dataesr/scientific-paragraphs-categorization huggingface dataset:
Niche Evolution Our estimates of both Pagel statistics showed distinct evolutionary patterns (Fig. 2c ; Supplementary Appendix S15 available on Dryad). We found low values of , indicating low phylogenetic signal (i. e. , a recent accelerated evolution), for the habitat preference (Fig. 2c ), and high phylogenetic signal for the dispersal niche and life form, suggesting that these niche characteristics have diversified early. For the pollination niche, estimates of were more spread out, with a lower 5% quantile of 0. 2, a higher 95% quantile of 1. 01, and a median value of 0. 99; this also indicated a relatively high phylogenetic signal (Fig. 2c ). Estimates of the statistic were close to 0 for the habitat preference (indicating a punctual evolution), and close to 1 for the dispersal niche and life form, respectively (indicating more gradual evolution).
For the pollination niche, scaled between 0. 35 (5% quantile) and 0. 99 (95% quantile), with a median value of 0. 69. The best-fit evolutionary model identified in our ancestral state reconstruction analyses was the "ER" model for each niche/trait data set (Supplementary Appendix S16 available on Dryad). The reconstructed ancestral habitat preference of Oxera was ambiguous: forests on both ultramafic and non-ultramafic rocks were together reconstructed with a high likelihood (forested vegetation was recovered as ancestral for this node with cumulated likelihoods of both forest types of ca. 0. 57). However, the ancestral pollination, dispersal, and life form were inferred with much less ambiguity; the Oxera ancestor was very likely a robust liana with gullet flowers producing small rounded fruits (Supplementary Appendix S17 available on Dryad).
Analyses of stochastic character mapping allowed us to estimate that very few pollination, dispersal, and life form shifts occurred during the evolution of Oxera (up to two shifts per time bin of 0. 5 Myr; Fig. 2b ), and that most of these trait shifts occurred between 2 Ma and 0. 5 Ma for pollination, and following 3 Ma and 3. 5 Ma for dispersal and life form, respectively. Habitat shifts occurred between 9 Ma and present, but from 4 Ma onward their number increased markedly, finally reaching 17 shifts between 0. 5 Ma and the present. The best-fitting model of trait-dependent species diversification identified for habitats had speciation and transition rates all equal, a null extinction rate (Supplementary Appendix S4 available on Dryad), and no discernible effect of any habitat type. For the pollination syndromes, dispersal types and life forms, the best-fitting model was that with a null extinction, transition rates all equal, and a particular character state in which speciation rates were significantly different from other states (Supplementary Appendix S4 available on Dryad).
The Kernel density plot of range overlap through all possible species pairs (in black) and all possible sister species pairs (in grey) in New Caledonian Oxera. deviation of 0. 357), suggesting a high level of allopatry between all species. The kernel density plot highlighted two range overlap frequency peaks, the highest located for a range overlap of 0 and the shortest to 1 (Fig. 3 ). Age range correlation analyses showed that the slope of range asymmetry through time was significantly positive for linear regressions (all P-values <0. 05 across RD trees, Supplementary Appendix S19 available on Dryad). For range overlap and habitat distance, linear regression slopes with divergence times were negative in both cases but not significant. Different Oxera subclades highlighted distinct patterns of geographical overlap (Fig.
An Early Burst of Diversification Our study shows that the genus Oxera is a quite recent and rapid plant radiation that initiated during the late Miocene, and that most of the New Caledonian subclades within Oxera began to diversify in the early Pliocene (Table  2 , Fig. 2 ). It is noteworthy that this New Caledonian radiation occurred long after the emergence of Grande Terre about 37 Ma  (Cluzel et al. 2012). Thus, the radiation of Oxera originated in the archipelago via long-distance or stepping-stone dispersal, but was not triggered by Gondwanan fragmentation. This continental dispersal to the New Caledonian archipelago was probably aided by the ancestral dispersal type (i. e. , small rounded fleshy fruits; Supplementary Appendix S17 available on Dryad), which may be the most efficient dispersal mode in the group.
