Vigna radiata var. radiata) as a test case, we investigated the genomes of more than 1000 accessions to illustrate climatic adaptation’s role in dictating the unique routes of cultivation range expansion. Despite the geographical proximity between South and Central Asia, genetic evidence suggests mungbean cultivation first spread from South Asia to Southeast, East and finally reached Central Asia. Combining evidence from demographic inference, climatic niche modeling, plant morphology, and records from ancient Chinese sources, we showed that the specific route was shaped by the unique combinations of climatic constraints and farmer practices across Asia, which imposed divergent selection favoring higher yield in the south but short-season and more drought-tolerant accessions in the north. Our results suggest that mungbean did not radiate from the domestication center as expected purely under human activity, but instead, the spread of mungbean cultivation is highly constrained by climatic adaptation, echoing the idea that human commensals are more difficult to spread through the south-north axis of continents.While the domestication process has been investigated in many crops, the detailed route of cultivation range expansion and factors governing this process received relatively little attention. Here, using mungbean ( Mungbean, also known as green gram, is an important crop plant in China, India, the Philippines and many other countries across Asia. Archaeological evidence suggests that humans first cultivated mungbeans from wild relatives in India over 4,000 years ago. However, it remains unclear how cultivation has spread to other countries and whether human activity alone dictated the route of the cultivated mungbean’s expansion across Asia, or whether environmental factors, such as climate, also had an impact.To understand how a species of plant has evolved, researchers may collect specimens from the wild or from cultivated areas. Each group of plants of the same species they collect in a given location at a single point in time is known collectively as an accession. Ong et al. used a combination of genome sequencing, computational modelling and plant biology approaches to study more than 1,000 accessions of cultivated mungbean and trace the route of the crop’s expansion across Asia.The data support the archaeological evidence that mungbean cultivation first spread from South Asia to Southeast Asia, then spread northwards to East Asia and afterwards to Central Asia. Computational modelling of local climates and the physical characteristics of different mungbean accessions suggest that the availability of water in the local area likely influenced the route. Specifically, accessions from arid Central Asia were better adapted to drought conditions than accessions from wetter South Asia. However, these drought adaptations decreased the yield of the plants, which may explain why the more drought tolerant accessions have not been widely grown in wetter parts of Asia.This study shows that human activity has not solely dictated where mungbean has been cultivated. Instead, both human activity and the various adaptations accessions evolved in response to their local environments shaped the route the crop took across Asia. In the future these findings may help plant breeders to identify varieties of mungbean and other crops with drought tolerance and other potentially useful traits for agriculture. Photoperiod-H1 (Ppd-H1) resulting in the non-responsiveness to longer daylengths were likely associated with the historical expansion to high-latitude regions , also known as green gram, is an important grain legume in Asia  the mungbean mini-core collection of the World Vegetable Center (WorldVeg) genebank, (ii) the Australian Diversity Panel (ADP), and (iii) the Vavilov Institute (VIR), which hosts a one-century-old collection enriched with mid-latitude Asian accessions that are underrepresented in other genebanks, many of which were old landraces collected by Nikolai I. Vavilov and his teams in the early 20th century . These gUsing DArTseq, we successfully obtained new genotype data of 290 mungbean accessions from VIR The genetic structure was investigated based on the 10,359 LD-pruned SNPs. Principal component analysis PCA,  showed aV. radiata var. sublobata (Wild hereafter) as the outgroup, the accession-  or SEA and EA form a clade relative to SA and CA , again suggesting EA and CA to be closest. With regards to the relationship among Wild, SA, SEA, and EA, f4 tests suggest SEA and EA form a clade relative to Wild and SA . Notably, both TreeMix  suggest gene flow between SEA and EA. Consistent with archeological evidence of SA domestication, the nucleotide diversity (π) decreased from SA (1.0×10–3) to SEA (7.0×10–4) and EA (5.0×10–4), while the CA group has lowest diversity . Given this, the phylogenetic relationship  is consir=0.466, P=0.010), followed by SEA . No such association was found for EA  or CA . In addition, the southern groups (SA and SEA) together  have a much stronger pattern of isolation by distance than the northern groups  of eight bioclimatic variables  are higher than the tails of SNP STF, suggesting trait evolution driven by divergent selection , CA consistently exhibits a significantly higher root:shoot ratio, a phenotype that is potentially adaptive to its native environment of lower water supply  contains poems dating between the 11th and 7th centuries BCE near the lower and middle reaches of the Yellow River. While crops , vegetables, and many other plants have been mentioned, mungbean was not recorded. This is consistent with our results that mungbean had not reached the northern parts of East Asia at that time (the EA group diverged from the SEA group at around 2.7 kga). The first written record of mungbean in China is in an agricultural encyclopedia Qimin Yaoshu , whose spatiotemporal background (~1.5 kya near the lower reaches of Yellow River) is again consistent with our estimated origin of the EA group.Our results suggest that the expansion of the mungbean cultivation range may be associated with the novel phenotypic characteristics potentially adaptive to the new environments. This proposal would be rejected if the novel phenotypic characteristics appeared very recently. In support of our proposal, Xiangshan Yelu  recorded that mungbean from the southern parts of Asia had higher yield and larger grains than those in northern China (Chinese text and translation in Supplementary note). Similarly, Tiangong Kaiwu  mentioned that mungbean must be sown during July and August (Chinese text and translation in Supplementary note). The record suggests that the daylength requirement restricts the sowing period of mungbean in the north. Together with the dry summer  and soonUsing mungbean as a test case, we combined population genomics, environmental niche modeling, empirical field and laboratory investigation, and ancient Chinese text analyses to demonstrate the importance of climatic adaptation in dictating the unique patterns of cultivation range expansion after domestication. In this study, we focus on how or when mungbean could be established as part of local agriculture throughout Asia. We showed that after leaving South Asia, mungbean was likely first cultivated in Southeast Asia, East Asia, and finally Central Asia. We acknowledge that our data do not allow us to specify the number of previous out-of-India events that did not leave traces in modern genetic data or their exact routes (e.g. whether mungbean expanded from South to Southeast Asia through the land or maritime routes). While there might be multiple attempts to bring mungbean out of India as a commodity for consumption, our results suggest all present-day non-SA accessions have a common out-of-India origin.Combining archeological records, population genetics, and niche modeling  and 3, oIn this study, we suggest that the ability to disperse may not be an essential factor restricting mungbean spread from South to Central Asia. Cultivated mungbean has lost the natural ability of pod shattering to disperse seeds, and they mostly traveled through landscapes by human-mediated seed exchange or commerce. Evidence of long-distance human-mediated dispersal of mungbean was available. For example, mungbean seeds have been found near the Red Sea coast of Egypt during the Roman (AD 1–250) period . As earlDespite the profound impact of human-mediated dispersal on the spread of these and many other crops , in mungIn addition to the constraint of soil moisture, other factors may have contributed to the selection of short-season accessions in the north. In the short summer seasons of much of Central Asia, short crop cycling is a requirement. In Uzbekistan, mungbean is often sown in early July after the winter wheat season and harvested before mid-October to avoid delays in the next round of winter wheat and escape frost damage. Therefore, fast-maturing accessions are essential for this production system . SimilarAbout accession sampling and climatic niche modeling, we recognize that not all samples have available spatial data, and we do not have samples from some parts of Asia. For example, while most samples of the SEA group were collected from Taiwan, Thailand, and Philippines, we do not have many samples from the supposed contact zone between SA and SEA (Bangladesh and Myanmar) or between SEA and EA (southern China). If more samples were available from these contact zones, the modeled niche space between SA and SEA and between SEA and EA would be even more similar than the current estimate, strengthening our hypothesis that niche similarity might facilitate the cultivation expansion. On the other hand, clear niche differentiation between SA and CA was evident despite the dense sampling near their contact zone. Based on the Köppen climate classification, South Asia could be roughly separated into two major zones, with the eastern zone slightly more similar to Southeast Asia . This paOur study demonstrates that mungbean’s cultivation range expansion is associated with climatic conditions, which shaped the genetic diversity and contributed to adaptive differentiation among genetic groups. The climatic differences likely also resulted in farmers’ differential emphasis on using it mainly as a grain or green manure crop, further intensifying the phenotypic diversification among regional mungbean accessions that could be used as an invaluable genetic resource for genetic improvement in the future.V. radiata var. radiata) accessions were provided by the VIR. Most of the accessions are mainly landraces collected during 1910–1960 and are considered these accessions as the oldest cultivated mungbean collection from VIR  accessions