Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.The rubber tree [ This increase has occurred partially in response to the major alterations caused by the development of human settlements in the areas of origin of the related wild species. Among the numerous existing collections, those involving perennial crops (either forestry or fruit crops) are especially difficult to establish. Moreover, these collections are expensive to manage due to the large areas that are required to maintain the accessions, such as the ex situ collections of grapevines  with a The distance-based model was implemented in the DARwin 5.0.158 software . A dissiThe maximization strategy  implemenWe confirm that no specific permits were required to collect the leaves used in this study. This work was a collaborative study developed by researchers from APTA (Brazil), CIRAD (France), EMBRAPA (Brazil), IAC (Brazil), UESB (Brazil) UNESP (Brazil) and UNICAMP (Brazil). Additionally, we confirm that the field studies did not involve endangered or protected species.As explained in the previous section, the allelic sizes of the PCR products were estimated using the following two technologies: LI-COR technology (electrophoresis in polyacrylamide gels) for 353 accessions and ABI3500 (capillary electrophoresis) for the remaining 764 accessions. Although both technologies are accurate and reliable, deviations may exist between the data obtained from these two sources due to the use of different calibration curves. The analysis of common control genotypes using both technologies allowed us to standardize the sizes of the different allelic products for each microsatellite marker. Moreover, the presence of 52 pairs of accessions among the analyzed samples identified under the same name and analyzed with the two technologies helped us to confirm the goodness of data homogeneity. Among these 52 pairs of homonymic accessions, 26 were identical, 22 exhibited less than 5 differences among the 26 allelic forms , and 4 differed for at least 5 alleles. Further analyses based on a matrix of dissimilarity (see below) suggested that only these last 4 pairs corresponded to genetically distinct genotypes to which identical names were erroneously assigned.We computed diversity statistics across all 1,117 of the individual accessions and within each of the two subgroups obtained in the analyses using the STRUCTURE software . The oveO) was 0.64 (ranging from 0.57 to 0.69); this value was slightly higher in cluster 1 than in cluster 2. The genetic diversity (HE) was higher than HO in all cases. The analysis revealed a high HE level ranging from 0.63 (Wickham group) to 0.84 (Pará group) with a mean of 0.76. Consequently, the Wright’s fixation index (F) values were positive, with a mean of 0.16 obtained for the accessions overall. The heterozygosities (HO and HE) were similar in both of the subgroups, although cluster 2 displayed higher indices of fixation (F = 0.20 in cluster 1 and F = 0.25 in cluster 2).For all of the accessions, the mean observed heterozygosity . A comparison of the number of private alleles from cluster 1 (18) and cluster 2 (97) showed that the latter contained a larger number of private alleles  suggested that two genetic clusters (K = 2) were sufficient to interpret our data ; the resHevea spp. A further STRUCTURE analysis of these two primary clusters of genotypes also indicated partitioning of both cluster 1 and cluster 2 into 2 subgroups. (The level of clustering (K = 2) reflects the primary division of subgroup cluster 1, consisting of the varieties of the advanced breeding germplasm originating from the Wickham and Mato Grosso accessions. Cluster 2 was formed by the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and bgroups. . HoweverHevea spp. were placed into one group, while the remaining populations belonged to the group formed by the Wi, MT and Wi × AM wild accessions.Additionally, the separation of the groups was also estimated using PCoA  based onvs. MT/C/S/25 or RO/C/9/45 vs. RO/C/9/48). Therefore, misidentifications due to human mistakes can be reasonably hypothesized to have occurred during the process of multiplication or transfer of accessions from one ex situ collection to another. In two cases, the accession names were completely different.The dissimilarity matrix computed with DARwin 5.0.158 was used to identify putative unexpected duplications of genotypes under different accession names. A total of 13 pairs and 2 triplets of accessions were found to be present with a high degree of genetic similarity. All of the concerned accessions were from the oldest and most widespread surveys conducted in 1974 (by EMBRAPA/IRCA) and 1981 (by IRRDB). In the majority of cases, these accessions were registered under almost identical names . However, the hybrids (21 H. brasiliensis × H. benthamiana and 100 H. brasiliensis × H. guianensis) were not separated from the genotypes of the Amazonas group  ranged from 0.008 (between the Amazonas and PA) to 0.099 (between the Wi and MD). Each of the pairwise values was significantly different from zero according to tests based on 9,999 random permutations (p ≤ 0.001)  to 0.20 (between the Wi and MD). However, the sample sizes from MD are relatively small compared to the other accessions, which may influence the Fst values. In terms of the population structure between the groups recognized in this study, the GST between cluster 1 and cluster 2 estimated from AMOVA was 0.018 (P < 0.01).Although most of the genetic variance occurred within the accessions, the differentiation of the accessions and groups was highly significant (p ≤ 0.001). The pairwise G≤ 0.001) . This fiHevea spp. (9.1%), Para (8.1%), Mato Grosso (7.1%) and Madre de Dios (2%). The alleles identified in this study were fully represented in these core collections. Additionally, our COREFINDER analysis highlighted that 85% (84 accessions) of the entire core collection was represented by the rubber tree accessions grouped in cluster 2, whereas cluster 1 contributed a smaller percentage (11%) to the core collection; the accessions that were considered a mixture  contributed to only 4% (4 accessions) of the core collection.A core collection was assembled for the rubber tree germplasm to represent all of the genetic diversity identified in this study. The 408 alleles identified at the 13 microsatellites used in this study were fully represented by as few as 99 accessions (the best of 10 runs) . The corHevea. This study was based on more than 1,100 accessions sampled at 7 ex situ collection sites located in Brazil and French Guiana. Nearly 500 accessions from the collecting survey conducted in 1995 in the Brazilian states of Amazonas and Pará that had never been previously described were included in this study. The other accessions mostly came from the states of Acre, Mato Grosso or Rondônia and were obtained in surveys performed in 1974 and 1981. Since that time, the accessions have been conserved in different ex situ collections. In recent decades, this latter group of accessions has potentially been transferred from one collection site to another, with all of the possible associated risks regarding traceability. For example, the accessions kept at the French Guiana collection site were primarily contributed by the CNRA collection site at Bimbresso in Côte d’Ivoire, where they had been sent soon after the respective prospection [The present study is the most comprehensive study ever performed on the population genetics of the genus spection . Some ofo of 0.64 across the entire accession set. These values were slightly higher than those detected by Le Guen et al. (2009) (Ho = 0.59). Lam et al. (2009) have detected an average heterozygosity of 0.20 using random amplified polymorphic DNA (RAPD) markers in Hevea genetic resources in Vietnam. These differences in genetic diversity values might be attributable to the types of germplasm that were analyzed. Lekawipat et al. (2003) have used microsatellite markers to detect the diversity in 40 Wickham and 68 Amazonian accessions using 170 alleles from 12 microsatellite markers dispersed among all of the genotypes. Similar results were observed in our study, in which an average of 14 alleles were available per locus; this diversity can be attributed to the high variability of Amazonian accessions.The results from this study reveal high levels of genetic diversity among the accessions, which is consistent with previous studies ,33 and tST and FST values revealed low genetic differentiation between the groups, with the exception of the Wickham accessions, which showed greater differentiation compared to the other studied groups  have obtained a similar value (FST = 0.12) upon analyzing ex situ collections of wild rubber trees. Gouvea et al. (2010) have studied clones from controlled-cross and open pollinated progenies and reported high values of genetic differentiation (GST = 0.61). Lower genetic differentiation indicates higher gene flow between populations, indicating that a majority of the genetic diversity is preserved within populations.An outcrossing breeding system, long life cycle and large geographic range may have helped to shape the high genetic diversity of Hevea spp. were discretely separated from the other populations to form cluster 2. However, due to the small number of samples analyzed (only seven Hevea spp. genotypes were included in this group), this result should be interpreted with caution. The observed heterozygosity was slightly higher in cluster 1  than in cluster 2 ; nevertheless, the number of different alleles was greater in cluster 2, which can be explained by the greater diversity of the different species present in this cluster.A population structure analysis using the software package STRUCTURE revealed the presence of two primary groups in our set of accessions. This result partially agrees with the results obtained through PCoA  analysisPrior analyses by Le Guen et al. (2009) have demonstrated a distinct separation between the Acre and Rondônia groups and the Mato Grosso group. Although only a few Wickham accessions were included among the samples, these clones appeared to be closer to the Mato Grosso accessions. Our analysis of 55 additional Asian accessions confirmed the genetic similarity between the Wickham and Mato Grosso accessions. The most obvious division in the analyzed accessions occurred between the Mato Grosso and Wickham clones; these clones formed one group, while the other accessions grouped together in a second cluster.One explanation for this result is that the accessions are from geographically distant populations. However, these two groups are located in the same hydrographical network, which originates downstream of the Tapajos River ,34,35.H. brasiliensis separated by distances within catchments and incurred the isolation in populations with distances that exceeded the size of a catchment [Hevea pollen can generally be dispersed by these pollinating agents in the course of open pollination. Yeang et al. (1999) [Hevea pollen can be transported fairly considerable distances by pollinating agents. The regression model in this study suggested a theoretical range of 0±3 to 1±1 km, although very few pollen grains would be expected to reach this limit.Determining a structure within the accessions of Amazonas, Rondônia, Acre, Madre de Dios and Pará is more difficult. One possible explanation for this difficulty is that long-distance gene