Following this dispersal to New Caledonia, the successful establishment of ancestral Oxera may have been facilitated by the climbing habit of its ancestor (robust woody liana identified as the ancestral state; Supplementary Appendix S17 available on Dryad), which is believed to allow the occupation of a broad range of local environments  (Gianoli 2004 ). The finding that the ancestral colonizer of extant New Caledonian Oxera was reconstructed as having a liana life-form with fleshy fruits makes it a quite unique case since the liana form is generally associated with wind dispersal  (Givnish 2010) , implying dispersal limitations over water, and that the liana niche in islands remains often empty. Diversification analyses identified an early burst of diversification (BAMM analyses; Fig. 2a  and b , Supplementary Appendix S12 available on Dryad), likely located between the divergence of the Oxera ingroup and its sister lineage Hosea (ca.
12 Ma) and the crown node of Oxera within New Caledonia (ca. 4. 5 Ma). This late Miocene/early Pliocene burst of species diversification indicates that Oxera underwent an initial period of rapid cladogenesis, especially in New Caledonia, concordant with an initial decreasing of extinction rates; Figure  2b , Supplementary Appendix S12 available on Dryad. This coincides with the origination and early diversification of other major New Caledonian radiations (e. g. , Psychotria clade NC2), and especially lineages typical of sclerophyllous vegetation types (e. g. , Thiollierea; Table  2 ). This period of intense species diversification is concordant with the global onset of Pliocene glaciations  (Zachos et al. 2001)  as well as the temperature declines and severe aridification recorded in the South Pacific during the Pliocene  (Karas et al.
An Explosive Species Diversification, with Early Divergence in Biotic Niches The rate of species diversification estimated for Oxera is exceptionally high, and represents the fastest known New Caledonian plant radiation, rivalled only by Thiollierea  (Manns et al. 2012 ; Table  2 ). Estimated speciation rates within Oxera are comparable to the fastest island plant radiations documented in previous studies (e. g. , Bidens in Hawaii or Echium in Macaronesia; Table  3 ). The detected early burst of diversification has been followed by a rather constant diversification, as inferred from BAMM and ML Treepar analyses even under weak divergence origination scenarios (Supplementary Appendices 12 and 14 available on Dryad); this may reflect the ongoing challenge within the evolutionary biology community to realistically model diversification processes, especially extinction  (Stadler 2011; Morlon 2014 ).
Nevertheless, it seems that since its origination Oxera has continued to diversify under constant speciation and rather null extinction, as exemplified by the exponential increase of species lineages through time (Fig. 2a ). Trait-dependent diversification models suggest that no specific adaptation has disproportionately favored speciation in Oxera (all biotic traits had equal speciation rates; Supplementary Appendices S4 and S18 available on Dryad), excepting perhaps the slender liana life form (acquired with the emergence of the neriifolia, pulchella, and oblongifolia subclades; see Table  4 , Fig. 2a , Supplementary Appendix S18 available on Dryad), which is found in open sclerophyllous vegetation and exhibits high speciation rates probably because open habitats have increased in concert with Pliocene and Pleistocene cooling while remaining spatially fragmented (see below).
The decelerated diversification of pollination syndromes, dispersal niches, and life-forms (revealed by a rather high phylogenetic signal; Fig. 2c ) likely indicates that all or most of these niches previously vacant were ultimately filled during the early history of the clade. Our comparative analyses indicate that from the late Pliocene to early Pleistocene, the major Oxera lineages (i. e. , the seven New Caledonian subclades plus O. morierei) had already originated (Fig. 2a ), most of them occupying a unique niche combination. It is important to note that all recovered Oxera subclades were robust to contrasting phylogenetic signal between nuclear and plastid genes (Supplementary Appendix S8 available on Dryad). Hence, each Oxera subclade robustly holds a unique trait combination (Table  4 ), excepting perhaps the neriifolia and oblongifolia subclades, which similarly exhibit slender lianas, bilabiate flowers and small rounded fruits.
4; Supplementary Appendix S19 available on Dryad) indicating that given the recent radiations of Oxera, most sister species have remained in allopatry, and that secondary sympatry may not have yet occurred in most sister species pairs. The examination of geographic and ecological overlap between species pairs suggests that local species coexistence may in fact be very rare in Oxera. Among the 96 putative pairs of species (within the seven New Caledonian subclades), only five pairs potentially coexist locally, although this has never been noted after years of field observations (Gâteblé, pers. obs. ). For example in the oblongifolia subclade (which exhibits largely sympatric species), each species grows in a specific set of environmental conditions, excepting the ubiquist O. oblongifolia (Fig.