were included as an outgroup. While all accessions used in this study have the country of origin information, only those from VIR have detailed longitude and latitude information. Therefore, for analyses connecting genetic information and detailed location , only the VIR samples were used.DArTseq data of 521 accessions from the ADP  and 297 The major goal of this study is to investigate the patterns of population expansion and the underlying ecological causes instead of detailed haplotype analyses of specific genomic regions. For this goal, genomewide SNPs provide similar information as whole-genome sequencing, as have been shown in other species. Compared to other genotyping-by-sequencing technologies, DArTseq has the additional advantage of less missing data among loci or individuals, providing a more robust estimation of population structure.2r threshold of 0.5 in PLINK (Trimmomatic version 0.38  was usedin PLINK . This dahttp://tree.bio.ed.ac.uk/software/figtree/).Population structure was investigated based on 10,359 LD-pruned SNPs using ADMIXTURE  with theV. radiata var. sublobata as an outgroup with a block size of 20 SNPs to account for the effects of LD between SNPs. We estimated one as the optimal number of migration events using the ‘OptM’ in R (The relationships and gene flow among the four inferred genetic groups were further assessed by TreeMix version 1.12  using 43tM’ in R . Bootstrxyd and STF) were estimated in 10 kb windows with pixy version 1.2.7.beta1 (Nucleotide diversity (π) and genetic differentiation  and a target population C. In ‘outgroup f3 statistic,’ C is the outgroup, and positive values represent the shared genetic drift between A and B. In ‘admixture f3 statistic,’ negative values indicate that the C is admixed from A and B. For f4 statistics, f4 measures the shared genetic drift between B populations and C and D after their divergence from outgroup A. A positive value indicates that the B population shares more alleles with D, and a negative value indicates that the B population shares more alleles with C. We used two Mb as a unit of block-jackknife resampling to compute SEs. The Z-scores with absolute values greater than three are considered statistically significant.To investigate the relation among inferred genetic groups, sion 7.0 . The f3 To examine the role of geographic distance in shaping spatial genetic differentiation, Mantel tests with 1000 permutations were performed for each of the ADMIXTURE-inferred genetic groups (separately for the groups defined by Q≥0.7 or Q≥0.5) using ‘ade4’ in R. Pairwise genetic distance between accessions was estimated based on all sites while the great circle geographic distance was determined using ‘fields’ in R. In addition, the same analysis was conducted for southern and northern groups to examine if there was a south-north pattern of differentiation.–8 which was within the range of mutation rates used in eudicots (V. radiata var. sublobata) as the ancestral allele. The model was run independently 100 times, each with 100,000 simulations. After obtaining the run with the highest likelihood, we performed parametric bootstrapping 100 times to obtain the 75% CIs of each parameter based on the previous study of Based on the shape of the phylogenetic tree, we used fastsimcoal2 , which deudicots . The modhttps://www.gbif.org/), were used for the analysis. Using the longitude and latitude information, we extracted the Köppen climate zones , in combination with additional presence records obtained from the Global Biodiversity Information Facility . To minimize redundancy and model overfitting, pairwise Pearson correlations between the 19 bioclimatic variables were calculated using ENMTools version 1.4.4 , reproduction , and plant size  were included. Trait values were inverse normal transformed. The ANOVA was performed to test for inferred genetic groups differences for each trait using R software (version 4.1.0).A total of 52 accessions with ancestry coefficients Q≥0.7 from three genetic groups  were selected for experiments of seedling-stage drought response. The experiment was laid out in a completely randomized design with three replicates of each accession under two treatments (control/drought). The experiment was conducted in two independent batches, and the whole experiment included 624 plants (52 accessions × 2 treatments × 3 plants per treatment × 2 batches).–2s–1 and relative humidity at 60 ± 5%. The seedlings were then transplanted to a hydroponic system with half-strength Hoagland nutrient solution  and were grown for 6 days before drought stress started. The nutrient solution was changed on alternate days, and the pH of the solution was adjusted to 6.0 with 1 M KOH or 1 M HCl.Mungbean seeds were surface-sterilized with 10% bleach for 10 min and rinsed with distilled water for three times. Seeds were treated with 70% ethanol for 5 min and washed three times in distilled water. The sterilized seeds were germinated on wet filter paper in petri dishes for 3 days. The experiment was conducted in a 740FLED-2D plant growth chamber  at a temperature of 25 ± 1°C and 12 hr of photoperiod (light ratios of red: green: blue 3: 1: 1) with light intensity 350 µmol mFor drought treatment, seedlings of mungbean were exposed to polyethylene glycol (PEG)-induced drought stress for 5 days. The solution of PEG6000 with an osmotic potential of –0.6 MPa was prepared by adding PEG6000  to the nutrient solution according to At the end of the experiment, plants were evaluated for SDW and root dry weight, measured on digital balance after oven-drying at 70°C for 48 hr. All traits were analyzed by mixed-model ANOVA with the treatment (control/drought) and the genetic group as fixed effects. The models included accessions as a random effect nested within genetic groups and a random effect of batches. Tukey’s test was conducted to compare genetic groups. All statistics were performed using JMP v13.0.0 .STQ) was calculated separately with respect to each treatment. Our root and shoot weight experiment used a selfed-progeny design, using the self-fertilized seeds from each accession as replicates, as recommended for partially inbred species (STQ = VB/(VB+VFam), where VB is the among-population variance component, and VFam is the within-population among-family variance component (STQ = (1+f)VB/([1+f]VB +2 VAW) (f is the inbreeding coefficient (estimated by VCFtools as 0.8425), VB is the among-population variance component, and VAW is the additive genetic variance within genetic groups estimated by the kinship matrix using TASSEL software  , where fsoftware . The res This is an important interdisciplinary effort, with compelling genetic evidence, that informs on the spread of an important crop. The work will be of broad interest to those studying the domestication and dissemination of cultivated plants. In the interests of transparency, eLife publishes the most substantive revision requests and the accompanying author responses.Decision letter after peer review:[Editors’ note: the authors submitted for reconsideration following the decision after peer review. What follows is the decision letter after the first round of review.]eLife.Thank you for submitting the paper "The climatic constrains of the historical global spread of mungbean" for consideration by First we would like to apologize for the length of time it took to reach this decision. We had hoped to get input from another archaeologist who had agreed to review but in the end did not submit a review. We had a rather long discussion of the work, plus several of the people involved were on vacation.Your article has been reviewed by 3 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and a Senior Editor. The following individual involved in the review of your submission has agreed to reveal their identity: Jeffrey Ross–Ibarra (Reviewer #1).Comments to the Authors:eLife.We are sorry to say that, after consultation with the reviewers, we have decided that this work will is not acceptable for publication in The first two reviewers, both geneticists with experience in plant domestication, were excited about the topic and the interdisciplinary approach taken. But both raised a number of concerns about the methods and approaches used, which would require substantial additional work to address. The third reviewer, an archaeologist, raised real concerns about how well the paper has incorporated existing data into interpretation and analysis.eLife. Having said this, there was broad interest in the work and the topic, and we would reconsider, albeit as a new submission, an extensively revised paper, which would likely look very different from the study at hand.In the end, given the number of concerns raised on both the genetic and archaeological fronts, I'm sorry to say that we have decided that this work in its current form will not be considered further for publication by We are sorry about this outcome, but hope that the comments will be helpful for submission elsewhere.Reviewer #1 (Recommendations for the authors):The authors provide an ambitious interdisciplinary analysis of the post–domestication spread of mungbean. I believe the authors' general thesis is correct, and the various data they provide are all consistent with their model.Nonetheless, there are some issues with analysis and interpretation, and in general, the data don't provide definitive evidence that allows claims about drought or the importance of the environment.All of the evidence and analysis presented are consistent with the authors' proposed SA–SEA–EA–CA model. The f3 results are particularly convincing. I struggle, however, with how the data definitively show environment was more important than human movement. Some text shows, for example, that trading or demic movement between SA and CA was frequent would make clear that mungbean 'could' have moved SA–>CA via humans but didn't. Otherwise, could the SA–SEA–EA–CA model simply reflect historical movements/expansions of people in those directions/times?On a similar note, the paper claims that drought was the most important factor limiting the mungbean movement. The phenotypic data certainly suggest adaptive differences in traits related to drought and drought differences in phenotype in an experimental setting, but additional evidence would be helpful to convince that drought is the key factor. The authors note the importance of daylength differences, for example – how do we know daylength wasn't the limiting factor ?Methods Recommendations– It's difficult in some places to know which SNP data set is used where. Are the LD–pruned SNPs used to estimate LD decay? The methods say there are 67K sites (including monomorphic) but there are 41K SNPs. This would imply that 2/3 of the sites are polymorphic. That can't be right so I must be misunderstanding something. Are these monomorphic sites also used for estimating nucleotide diversity (see the issue with VCFtools below)? For fastsimcoal, do you include sites where the derived allele is frequency=0 and where the derived allele is frequency 1?