vercchiarai . And, foraffonei . About traffonei .P. raffonei [Here are reported the results of the first climbing expedition by a biologist on La Canna in 2020, aimed at collecting updated information on the size, morphology, and genetic variability of the tiniest population of the Aeolian wall lizard. The first goal of the expedition was to secure fresh tissue samples from La Canna lizards to generate the first complete genome of raffonei  and popuSample and data collection required climbing the La Canna stack. The expert alpine guide Lorenzo Inzigneri (LI) planned, directed, and coordinated all the climbing activities, from the intensive training sessions of the author (DS) in the Dolomite mountains to the climb planning and execution. The climbing ascent started on the 31st of July 2020 at 6:30 a.m. and was performed in two pitches of about 30 m each, the first toward a small belay edge, and the second up to the sampling spot: a small gently sloping terrace at a 50 m elevation on the eastern side of the stack. LI climbed as lead bolting the route, and DS as top-roped. Sampling was performed by DS constantly secured by LI, who set up a belay station with fixed bolts to sample in safety . Soft frnd4) gene fragment was amplified by polymerase chain reaction (PCR). This fast-evolving marker has been fruitfully used in several phylogeographic and phylogenetic studies on lizards, including Podarcis [2 (50 mM), 0.5 µL dNTPs (10 mM), 0.5 μL each primer (25 mM), 1 U of BIOTAQ DNA polymerase (Bioline), and approximately 50 ng genomic DNA. Amplification conditions consisted of a predenaturing step of 3 min at 94 °C, followed by 35 cycles of a denaturing step of 30 s at 94 °C, annealing at 50 °C for 30 s, extension at 72 °C for 45 s, and the final extension at 72 °C for 5 min. Purification and sequencing of PCR products were carried out by a commercial company, GENEWIZ .Total genomic DNA was extracted from alcohol-preserved tail tip tissue following standard high-salt protocols . The mitPodarcis ,18,19,20Podarcis . Amplifip-distance) between samples analysed in this study and sequences obtained from GenBank were calculated with MEGA v.7 [h) and nucleotide diversity (π) with their standard deviations (SD), using DNASP 5 5.10.01 [Podarcis populations compiled from previous phylogeographic studies [nd4 and partial HistRNA).Sequences were aligned with MAFFT v.7  using thMEGA v.7 . Genetic 5.10.01 , and com studies ,27,28,29 studies , only poPlots shown in this study were generated with ggplot2  in R 3232.2. A few large basaltic stones, and around twenty individuals of the plant Malva veneta , offer refuges to lizards. An active nest of the Eleonora’s falcon, Falco eleonorae, with a female brooding two eggs, was observed in a rock niche in the southern side of the study area. A total of 31 lizard individuals were observed in a sampled area of ~18 m2. Using the same index as [−2, more than double the value estimated by the previous study for the same area (0.8 m−2). The use of baits to attract lizards and the higher sampling effort might explain the increased detection efficiency of this study. Sixteen individuals were captured, ten females and six males, all adults; juveniles or subadults were not observed. Fifteen individuals (94%) had mites in one or more of the following three regions: around forelimbs (81%), on the side of the collar (31%), or on the tympanic area (19%). Seven lizards (44%), all females, showed ventral bite marks. Six individuals (38%) showed regenerated tails, and one showed a missing toe . All individuals (100%) showed malformations in cephalic scales (pileus), especially in the parietal area, varying from deformation of a few scales  to a crumpled-bumpy amorphous structure extending over most of the pileus with loss of the scutellation pattern , lying on the side of the rock wall, and a high of ~5 m, including the flat and gently sloping portion of the terrace before the cliff overhang, for an approximate surface of 18 mindex as , individ pattern .Based on observations and capture data, I can tentatively discuss previous observations and population size estimates. During the first climbing expedition on La Canna, five alpinists, led by L. Battineschi, observed a couple of fearless lizards and, surprisingly, snakes . Both li2, indicates that the latest guess of 20–30 individuals by Capula and Lo Cascio [The size of the La Canna population was reported to be of 20–60  or 20–30o Cascio  was probo Cascio , the numP. raffonei  of females (N = 9) range from 64 to 80 mm mean = 73.7 mm) and include the value observed for the single female (n.34-M.Z.U.P.: 73 mm) measured by Di Palma . At this.7 mm andP. raffonei from the population of Strombolicchio, which corresponds to a low intraspecific divergence (0.6% uncorrected genetic distance) compared to other wall lizards [nd4 genetic diversity estimates was possible for 16 insular populations of five congeneric species , and nucleotide diversity ranged from 0 to 0.00283 . Lack of haplotype and nucleotide diversity was also observed in four populations of three Podarcis species inhabiting a sea stack , two tiny islets . and a relatively larger island , although in all these cases, the population size was smaller (N < 7) than La Canna (N = 15). On the other hand, five populations inhabiting the tiny (<1 km2) or tiniest  islets show from low to high haplotype and nucleotide diversity . Therefore, besides the limitation of estimates based on a short gene fragment, and of uneven sampling strategies , in addition to island size, other factors may contribute to the lack of genetic diversity of the La Canna and other Podarcis populations. Probably, the extremely poor and reduced habitat available on La Canna  is the main determinant factor for the small size of this population, resulting in severe genetic drift and inbreeding that, in turn, can result in reduced fertility, hatchling success, offspring survival, and individual fitness [A single haplotype was found at the gene fragment in the sequenced individuals. The haplotype found in the La Canna population is five substitutions different from the haplotype sequenced by Salvi et al. ,44 in tw lizards ,26,28,45 lizards . Compari species b, includs clades . The num fitness . The hig fitness ,50,51. I fitness ,54,55,56Beside the collapse of the La Canna stack itself, deleterious effects of low genetic diversity and inbreeding depression might represent the more immediate threat to the persistence of La Canna population.The tiny population size of La Canna is associated with a collapse of genetic variability and inbreeding depression. Drone-based remote sensing imagery may provide a suitable and cost-effective approach for monitoring the size and the status of this population. Research in progress on the effect of deleterious mutations associated with inbreeding depression  will provide key information for guiding conservation actions that include ex situ strategies and genetic rescue through outbreeding programs.