4 ). Contemporary species coexistence is probably prevented by the recent interplay of allopatry and parapatry due to habitat shifts and environmental oscillations that have caused cycles of forest expansion and retraction. With Oxera being mainly a forest-adapted group (25 of 38 species confined to forests, and forest habitat identified as ancestral; Supplementary Appendix S17 available on Dryad), it is likely that vegetation cycles along the complex topographical gradients of New Caledonia have triggered spatial divergence and probably speciation. This process has been further amplified by the limited dispersal ability of Oxera since its dispersers are relatively sedentary. Such processes of vegetation oscillations along steep physical gradients, sometimes creating barriers to dispersal, is now considered to be a major driver of clade diversification, as demonstrated in recent theoretical simulations  (Aguilée et al.
ACKNOWLEDGEMENTS The authors would like to thank all the people who provided plant material, access to specimens or bibliography:  Laurence Ramon ,  Chanel Sam , and  Stéphanie Stephens  (PVNH);  Felix Forest ,  Edith Kapinos , and  Helen Fortune Hopkins (K) ;  Vicki Funk  and  Carol Kelloff (US) ;  Darren Crayn  (CNS);  Josephine Milne  and  Wayne Gebert  (MEL);  David Middleton  and  Nura Abdul Karim (SING) ;  Jérôme Munzinger  and  Jacqueline Fambart-Tinel (NOU) ;  Christiane Anderson  (MICH); and the  IAC's team , especially  Jacqueline Ounémoa ,  Virginie Lemay ,  Donny Wamytan ,  Laurent Demaret ,  Michel Moenteapo ,  Edmond Poitchili ,  Nicolas Anger ,  Hervé Vandrot , and  Hélène Udo , for having collected, propagated and grown all New Caledonian Oxera species over the past 10 years.
Di erent factors. Figure a illustrates the aggregated regional PV di usion trends in MF, SE and RR ABMs assuming that economic, environmental, social and comfort factors influence individual decisions of households. Here we tested how adding information as a decisive factor impacted the emergent PV di usion rates in each version of the TPB-ABM architecture  (Figure ). In this set of simulation experiments the lack of information comes as agents' uncertainty regarding the financial aspects. The key variable r inf was parameterized using secondary data on time spent to clarify financial aspects of a PV system and its performance  (Rai & McAndrews ). Instead of assuming that households were perfectly informed of PVs performance and their financial consequences, we assumed that a population of agents was heterogeneous in the level of information they possess.
Di erent data. Lastly, we ran analyses to explore how PV di usion curves change with a distribution of r inf (Figure ), with each agent keeping their individual mean value. When information was represented as costs, most of the runs across our ABMs and distributions showed no qualitative di erences compared to no information' case, except RR ABM. Thus, in addition to the latter case, we discuss only the variability in results of the three ABMs with information represented as uncertainty under the four distributions of r inf  (Figure ). ). In the case of MF ABM, the di usion rate of PV with information biases parameterized using Poisson, Uniform and Normal distributions and multi-modal distribution that follows the patterns from the secondary data source nearly match the base case with no information (black horizontal line in Figure  a ).
The implementation of the inaccuracy of information caused changes in the steady state PV share for all ABM architectures. The introduction of information costs however, made no significant di erence for MF and SE ABMs, while for RR ABM the system behaviour depended on the distribution of information among individual households. Therefore lastly, we ran three TPB-ABMs varying in architecture, each with two alternative representations of information where a crucial stochastic parameter is initiated following four di erent data distributions with individual agents' same average value. Our results indicated qualitative and quantitative di erences in the emergent outcomes such as technology di usion rates with changes across model variations ranging from % to % and a steady state being reached on step vs not being reached even a er periods.