– It would be good to modify the language of the MaxEnt modeling. While MaxEnt may show that the modern mungbean does not currently grow in conditions similar to those during the Holocene at a certain spot on the map, this is not the same as saying the plant could not have grown there. For example, if we were to model MaxEnt on modern CO2 concentrations, we would come to the conclusion that modern mungbean could not have grown anywhere during the Holocene. I don't think necessarily the methods need to be changed, but it would be good to change the language here to be less definitive.– Although dominance is less of a concern in inbred species, I believe it is still incorrect to assume that using Vg is equivalent to Va in Qst. The epistatic variance could still be important, for example, and my brief internet search suggests mungbean isn't 100% selfing either. The authors have SNP data for all the individuals phenotyped, so it should be doable to estimate Va using kinship matrices and thus do a correct Qst analysis.– VCFtools calculates nucleotide diversity assuming every bp in a window has been sequenced. This will lead to incorrect estimates of π and Fst. See https://pubmed.ncbi.nlm.nih.gov/33453139/ for details and one potential fix if you have a vcf with invariant sites, or https://github.com/RILAB/mop for another if you just have bams + variable vcf.– an NJ tree  is just a clustering algorithm and shouldn't be interpreted as providing information on the timing or order of evolutionary events. (lines 119–123)– If the growing season is known and is what is most relevant for the crop (line 190), these should be used for most analyses or a justification for using annual data should be provided– I can't find the total length of time plants were grown for the drought stress experiment. The text reads as if it were 9 days?Reviewer #2 (Recommendations for the authors):The study aims to understand the diffusion of the Mugbean population in Asia using genomic and phenotypic data. The authors used phylogeny, analysis of population structure, model–based inference, quantitative genetics, and niche modeling to understand the diffusion of Mugbean and proposed a scenario where diffusion is strongly constrained by climate, and partially by geographical.I found the study very interesting with a mix of different methodologies from genomics to niche modeling and quantitative genetics. Few others studies used similar approaches but it is rather unique for the study of diffusion to combine these different approaches and bring up very interesting results. I have several comments on the methods so the results are better supported for the genetic part, for the phenotypic part, I am not sure the author will be able to support their claims, as the method they used might inflate variance in their estimations.Main comments:Phylogeny. Phylogeny is not really an appropriate method per see for intra–diversity study, phylogeny analysis could be used but the basic assumptions of the method are often inadequate, so the result should be put in context. A better method to do phylogeny–like inference is the TREEMIX approach based on the relationship of population integrating drift. I suggest the authors add this complementary analysis.Model inference. Here, I would have liked a statistical comparison of the different scenarios. FastSimcoal allows for estimated probability of models/scenarios and it would be an independent validation to have such a comparison of models.The inference of the model is dependent on mutation rate (unknown), notably on the time of divergence. The author used 10–8 but it is neither discussed nor justified.Analysis of structure.The author led aside from further studying individuals with ancestry lower than 70% in a given group. The analysis of structure could lead to such ancestry because of admixture or isolation by distance. One is secondary contact based on recent (or not) gene flow between genetic groups, the author is related to diffusion across the landscape. A large fraction of individuals in the PCA seems to me more likely related to isolation by distance . How this will impact the analysis of correlation by geographical distance if such individuals are not considered? The authors should perform the analysis of the Mantel test with all individuals to assess the impact of their choices.Quantitative analysis of QST. The author used the genetic variance and not the additive variance. The reasoning behind that is not explained, neither the inflation created by this broad sense QST. Authors have concluded that the "extent to which comparisons between FST and broad–sense QST are appropriate remains unknown" .Reviewer #3 (Recommendations for the authors):The paper aims to look at the domestication, post–domestication spread, and adaptation of mungbean (Vigna radiata) across Asia through the use of genetic data from landraces and accessions in see and genebanks.The genetic aspects of this paper are a strength – there is a lot of work that has been done putting together a range of datasets allowing for inter–collection comparison and comparison of collections made by different institutes with their varying goals, sampling strategies, and dates of collecting. Mapping this diversity, think about how drift has occurred and why is something that needs to be done, especially in mungbean  as they are often overlooked in literature.However, the main stated goal of the paper – to look at the domestication, post–domestication, and adaptations to climate change as this crop was moved around – is where it falls short. There is little engagement with the deep archaeological literature on both domestication as a process, post–domestication use and spread of mungbean (and other South Asian crops and those involved in the Silk Routes trade pathways), and the complexity of climate reconstructions and climate change over the stated period of interest/regions of interest. Works by Spengler and d'Alpoim Guedes for example are missed with regards to the Silk Routes debates, and literature by Fuller, Murphy given only short sentences as background for what is a very complex background regarding where and when mungbean is thought to have been domesticated. There is little reflection on the context of the two/three possible origins for mung , how this interacts with the Southern Indian Neolithic and Indus regions, and how the changing cultural dynamics may have contributed to the processes of domestication, post–domestication change and the spread of different varieties. Without this background, it is hard to then move into discussing modern genetic data with a view to past patterns, for example with thinking about how climate may have affected change, given that the debates around the 4,2k event are extremely complex within these, let alone thinking pan–Asian and trying to link potentially 'drifted' genetic data today to these deep–time events. This comes across in the timescales given to the genetic data, as without the context of the where and when from archaeology, we see dates such as those given in Figure 2B that suggest domestication for South Asia moving to South East Asia at c.6kya (4000BC), which is when we still think they were under domestication within South Asia. The region is also not pinned down for where in South Asia these specific 'domesticated' mung are coming from to go to South East Asia, and the routes, yet arrows and big circles are added in Figure 2A. This shows the issue of not using that important context from archaeology.A further issue arises from thinking about the climate data. By conflating vast areas , when applying climate modelling there has been an oversimplification, which makes any discussion of mung bean adapting to climate post domestication difficult to sustain. In line 184 for example, there is a suggestion on the role of the 6.2k event in Central Asia . While there are a few datasets as cited in the paper that show some impacts of wetter climates in some regions of Central Asia for a wetter 6,2k event this is by no means a universal impact, and regional data points are needed. We can see this when looking to the Indus and the impact of the 4.2k event as another example, again a point that needs refining in order to make such claims about mung domestication, let alone post–domestication adaptations.Overall the thrust of the paper – domestication, post–domestication, and the spread of agriculture – are overshadowing what is actually a far more interesting point, hidden in lines 87–89: this data could be "used this resource to investigate the global history of mungbean after domestication […looking at the …] phenotypic characteristics for local adaptation to distinct environments." This perhaps is where the paper is most interesting, and reframing it in this context would be truly exciting, looking at the diversity of the crop, how it is now adapted to diverse environments, and what this might mean for long–term sustainability in cropping systems.This paper sadly is losing some very interesting genetics data in complex and poorly explained mung history.– The lack of engagement with archaeological data and the misunderstanding of the chronology of mung use in the past makes it very difficult to tally the results with the interpretations and discussions. This MAJOR point has been unpacked in more detail above and must be addressed in order to reduce the oversimplification of the background and remove the concerning premise that no one has done much work on ancient mung use (as stated up to l.77). While it has not had as much work as the cereals, there is still work being done on it, looking at its domestication regions, secondary domestication changes and spread across South Asia and then into different parts of Asia.– Data seems to have been massaged to make it fit with the climate modelling in various regions , and to also make mung seem to be spreading before the domestication event itself. More engagement with the archaeological discussions on mung domestication is needed and discussions of what domestication is as a process .– Terms like cultivar and variety and landrace are used interchangeably. These must be defined in the paper. How they fit in with notions of domestication and post–domestication agricultural behavior must also be unpacked.