Future research should focus on how (lack of) information impacts individual decisions, for example on energy technology adoption, and how trust and search time and/or costs influence individual behaviour. Studying this empirically on large datasets will help di erentiating between competing theories. Standardization and modular approach for alternatives: Theories of human decision-making in various contexts provide an essential ground for understanding cause-e ect links between stimuli or barriers and individual actions, and feedbacks between individual decisions and social norms or policies. As such they serve as microfoundations for designing agents' behavioural rules necessary for any solid academic use of the ABM method. Moreover, results of theory-grounded ABMs can be directly compared to conventional analysis (empirical, statistical or analytic) driven by the same theory, that serves as a natural benchmark for comparison with advanced agent-based simulations.
An agent-based model to study energy technology di usion in the Netherlands The ABM, which we take as a basis for testing the four types of di erences -in architecture, factors, representations and data -is developed to study the di usion of renewable energy among households (Tariku ; Muelder ). We refer to this base version as to the MF ABM (a er the authors). The MF ABM is designed to study the aggregated outcomes of individual household decisions regarding PV installation in a municipality of Dalfsen, which is one of the pioneering green municipalities in the Netherlands. There are agents that represent houseowners of various income classes spread over the spatial landscape. The model is coded using NetLogo (Wilensky ); the model code is available online, under this link. We use GIS data, data on income distribution and accommodation sizes provided by the Dalfsen municipality  (Boer ).
Households' decisions in the original SE study depend on such factors as environmental attitudes, savings and social influences of a household, and the ease of use, compatibility with infrastructure of the technology and installation costs of the technology. Some factors used in the original SE study were omitted due to the irrelevance for our case (e. g. characteristics of multiple technologies since only solar panels are considered as a single technology in question) or due to a lack of data (e. g. no savings data). In the original SE study savings factor was part of the utility function and, thus, had an allocated weight. To represent the economic factor in SE ABM we replace savings by the payback assessment, which is weighted with w eco when estimating overall utility. The environmental and social components in SE ABM have the same representations as in MF ABM (Equation and Equation , Table ).
When transferring the RR study into the RR ABM, we omit the latter two measures due to data absence in the Dutch case-study. Further, the RR study measures social influence as the contribution of neighbors and other acquaintances to an individual household attitude towards PVs. Specifically, the number of PVs installed in the neighborhood, combined with the confidence obtained from neighborhood systems and the number of contacts with PV owners who are not in the household's neighbourhood all contribute to the social factor of agents' decision-making. The RR study does not have psychological comfort or aesthetics factor included in their households agents decision-making. Thus, u cof comes as a new factor in RR ABM. All four factors in RR ABM are measured in the same way as in MF ABM (Table ).
Recent genome-wide association studies (GWAS) have only identified a handful of loci for DKD, albuminuria, or estimated glomerular filtration rate (eGFR) in individuals with diabetes  [7] [8] [9] [10] [11] [12] [13]. Potential reasons for the limited success include small sample sizes, modest genetic effects, and lack of consistency of phenotype definitions and statistical analyses across studies. Through collaboration within the JDRF Diabetes Nephropathy Collaborative Research Initiative (DNCRI), we adopted three approaches to improve our ability to find new genetic risk factors for DKD: 1) assembling a large collection of T1D cohorts with harmonized DKD phenotypes, 2) creating a comprehensive set of detailed DKD definitions, and 3) augmenting genotype data with low frequency and exome array variants.
Variants previously associated with DKD We investigated the effect of variants previously associated at genome-wide significance with renal complications in individuals with diabetes  [8] [9] [10] [11] [12] [13] 28. Acr ss the ten sub-phenotypes in our meta-analysis, we found evidence of association for seven of nine examined loci (P<0. 05, Figure  S5 ): We replicated two loci that were previously discovered without overlapping individuals with the current study: SCAF8/CNKSR3 rs12523822, originally associated with DKD (P=6. 8×10 -4 for "All vs ctrl")  8  ; and UMOD rs77924615, originally associated with eGFR in both individuals with and without diabetes (P=5. 2×10 -4  for "CKD")  20. Associations at the AFF3, RGMA-MCTP2, and ERBB4 loci, identified in the GEnetics of Nephropathy-an International Effort (GENIE) consortium  12  , comprised of a subset of studies included in this current effort, remained associated with DKD, though the associations were attenuated in this larger dataset (RGMA-MCTP2 rs12437854 P=2.