– "how the domesticated forms later expanded to a broader geographical area has also been detailed in several species, including maize , rice , tomato , chickpea , and lettuce ." – these are unusual choices of case study to make a point as many (maize and rice as key examples) are not accepted as well defined and remain highly controversial. These are genetics papers, and demonstrate the lack of familiarity with the archaeological context of domestication. A quick glance at the literature around them will illustrate that they are poor choices of case studies to make this point as they too are highly controversial.– "It is also unclear whether the expansion of most crops strictly follows the longitudinal axis of the continents  or whether or why some are able to cross different climatic zones." – again poor knowledge of the archaeological context of these debates, and the reliance on Diamond is concerning as he is not an archaeologist. See works by Lister on barley and Lui on wheat as a good starting point.– Debate on wild progenitor of mung bean needs to be explored. while sublobator is a likely candidate it should be explained in the paper that there are other possible options, and then why it was chosen here, with citations.– The figures are difficult to use. This comes back to the conflation of space and time outlined in the public review. There are big circles on the maps covering the dots which I presume are either archaeological sites or accession points of the sampled beans(?! unclear), and then very odd choices of illustrating change over time. The figures are small and hard to see and require very long text in the figures to make them useable.– Some aspects of basic geography have been overlooked to make climate the most important variable; l.166–7 "Given that geographic barrier might not be the most important factor". I find it hard to believe that both the Himalayas and major flood basins like the Brahmaputra would not be an issue, as would issues of day length when moving things north–south.– In dealing with issues of climate change and adaptation some discussion of tolerance is needed. there must be a discussion (and a table perhaps) of the different watering, salination, temperature, etc. tolerance of the mung bean(s) under consideration to make the claims justified.– Within the methods, the sampling strategy was hard to follow. This needs a more careful and clear description of decisions made: exactly where did the accessions come from geographically? how did their spread affect the dataset? Is there geographic clustering, did you compensate for that? how does the sampling potentially bias your data? a map would be useful.– Fair and open protocols dictate that all methods must be stated: "Genomic DNA was extracted from a single plant per accession using QIAGEN Plant Mini DNA kit according to the manufacturer's instruction with minor modification." If you modified the protocol then you have to outline what you did so it can be reproducible and the data comparable.– "Climate data for conditions between 1960–1990 were downloaded from the WORLDCLIM 1.4 database" – how was this dataset determined? why 30 years and not more? give citations to explain this decision, and look to other modelling efforts to check comparability.– "19 bioclimatic variables" – what are these? why were they chosen? a table and explanation are needed.– "excluding one of the two variables that have a correlation above 0.8 (Supplementary file 4)" – why? explain the reasoning for exclusion.– Throughout the dataset has relied on "In total, our dataset contains more than one thousand accessions (1092) and covers worldwide diversity of mungbean representing a wide range of variation in seed colour" however at no point is there a discussion of whether these are modern variants of historic landraces and how this was assessed. This has a big impact on any discussion of "ancient" adaptations, and there must be a discussion of how you tested to see if the genetic changes you see are more recent or past changes and how the genetic clock was applied.As noted in the public review, a far more interesting aspect than trying to tie into domestication/post–domestication and chronological vagaries are the points made in lines 87–89: this data could be "used this resource to investigate the global history of mungbean after domestication […looking at the …] phenotypic characteristics for local adaptation to distinct environments." Thinking about the value of this dataset for the preservation of diversity, and how diversity links to localised adaptations today and to sustainable cropping now is critical, and I suggest this could be the way to reframe things.eLife. Your revised article has been evaluated by Detlef Weigel as Senior and Reviewing Editor.Thank you for resubmitting your work entitled "Environment as a limiting factor of the historical global spread of mungbean" for further consideration by The manuscript has been improved but there are some remaining issues that need to be addressed, as outlined in the comments of Reviewer #1 below.Reviewer #1:I found this study to be one of the rare to combine genomic data, climate data, phenotypic data to decipher the diversity of adaptation of plants, and try to build up scenario of their diffusion. Previous recommendations were mainly answered, and I am personally satisfied with this new version of the manuscript. At this stage I recommend acceptance of the paper as soon as the concern is addressed.Data availability:I was not able to access the bioproject PRJN809503, is the data already available or not? Neither a biosample I try to access for a check.Neither I was able to access DRYAD data.The authors provide a link to fastq data but I could not find a fastq file link in Noble et al. or Breria et al. How did the authors merge the data? If they merged the data based on Table S1 or Noble et al. why did they find more SNPs than Noble et al. with a 10% missing rate? Since some authors are common between these studies a clear path to access to the whole dataset should be available to the community. [Editors’ note: the authors resubmitted a revised version of the paper for consideration. What follows is the authors’ response to the first round of review.]Reviewer #1 (Recommendations for the authors):The authors provide an ambitious interdisciplinary analysis of the post–domestication spread of mungbean. I believe the authors' general thesis is correct, and the various data they provide are all consistent with their model.1. Nonetheless, there are some issues with analysis and interpretation, and in general, the data don't provide definitive evidence that allows claims about drought or the importance of the environment.All of the evidence and analysis presented are consistent with the authors' proposed SA–SEA–EA–CA model. The f3 results are particularly convincing. I struggle, however, with how the data definitively show environment was more important than human movement. Some text shows, for example, that trading or demic movement between SA and CA was frequent would make clear that mungbean 'could' have moved SA–>CA via humans but didn't. Otherwise, could the SA–SEA–EA–CA model simply reflect historical movements/expansions of people in those directions/times?et al. 2021), suggesting the prevalence of crop exchange. Human-mediated long distance dispersal of mungbean seeds also happened, as mungbean seeds have been found near the Red Sea Coast of Egypt during the Roman period . Despite the prevalence of exchange, we note in Discussion: “Despite this, in Bronze-age archaeological sites north of Hindu Kush, cereals were frequently observed. Legumes (such as peas and lentils) were observed to a lesser extent, and South Asian crops were not commonly found . Interestingly, archaeologists suggested legume’s higher water requirement than cereals may be associated with this pattern, and pea and lentil’s role as winter crops in Southwest Asia may be associated with their earlier appearance in northern Central Asia than other legumes .” Our study of genetics, climate, and plant traits therefore support conclusion from archaeological studies.Thank you. In the previous version we put most of the information in Discussion, and now we elaborated this point. Specifically, we emphasized studies that as early as about 4kya, Central and South Asia was connected through a complex exchange network linking the north of Hindu Kush, Iran, and the Indus River Civilization . Later, there was archaeological evidences that diverse crops from West, South, and East Asia have been cultivated in northern Pakistan , Intercultural Relations between South and Southwest Asia. Studies in Commemoration of E.C.L. During Caspers (1934–1996), Oxford: Archaeopress pp. 29–42Lamberg-Karlovsky CC 2002. Archaeology and language: The Indo-Iranians. Current Anthropology 43:63–88Lombard P 2020.The Oxus civilization/BMAC and its interaction with the Arabian Gulf. A review of the evidences. In: Lyonnet B and Dubova NA (eds.), The world of the Oxus civilization, London: Routledge pp. 607-637Lyonnet B 2005. Another possible interpretation of the Bactro-Margiana Culture (BMAC) of Central Asia: The tin trade. In: Jarriage C and Lefevre V (eds.), South Asia Archaeology 2001, Volume 1: Prehistory, Paris: Editions recherche sur les civilisations pp. 191-200et al. 2014. Agriculturalists and pastoralists: Bronze Age economy of the Murghab alluvial fan, southern Central Asia. Vegetation History and Archaeobotany 23:805-820Spengler et al. 2018. Arboreal crops on the medieval Silk Road: Archaeobotanical studies at Tashbulak. PLOS ONE 13(8):e0201409Spengler et al. 2021. The southern Central Asian mountains as an ancient agricultural mixing zone: new archaeobotanical data from Barikot in Swat valley of Pakistan. Vegetation History and Archaeobotany 30:463-476Spengler Van der Veen M and Morales J 2015. The Roman and Islamic spice trade: New archaeological evidence. Journal of Ethnopharmacology 167:54-632. On a similar note, the paper claims that drought was the most important factor limiting the mungbean movement. The phenotypic data certainly suggest adaptive differences in traits related to drought and drought differences in phenotype in an experimental setting, but additional evidence would be helpful to convince that drought is the key factor. The authors note the importance of daylength differences, for example – how do we know daylength wasn't the limiting factor ?Thank you. The main thesis of this study is that environmental adaptation may be an important factor. We used drought  as a test case and chose root/shoot traits and field phenology as supporting evidences. We wish to note that we do not claim drought to be the most important. We believe mungbean was influenced by the join effects of multiple environmental factors: In the north, there is a limited duration for sowing (due to daylength), and the soon-arriving fall frost (temperature) further limited the growing season. During this period the water availability is also low (drought). The rapid phenology therefore appears to be important for adaptation to the short growing season (caused by daylength and temperature) and declining water availability (drought). We have rephrased the point throughout the manuscript.Methods Recommendations3. It's difficult in some places to know which SNP data set is used where. Are the LD–pruned SNPs used to estimate LD decay? The methods say there are 67K sites (including monomorphic) but there are 41K SNPs. This would imply that 2/3 of the sites are polymorphic. That can't be right so I must be misunderstanding something. Are these monomorphic sites also used for estimating nucleotide diversity (see the issue with VCFtools below)? For fastsimcoal, do you include sites where the derived allele is frequency=0 and where the derived allele is frequency 1?We apologize for the error. After quality filtering, in total there are 1248K sites, among which 34K are SNPs. The nucleotide diversity, pairwise genetic distance, and all related analyses have been re-done using the estimates incorporating monomorphic sites. For fastsimcoal, we included monomorphic sites. The previous information  was a typo. The LD decay was calculated using the SNP sites without LD-prune. We have revised the manuscript throughout.4. It would be good to modify the language of the MaxEnt modeling. While MaxEnt may show that the modern mungbean does not currently grow in conditions similar to those during the Holocene at a certain spot on the map, this is not the same as saying the plant could not have grown there. For example, if we were to model MaxEnt on modern CO2 concentrations, we would come to the conclusion that modern mungbean could not have grown anywhere during the Holocene. I don't think necessarily the methods need to be changed, but it would be good to change the language here to be less definitive.Thank you. After considering this and the comments of reviewer 3, we have removed the mid-Holocene niche modeling results. In this revision we focus on comparing the potential range overlap in current conditions.5. Although dominance is less of a concern in inbred species, I believe it is still incorrect to assume that using Vg is equivalent to Va in Qst. The epistatic variance could still be important, for example, and my brief internet search suggests mungbean isn't 100% selfing either. The authors have SNP data for all the individuals phenotyped, so it should be doable to estimate Va using kinship matrices and thus do a correct Qst analysis.ST = VB / ( VB + VFam ) , where VB is the among-group variance component and VFam is the family-level variance component within genetic groups. This is the method originally used in our study as well as in many Arabidopsis thaliana  and Medicago truncatula  studies. To accommodate the possibility that mungbean is not completely selfing, we also applied the equation QST = (1+f) VB/ ( (1+f) VB + 2VAW ) from Goudet and Büchi (2006), where f is the inbreeding coefficient (estimated by VCFtools as 0.8425), VB is the among-population variance component, and VAW is the additive genetic variance within populations estimated by the kinship matrix using TASSEL. The results and conclusions are shown in this revision and are similar to our previous version.Thank you. Goudet and Büchi (2006) showed that for partially inbred species, the selfed-progeny design (as in our study) is more suitable than the half-sib design. With selfed progeny, Goudet and Büchi (2006) suggested using Qet al. 1996. Genetic markers and quantitative genetic variation in Medicago truncatula (Leguminosae): a comparative analysis of population structure. Genetics 143:1795–1805Bonnin STQ, an estimator of population differentiation for quantitative traits. Genetics 172(2):1337-1347Goudet J and Buchi L 2006. The effects of dominance, regular inbreeding and sampling design on et al. 2013. Among- and within-population variation in flowering time of Iberian Arabidopsis thaliana estimated in field and glasshouse conditions. New Phytologist 197(4):1332–1343Mendez-Vigo et al. 2005. Genetic variability in natural populations of Arabidopsis thaliana in northern Europe. Molecular Ecology 14:137–148Stenoien et al. 2021. Polygenic adaptation of rosette growth in Arabidopsis thaliana. PLOS Genetics 17(1):e1008748Wieters 6. VCFtools calculates nucleotide diversity assuming every bp in a window has been sequenced. This will lead to incorrect estimates of π and Fst. See https://pubmed.ncbi.nlm.nih.gov/33453139/ for details and one potential fix if you have a vcf with invariant sites, or https://github.com/RILAB/mop for another if you just have bams + variable vcf.STF) using all invariant sites. The results have been updated.We re-generated the vcf including invariant sites and excluded sites with high missing proportion. We used pixy  to calculate nucleotide diversity (π) and genetic differentiation (Korunes KL and Samuk K 2021. PIXY: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Molecular Ecology Resources 21(4):1359-13687. An NJ tree  is just a clustering algorithm and shouldn't be interpreted as providing information on the timing or order of evolutionary events. (lines 119–123)f3 tests and f4 tests to investigate the relationship among these genetic groups. All results are consistent with our previous results of )).Following the suggest from Reviewer 2, point 2, we used TREEMIX to build the population-level relationship. In addition, we used methods such as outgroup 8. If the growing season is known and is what is most relevant for the crop (line 190), these should be used for most analyses or a justification for using annual data should be providedWhile mungbean could be grown in the summer/early fall for most of Asia, in the southern part of Asia mungbean are occasionally grown in winter/spring. Due to the discrepancy of growing season between the northern and southern parts of Asia, we therefore performed parallel analyses, one using annual data and the other using temperature and precipitation from May, July, and September as growing season data. Both results are presented in the revised manuscript.9. I can't find the total length of time plants were grown for the drought stress experiment. The text reads as if it were 9 days?We revised the Materials and methods section. The seedlings were grown in nutrient solution for 6 days before being subjected to drought stress. For drought treatment, seedlings of mungbean were exposed to polyethylene glycol (PEG)-induced drought stress for 5 days as illustrated in Reviewer #2 (Recommendations for the authors):The study aims to understand the diffusion of the Mugbean population in Asia using genomic and phenotypic data. The authors used phylogeny, analysis of population structure, model–based inference, quantitative genetics, and niche odelling to understand the diffusion of Mugbean and proposed a scenario where diffusion is strongly constrained by climate, and partially by geographical.1. I found the study very interesting with a mix of different methodologies from genomics to niche modeling and quantitative genetics. Few others studies used similar approaches but it is rather unique for the study of diffusion to combine these different approaches and bring up very interesting results. I have several comments on the methods so the results are better supported for the genetic part, for the phenotypic part, I am not sure the author will be able to support their claims, as the method they used might inflate variance in their estimations.Thank you. For the phenotype part, in this revision we applied a method that specifically addressed additive genetic variance and the potential issue that mungbean is not fully inbred . The results are qualitatively similar and the conclusions are the same. Please refer to Reviewer 1, point 5 and Reviewer 2, point 5 for detail.Main comments:2. Phylogeny. Phylogeny is not really an appropriate method per see for intra–diversity study, phylogeny analysis could be used but the basic assumptions of the method are often inadequate, so the result should be put in context. A better method to do phylogeny–like inference is the TREEMIX approach based on the relationship of population integrating drift. I suggest the authors add this complementary analysis.f3 statistics and f4 statistics.Thank you. We have performed TREEMIX in Figure 2A. The relationship among these genetic groups was also supported by outgroup 3. Model inference. Here, I would have liked a statistical comparison of the different scenarios. FastSimcoal allows for estimated probability of models/scenarios and it would be an independent validation to have such a comparison of models.The inference of the model is dependent on mutation rate (unknown), notably on the time of divergence. The author used 10–8 but it is neither discussed nor justified.xyd, STF, outgroup f3 statistics, and f4 statistics. All results point to the same pattern that EA and CA are genetically closest, followed by SEA, and SA is the most diverged group. Regarding the tree shape, )) has strong supports from many independent analyses. We therefore mainly use fastsimcoal2 not as a tree-shape-testing method but as a method to estimate population divergence time based on this tree shape, which has strong support from many independent methods.Thank you. In addition to our previous results, in this revision we expanded the population structure inference section by incorporating and connecting independent analyses such as TREEMIX, We wish to note that the current tree shape is still consistent with multiple hypotheses of cultivar expansion , and testing different tree shapes would not necessarily distinguish among these hypotheses. Instead of using fastsimcoal2 to test different tree shapes, we employed the evidence from π, linkage disequilibrium decay, and isolation by distance to test these hypotheses.