Gene and gene set analysis We conducted gene-level analyses by employing two methods that aggregate SNP summary statistics over a gene region while accounting for linkage disequilibrium, MAGMA and PASCAL  29, 30. MAGMA identified five genes at a Bonferroni-corrected threshold (P<0. 05/18,222  ), SFXN4 associated with "Macro" (full model P=1. 65×10 -7 ), GLT6D1 associated with "ESRD vs. macro" (P=1. 49×10 -  ), and SNX30 associated with "All vs ctrl" (P=2. 49×10 -  ) (Table  S8 ). Although PASCAL did not identify any significant gene level associations, the five MAGMA-identified genes had P<5. 0×10 -4 in PASCAL (Table  S9 ). Both SFXN4 and CBX8 have been reported to be differentially methylated in patients with diabetes with and without nephropathy  31, 32. Additionally, we used MAGMA, PASCAL, DEPICT, and MAGENTA to conduct gene-set analysis in our GWAS dataset.
Expression and epigenetic analyses We interrogated gene expression datasets in relevant tissues to determine whether our top signals underlie expression quantitative trait loci (eQTL). We first analyzed genotype and RNAseq gene expression data from 96 whole human kidney cortical samples  42  and microdissected human kidney samples (121 tubule and 119 glomerular samples  43  from subjects of European descent without any evidence of renal disease (Figure  S8 ). No findings in this data set achieved significance after correction for multiple testing. ) with the MFF gene in blood, and rs118124843 near DDR1 and VARS2 had multiple significant eQTLs in blood besides VARS2 (P=1. 71×10 -  ; Table  S11 ). ), a transcription factor regulating adipocyte development, glucose and lipid metabolism; PPARγ agonists have been suggested to prevent DKD  44.
To ascertain the potential functional role of our top non-coding signals, we mined ChIP-seq data derived from healthy adult human kidney samples  45. SNP rs142823282 near TAMM41 showed enrichment for the histone marks H3K27ac, H3K9ac, H3K4me1, and H3K4me3, suggesting that this is an active regulator of TAMM41 or another nearby gene (Figure  S9 ). Interestingly, in recent work we have shown that DNA methylation profiles in participants with T1D with/without kidney disease show the greatest differences in methylation sites near TAMM41  46. To establish whether the expression of our top genes shows enrichment in a specific kidney cell type, we queried an expression dataset of ~50,000 single cells obtained from mouse kidneys  47. Expression was detected for six genes in the mouse kidney atlas: three (COL4A3, SNCAIP, and BMP7) were almost exclusively expressed in podocytes (Figure  5 ), supporting the significant role for podocytes in DKD.
Structural parameters measured by electron microscopy on biopsy included GBM width, measured by the electron microscopic orthogonal intercept method  17. SUMMIT consortium. The SUMMIT consortium included up to 5193 subjects with type 2 diabetes, with and without kidney disease, of European ancestry. All studies were approved by ethics committees from relevant institutions and all participants gave informed consent  13. Complete list of SUMMIT Consortium members provided in Table  S13. Genotyping. Samples were genotyped on the HumanCore BeadChip (Illumina, San Diego, CA, which contains 250,000 genome-wide tag SNPs (and other variants) and over 200,000 exome-focused variants. All samples were passed through a stringent quality control protocol. Following initial genotype calling with Illumina software, all samples were re-called with zCall, a calling algorithm specifically designed for rare SNPs from arrays.
Once calling was completed for all cohorts, our pipeline updated variant orientation and position aligned to hg19 (Genome Reference Consortium Human Build 37, GRCh37). Variant names were updated using 1000 Genomes as a reference. The data were then filtered for low quality variants (e. g. call rates <95% or excessive deviation from Hardy-Weinberg equilibrium) or samples (e. g. call rates <98%, gender mismatch, extreme heterozygosity). Principal Component Analysis (PCA) was performed separately for each cohort in order to empirically detect and exclude outliers with evidence of non-European ancestry. Genotypes were expanded to a total of approximately 49 million by imputation, using 1,000 Genomes Project (phase 3 version 5) as a reference. Genotyping of RASS cohort. All RASS participants contributed DNA for genotyping on the Illumina HumanOmni1-Quad and HumanCoreExome beadchip arrays.