-8 was within the range of mutation rates used in eudicots (literatures have used 1.43e-9 to 2.50e-8). We performed a parallel analyses using 2e-8, and the results are qualitatively similar, and we therefore retained the original results from 1e-8. The Upon checking the common mutation rates used in plant population genetics analyses, we found our original 1eAnalysis of structure.4. The author led aside from further studying individuals with ancestry lower than 70% in a given group. The analysis of structure could lead to such ancestry because of admixture or isolation by distance. One is secondary contact based on recent (or not) gene flow between genetic groups, the author is related to diffusion across the landscape. A large fraction of individuals in the PCA seems to me more likely related to isolation by distance . How this will impact the analysis of correlation by geographical distance if such individuals are not considered? The authors should perform the analysis of the Mantel test with all individuals to assess the impact of their choices.Thanks for the suggestions. We have re-perform the Mantel test following the suggestion, and the results consistent with our previous IBD analysis.5. Quantitative analysis of QST. The author used the genetic variance and not the additive variance. The reasoning behind that is not explained, neither the inflation created by this broad sense QST. Authors have concluded that the "extent to which comparisons between FST and broad–sense QST are appropriate remains unknown" .et al. (2008), it is unclear whether the comment pertains perdominately selfing species like mungbean. We therefore refer to Goudet and Büchi 2006 (https://pubmed.ncbi.nlm.nih.gov/16322514/), which has a complete treatment of the effect of inbredding and genetic variance estimates to STQ. In addition to the suggestion from Goudet and Büchi 2006 , we follow the suggestions in Reviewer 1, point 5 and estimated the new STQ using additive within-group genetic variance. The results are similar and the conclusions remain the same. Please also refer to Reviewer 1, point 5 for details.Thank you. Upon reading Pujol Reviewer #3 (Recommendations for the authors):The paper aims to look at the domestication, post–domestication spread, and adaptation of mungbean (Vigna radiata) across Asia through the use of genetic data from landraces and accessions in see and genebanks.The genetic aspects of this paper are a strength – there is a lot of work that has been done putting together a range of datasets allowing for inter–collection comparison and comparison of collections made by different institutes with their varying goals, sampling strategies, and dates of collecting. Mapping this diversity, think about how drift has occurred and why is something that needs to be done, especially in mungbean  as they are often overlooked in literature.1. However, the main stated goal of the paper – to look at the domestication, post–domestication, and adaptations to climate change as this crop was moved around – is where it falls short. There is little engagement with the deep archaeological literature on both domestication as a process, post–domestication use and spread of mungbean (and other South Asian crops and those involved in the Silk Routes trade pathways), and the complexity of climate reconstructions and climate change over the stated period of interest/regions of interest. Works by Spengler and d'Alpoim Guedes for example are missed with regards to the Silk Routes debates, and literature by Fuller, Murphy given only short sentences as background for what is a very complex background regarding where and when mungbean is thought to have been domesticated. There is little reflection on the context of the two/three possible origins for mung , how this interacts with the Southern Indian Neolithic and Indus regions, and how the changing cultural dynamics may have contributed to the processes of domestication, post–domestication change and the spread of different varieties. Without this background, it is hard to then move into discussing modern genetic data with a view to past patterns, for example with thinking about how climate may have affected change, given that the debates around the 4,2k event are extremely complex within these, let alone thinking pan–Asian and trying to link potentially 'drifted' genetic data today to these deep–time events. This comes across in the timescales given to the genetic data, as without the context of the where and when from archaeology, we see dates such as those given in Figure 2B that suggest domestication for South Asia moving to South East Asia at c.6kya (4000BC), which is when we still think they were under domestication within South Asia. The region is also not pinned down for where in South Asia these specific 'domesticated' mung are coming from to go to South East Asia, and the routes, yet arrows and big circles are added in Figure 2A. This shows the issue of not using that important context from archaeology.We appreciate the valuable comments. In this revision we discussed previous archaeological findings in Introduction and, as suggested, use the archaeological findings as the basis of our genetic investigation. Using genetic data, we re-constructed the evolutionary relationship among these major genetic groups. We showed that CA and EA to be genetically closest, followed by SEA, and SA is the most diverged group. As stated in our revised Results section, this observation is actually still consistent with several hypotheses, and we used further population genetics evidences to distinguish among these hypotheses. While our data suggested the general trend of SA-SEA-EA-CA, our investigation is limited by the amount of samples with detailed geo-referenced information.et al. 2022) that present-day worldwide cultivars, despite their geographic origin, have the same haplotype in the promoter region of VrMYB26a, a candidate gene controlling pod shattering in several Vigna species. This is consistent with a single origin of the loss of pod shattering phenotype common to present-day cultivars and suggests that while early mungbean cultivations happened independently, eventually one form with the loss-of-pod-shattering phenotype (and VrMYB26a haplotype) dominated and replaced others. Answering where the "domestication allele" of VrMYB26a originated or deciphering the relationship between present-day germplasms and ancient cultivation origins within India would require information from more geo-referenced ancient DNA, which would be out of the scope of this present study. On the other hand, we recognize the climate heterogeneity within South Asia. We performed new climatic analyses separating the SA group into two major regions based on the Köppen climate classification . The results remain similar.Indeed, archaeological evidences have shown multiple independent early cultivation of mungbean within South Asia. As the reviewer has pointed out, the present-day samples were ‘drifted’ from the ancient varieties. It is exactly because of this reason that we did not attempt to use the present-day samples’ detailed GPS coordinates to answer/discuss the issue about these independent origins of mungbean cultivation within South Asia. Due to the possibility of long-term seed exchange and replacement within South Asia, the samples collected in a specific location might not necessarily reflect the genetic information for ancient mungbean at the same locations. This is supported by our recent results . In our revision, we emphasized these routes are both compatible with our hypothesis. We wish to emphasize that we do not put much emphasis on the exact route of mungbean expansion, nor do we think there is only one wave/one route of the out-of-India event. There might be multiple attempts to bring mungbean out of India (which could not be answered unless with ancient DNA), and our focus in this study is whether or when mungbean could be grown and became part of the local agriculture throughout Asia. As in many other population genetics studies, if the previous waves were replaced by the later-arriving germplasms, our data could not provide information for the previous waves. We agree using big circles and arrows are too rough for the more complicated history of mungbean spread. We have modified this figure and prevent specifying a specific route without genetic evidence.We completely agree with the reviewer that modern samples are ‘drifted’ and do not necessarily reflect ancient conditions. It is exactly due to this reason that we did not attempt to pinpoint the detailed or specific route of the out-of-India event, either. The genetic data simply do not allow us to pinpoint, for example, whether mungbean expanded from South Asia to Southeast Asia / southern China through the land or maritime routes . Our work has similar aims and approaches to these studies. Similarly, questions such as “how many independent out-of-Africa events have happened”, “whether each of these originated from different locations within Africa”, or “the specific route of how anatomically modern human reached East Asia” would await studies incorporating ancient DNA from archaeological studies. For mungbean, we look very much forward to the chance of investigating these samples.About the estimated divergence time among genetic groups, we wish to note that the time estimates have high confidence intervals . Further, the time estimated was in units of generations instead of years (we modified the manuscript to clarify this). The growing season in the northern part of Asia is short, and we reasonably assumed one generation per year. This might not fit the whole Asia, since the southern parts of Asian have longer growing season and may allow more than one generation per year. Assuming one generation per year (as we naively did in the previous version) overestimated the divergence time for the southern groups. This is the limitation of current methods in this field, and we have acknowledged this in the manuscript.et al. 2016. Rice, beans and trade crops on the early maritime Silk Route in Southeast Asia. Antiquity 90(353):1255-1269Castillo et al. 2011. Across the Indian Ocean: The prehistoric movement of plants and animals. Antiquity 85(328):544-558Fuller et al. 2022. Distinct selection signatures during domestication and improvement in crops: a tale of two genes in mungbean. bioRxivLin et al. 2016. Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age. The Holocene 26(10):1541-1555Stevens 2. A further issue arises from thinking about the climate data. By conflating vast areas , when applying climate modelling there has been an oversimplification, which makes any discussion of mung bean adapting to climate post domestication difficult to sustain. In line 184 for example, there is a suggestion on the role of the 6.2k event in Central Asia . While there are a few datasets as cited in the paper that show some impacts of wetter climates in some regions of Central Asia for a wetter 6,2k event this is by no means a universal impact, and regional data points are needed. We can see this when looking to the Indus and the impact of the 4.2k event as another example, again a point that needs refining in order to make such claims about mung domestication, let alone post–domestication adaptations.Our study started from population genetic analyses, which separated the samples into four genetic groups. These genetic groups were separated purely based on genetic data without any geographic information, and their names  were given based on where most of the materials came from. Given this, each genetic group is a relatively homogeneous entity compared to worldwide genetic variation. We fully agree that each specific location has its own unique climatic conditions, but since the purpose of this study is to investigate what factors affect the divergence among these four genetic groups, we used each genetic group as a unit in climate analyses and aimed to identify which factors have larger among-group than within-group variation. We fully agree and recognize that the distribution ranges for some genetic groups have large environmental heterogeneity. For example, the EA group distributes from the Pacific Coast to Central Asia. This is why we separated the EA groups into the eastern and western halves to accommodate this issue. Another geographic region potentially with large environmental heterogeneity is South Asia. In this revision, we investigated the distribution of these samples based on Köppen climate classification. CA samples have relatively homogeneous distribution in a few Köppen zones with similar climatic characteristics, and so are SEA samples. Based on the patterns of SA and EA samples, we separated them into two groups each, resulting in a total of sis zones. We wish to emphasize that the major goal of this study is to investigate factors affecting the differentiation among these four genetic groups. Further subsetting the range into many small regions was not strongly supported by genetic evidence. Finally, niche modeling requires reasonable amount of samples to estimate the “tolerance environmental range”  of a group, and subsetting samples based on the unique climatic characteristics of each location is not suitable for this analysis.Note that in climatic modeling, we obtained the present-day environments from the present-day distribution of these present-day materials to identify their suitable “niche space”. Using this information, we predicted “where would be the suitable environment for these genetic groups under different climatic conditions” given the niche space information of each genetic group. The existence of the projected distribution for the CA group at 6.2kya (in the previous supplement figure) was merely a method to compare the climatic difference between 6.2kya and today, and this figure does not mean we thought the CA group already existed in the Central Asia geographical region at 6.2kya. We did not attempt to make mungbean seem already widespread at that time . The whole purpose of the analysis using 6.2k climate was to investigate whether the Central Asia geographical region may be a suitable habitat for plants from the SA group when the Central Asian climate might be slightly different from today. If so, that would reject our hypothesis. Due to the possibility of confusion, we removed this figure in the revision.To project the suitable distribution range, this niche modeling method requires the GIS layer with data in every 1km geographical grid, which is available for very limited number of time points. While mid-Holocene is the only close-enough time point with bioclimatic variables being modeled (http://www.worldclim.com/past), we agree this is a poor choice. We also agree detailed regional data would better reflect the spatial heterogeneity of climatic conditions, but this distribution modeling approach requires climate data for all geographical grids. We therefore removed the mid-Holocene niche modeling result.3. Overall the thrust of the paper – domestication, post–domestication, and the spread of agriculture – are overshadowing what is actually a far more interesting point, hidden in lines 87–89: this data could be "used this resource to investigate the global history of mungbean after domestication […looking at the …] phenotypic characteristics for local adaptation to distinct environments." This perhaps is where the paper is most interesting, and reframing it in this context would be truly exciting, looking at the diversity of the crop, how it is now adapted to diverse environments, and what this might mean for long–term sustainability in cropping systems.et al. 2014 and Spengler et al. 2018), here we provide supports from the genetics perspective. We have modified the manuscript to reflect the archaeological context.Thank you. We fully agree understanding the genetics, unique phenotypic characteristics, and local adaptation of these germplasms is important, and we sincerely hope to use our results to contribute to the goal of long-term sustainability and crop improvement. This is the topic of other research projects in our group. On the other hand, we also agree with the two other reviewers that using the genetic data to contribute to understanding of mungbean cultivation expansion is interesting. As the potential importance of environmental adaptation in determining crop cultivation range has been suggested in several archaeological studies . While it has not had as much work as the cereals, there is still work being done on it, looking at its domestication regions, secondary domestication changes and spread across South Asia and then into different parts of Asia.Thank you. In our revision, we have devoted a paragraph in Introduction for the archaeological results.5. Data seems to have been massaged to make it fit with the climate modelling in various regions , and to also make mung seem to be spreading before the domestication event itself. More engagement with the archaeological discussions on mung domestication is needed and discussions of what domestication is as a process .et al. (2014).We wish to emphasize that we did not massage the data in any way. For the 6.2k climate issue, please refer to our response to Reviewer 3, point 2. We have modified the introduction to reflect the reviewer’s point about Larson 6. Terms like cultivar and variety and landrace are used interchangeably. These must be defined in the paper. How they fit in with notions of domestication and post–domestication agricultural behavior must also be unpacked.We apologise that we have not made it clearer about the definition of cultivar, variety and landrace. In our work, we defined landraces if accessions are collected from the countries traditionally cultivating them and locally adapted as well as lack of formal genetic improvement, ie. those conserved in the Vavilov Institute, many of which were collected in the early 20th century. In order to avoid confusion, we revised all sentences to clarify these terms in relevant places across the text.7. "how the domesticated forms later expanded to a broader geographical area has also been detailed in several species, including maize , rice , tomato , chickpea , and lettuce ." – these are unusual choices of case study to make a point as many (maize and rice as key examples) are not accepted as well defined and remain highly controversial. These are genetics papers, and demonstrate the lack of familiarity with the archaeological context of domestication. A quick glance at the literature around them will illustrate that they are poor choices of case studies to make this point as they too are highly controversial.We have removed this citation and completely re-written this paragraph.8. "It is also unclear whether the expansion of most crops strictly follows the longitudinal axis of the continents  or whether or why some are able to cross different climatic zones." – again poor knowledge of the archaeological context of these debates, and the reliance on Diamond is concerning as he is not an archaeologist. See works by Lister on barley and Lui on wheat as a good starting point.Thank you. We have removed the citation to Diamond and re-written this part to reflect the rich archaeological works.9. Debate on wild progenitor of mung bean needs to be explored. while sublobator is a likely candidate it should be explained in the paper that there are other possible options, and then why it was chosen here, with citations.Vigna group . The constructed ITS-region-based trees revealed that V. radiata var. sublobata is closest to V. radiata.Molecular phylogenetic based on internal transcribed spaces (ITS) sequences was carried with the aim to resolve the taxonomic contradiction in Phaseolus-Vigna complex. Molecular Phylogenetic and Evolution 22(1):1-19Goel et al. 2001. Molecular evolution and phylogenetic implications of internal transcribed spaces sequences of nuclear ribosomal DNA in the 10. The figures are difficult to use. This comes back to the conflation of space and time outlined in the public review. There are big circles on the maps covering the dots which I presume are either archaeological sites or accession points of the sampled beans(?! unclear), and then very odd choices of illustrating change over time. The figures are small and hard to see and require very long text in the figures to make them useable.Thank you. We responded the space and time issue in Reviewer 3, point 1 and Reviewer 3, point 2. In this revision we removed the circles and arrows and moved the figures to supplement. We still keep some supplement figures with circles and arrows, but these figures  should be merely treated as simple illustrations of potential hybridization scenarios instead of detailed routes.11. Some aspects of basic geography have been overlooked to make climate the most important variable; l.166–7 "Given that geographic barrier might not be the most important factor". I find it hard to believe that both the Himalayas and major flood basins like the Brahmaputra would not be an issue, as would issues of day length when moving things north–south.Thank you. Since pods of mungbean cultivars do not shatter naturally, they have lost the natural ability to disperse seeds. We therefore focus on human activities when we discuss the ability to disperse. We are fully aware that it is difficult for human to cut through the Himalayas directly and we did not claim the Himalayas are not a barrier. Previously we put our argument mainly in Discussion, and here we elaborated part of the points in Results. Specifically, we emphasized that South and Central Asia was connected by a complex exchange network among north of Hindu Kush, Iran, and the Indus Valley. Between South and Southeast Asia, we did not assign a specific route, either. It is equally likely that mungbean spread through land or maritime routes. As emphasized in Reviewer 3, point 1, we focus on the relationship among the genetic groups instead of designating the exact routes. We have modified the manuscript reflect this.In this study, “geography” mostly refers to landscapes hindering human activity and the movement . We regard daylength  as a environmental factor that might limit the successful cultivation of mungbean in a new environment even though human had successfully transported mungbean there as seeds. We have rephrased this part to reflect the reviewer’s comment.12. In dealing with issues of climate change and adaptation some discussion of tolerance is needed. there must be a discussion (and a table perhaps) of the different watering, salination, temperature, etc. tolerance of the mung bean(s) under consideration to make the claims justified.Thanks for your comment. We have now revised the discussion comprehensively, mentioning that the precipitation in Central Asia is greatly below the lower limit of standard optimal conditions to grow mungbean in the south. To the best of our knowledge, this is the first study to systematically compare the phenotypic characteristics of different genetic groups in mungbean.13. Within the methods, the sampling strategy was hard to follow. This needs a more careful and clear description of decisions made: exactly where did the accessions come from geographically? how did their spread affect the dataset? Is there geographic clustering, did you compensate for that? how does the sampling potentially bias your data? a map would be useful.Thank you. We have clarified in Materials and methods that while all samples have the information of their countries of origin, only a subset of samples have the detailed longitude and latitude coordinates. These samples were used in the detailed analyses connecting genetic and location information . The genetic groups  were named from the geographic region where most of their members originated from, by considering both country and geographic coordinate information. Only samples from Asia were used. In this revision, we also put the accession location maps in supplement figures. About how the distribution of sample might affect our conclusion, we added the following note in Discussion:“We recognize that not all samples have available spatial data, and we do not have samples from some parts of Asia. For example, while most samples of the SEA group were collected from Taiwan, Thailand, and Philippines, we do not have many samples from the supposed contact zone between SA and SEA (Bangladesh and Myanmar) or between SEA and EA (southern China). If more samples were available from these contact zones, the modeled niche space between SA and SEA and between SEA and EA would be even more similar than the current estimate, strengthening our hypothesis that niche similarity might facilitate the cultivation expansion. On the other hand, clear niche differentiation between SA and CA was evident despite the dense sampling near their contact zone.”14. FAIR and open protocols dictate that all methods must be stated: "Genomic DNA was extracted from a single plant per accession using QIAGEN Plant Mini DNA kit according to the manufacturer's instruction with minor modification." If you modified the protocol then you HAVE to outline what you did so it can be reproducible and the data comparable.The modifications made during DNA extraction were added.15. "Climate data for conditions between 1960–1990 were downloaded from the WORLDCLIM 1.4 database" – how was this dataset determined? why 30 years and not more? give citations to explain this decision, and look to other modelling efforts to check comparability.2 (30s) resolution. Therefore, we directly used the available climate layers which were created based on climate conditions recorded between 1960 and 1990 to predict the geographic distribution of suitable habitats for cultivated mungbean. We have rephrased this part.Using the WorldClim database has now become a common practice in the field of environmental niche modeling. The WorldClim database used meteorological station data collected during 1960-1990 to extrapolate worldwide climatic conditions in about 1km16. "19 bioclimatic variables" – what are these? why were they chosen? a table and explanation are needed.Explanation of each bioclimatic variables used in this study are available on WorldClim website (https://www.worldclim.org/data/bioclim.html#google_vignette) and we have added a table in supplementary file 5. These are often used in species distribution modelling and any related ecological modelling techniques.17. "excluding one of the two variables that have a correlation above 0.8 (Supplementary file 4)" – why? explain the reasoning for exclusion.et al. 2022; Gao et al. 2021 and Zhao et al. 2019).The purpose of removing the highly correlated variables was to minimise the effect of multicollinearity, which could result in the overfitting of the model. This is the standard method in the field of ecological niche modelling and studies related to the environment variables :541-556Gao et al. 2019. Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil. Nature Communications 10:4201Zhao 18. Throughout the dataset has relied on "In total, our dataset contains more than one thousand accessions (1092) and covers worldwide diversity of mungbean representing a wide range of variation in seed colour" however at no point is there a discussion of whether these are modern variants of historic landraces and how this was assessed. This has a big impact on any discussion of "ancient" adaptations, and there must be a discussion of how you tested to see if the genetic changes you see are more recent or past changes and how the genetic clock was applied.et al. (2008), "The efforts of collectors such as N. I. Vavilov have prevented the extinction of some of these local ecotypes.", our use of the Vavilov institute collection is therefore important.Thank you. Our materials were directly obtained from worldwide stock centers, which house germplasms mostly collected during the 20th century. The missions of these stock centers are the collection and conservation of local landraces instead of developing or breeding novel varieties, and therefore our materials have limited numbers of “breeder lines” from recent artificial crosses. Since we focused on the comparison among the four genetic groups, recent admixture within the same group would have limited impact on the among-group pattern, and cross-group admixed accessions were excluded from most analyses. Similarly, despite generations of admixture, human geneticists could use contemporary human DNA and phenotypes to infer the divergence time and adaptation among major worldwide populations, as long as recently admixed individuals were excluded. In addition, as we noted in Introduction, the majority of accessions with detailed collection site information (from the Vavilov Institute) were collected during the early 20th century, before large-scale seed exchanges among worldwide stock centers. As noted by Jones We, however, acknowledge that genetic results from these materials collected during the 20th century may not reflect specific changes in specific time points in the past. This may be solved by ancient DNA analyses and is out of the scope of this current work. About divergence time, the fastsimcoal2 analysis was specifically used to address this issue while allowing potential gene flow among groups. Finally, we acknowledge that it may be difficult to estimate when the adaptive phenotypes originated. This may require specific modelling on whole-genome sequencing data and the identification of candidate genes, which would be out of the scope of the current study. Therefore, we used the descriptions in ancient Chinese texts about plant phenotypes as a supporting evidence to show some of these phenotypic characteristics appeared long time ago.et al. 2008. Approaches and constraints of using existing landrace and extant plant material to understand agricultural spread in prehistory. Plant Genetic Resources 6(2):98-112Jones 19. As noted in the public review, a far more interesting aspect than trying to tie into domestication/post–domestication and chronological vagaries are the points made in lines 87–89: this data could be "used this resource to investigate the global history of mungbean after domestication […looking at the …] phenotypic characteristics for local adaptation to distinct environments." Thinking about the value of this dataset for the preservation of diversity, and how diversity links to localised adaptations today and to sustainable cropping now is critical, and I suggest this could be the way to reframe things.Thank you. Please see our response to Reviewer 3, point 3.[Editors’ note: what follows is the authors’ response to the second round of review.]The manuscript has been improved but there are some remaining issues that need to be addressed, as outlined in the comments of Reviewer #1 below.Reviewer #1:I found this study to be one of the rare to combine genomic data, climate data, phenotypic data to decipher the diversity of adaptation of plants, and try to build up scenario of their diffusion. Previous recommendations were mainly answered, and I am personally satisfied with this new version of the manuscript. At this stage I recommend acceptance of the paper as soon as the concern is addressed.Data availability:I was not able to access the bioproject PRJN809503, is the data already available or not? Neither a biosample I try to access for a check.Neither I was able to access DRYAD data.Thank you for your valuable comments and suggestions. Regarding this comment specifically, all the sequences generated from this study was already deposited to NCBI (Bioproject PRJNA809503). As for phenotyping measurement data was also deposited to DRYAR. We can provide reviewer links  as below:NCBI:https://dataview.ncbi.nlm.nih.gov/object/PRJNA809503?reviewer=g4jqbn30fhpacs7di7vgj2b3okDRYAD:https://datadryad.org/stash/share/b5TO7fUNguxu0hMp6zx1cQZkBrCKzDmznCPvzf_CqEsWe will ensure the whole dataset is available to the public before publication online.The authors provide a link to fastq data but I could not find a fastq file link in Noble et al. or Breria et al. How did the authors merge the data? If they merged the data based on Table S1 or Noble et al. why did they find more SNPs than Noble et al. with a 10% missing rate? Since some authors are common between these studies a clear path to access to the whole dataset should be available to the community.We apologize for not describing this clearly in the manuscript. We re-preformed the SNP calling step for all accessions from Vavilov Institute (VIR), Australian Diversity Panel (ADP)  and the World Vegetable Center (WorldVeg) mini-core . Additionally, we included BioProject information to the published dataset by Noble et al. (2018) and Breria et al. (2020) under Data Availability (Line 643). The detailed information of the whole dataset as listed in