flow via seed flotation prevented the isolation of Amazonian populations of atchment . The rub. (1999)  have estHevea germplasm was conducted using isozyme markers in accessions from the 1981 IRRDB collection and Wickham group. The results of the isozyme analysis detected a total of 60 alleles in the 1981 IRRDB accessions and 26 alleles in the Wickham accessions. Based on these results, Chevallier (1988) affirmed that the genetic base of the Hevea germplasm 1981 IRRDB collection was prosperous and diversified. In contrast, the Wickham population showed a low level of genetic variability, which is a consequence of oriented selection within a narrow geographical origin over a period of years. Our results demonstrated a greater number of private alleles in cluster 2, which is composed of the wild germplasm  markers ,37 and PHevea genus. The first study using this material selected 150 genotypes to identify the most promising rubberwood-yielding genotypes and wild Hevea relatives conserved in the 1995 Hevea germplasm in Selangor, Malaysia. The genotypes and wild relatives that are considered vigorous and generate a high rubberwood yield can be exploited as promising planting material in breeding programs. In short, the expedition to collect wild Hevea relatives in 1995 was a worthwhile scientific activity to safeguard the most valuable genetic resources and improve future crops of the Hevea species [In 1995, an expedition was launched by RRIM to collect rubber seeds from Brazil. From this collection, approximately 50,231 seedlings were planted in Malaysia, including other species of the  species .ex situ germplasm collection presents great genetic potential for breeding, the collection remains underutilized. AMOVA demonstrated that 3% of the total genetic variance was present between the groups and 97% was within the groups, which could be explained by the large number of analyzed individuals in each group. Although the majority of the genetic variation occurred between the individuals within a group, the differences between the accessions and group differentiation were significant (p < 0.001). Our analysis revealed a high frequency of gene flow between the groups, with a genetic differentiation coefficient (GST) estimated to be 0.018.Although this Hevea spp. group. These genotypes may be incorporated in future breeding programs.The majority of the germplasm collection used in the current breeding programs was derived from the 1981 IRRDB collection expedition in the Amazon forests of Brazil, but 434 clones from the 1995 germplasm collection (Amazonas genotypes) showed 34 private alleles and high genetic variability, which stands out among the groups. Altogether, the groups contained 55 private alleles, of which 20 alleles were from the H. brasiliensis accessions and the other species from Amazonas was observed in the Structure analysis. However, using PCoA analysis, a possible discrete separation of Hevea spp. genotypes from the other genotypes of cluster 2 was observed. The results obtained by Lam et al. (2009) suggest that gene flow might exist between the districts, possibly due to the species’ outcrossing mode of reproduction and the dispersion of seeds by a network of rivers in the Amazon basin. However, this explanation should be treated with caution due to the small number of samples analyzed in that study.In addition to the high gene flow detected, no distinct separation among the Hevea species (13 H. benthamania and 4 H. pauciflora) or interspecific hybrids (21 H. benthamiana × H. brasiliensis and 100 H. brasiliensis × H. guianensis). This previous identification was based on the seed size, shape and layout pattern of the accessions. However, whether the trees from which the seeds were collected were hybrids or pure species pollinated by other species is not clear. No methods exist to easily determine whether an H. brasiliensis seed was generated by pollination from H. brasiliensis or H. guianensis. Our difficulty in structuring the Amazonas populations, even within the H. brasiliensis genotypes, mostly likely occurs because we are not observing a single species but a species complex consisting of at least H. brasiliensis, H. guianensis and H. benthamiana.In the present work, several Amazonas accessions were originally identified as other Hevea species have been generally assumed to be freely interfertile [H. camargoana × H. brasiliensis, and Gonçalves et al. (1982) have analyzed the progenies that issued from hand pollination through this type of crossing. Additionally, Hevea species might be considered a species complex due to the absence of a strict barrier to recombination between the species.Since the publication of the first papers on the subject, the rfertile ,39. PireHevea species indicate that the genus is a species complex with moderate differentiation between species. Moreover, the results suggest that these aspects are favorable for genetic introgressions using other Hevea species in the rubber breeding population, which is mainly based on H. brasiliensis.Recently, studies regarding the cross-species/genera transferability of SSR markers have been reported –43. AccoHevea genetic resources has been the establishment of ex situ gene banks that can represent a last resort for many species and varieties (including those of the Hevea genus), which would otherwise die out as their habitats are destroyed [The conventional solution for the conservation of estroyed . The conHevea spp. accessions were collected from 8 Rôndonia regions that have most likely been deforested during the last 30 years, resulting in a huge loss of the important Hevea spp. germplasm. Considering the deforestation scenario in Amazonia (and particularly in Rondônia), the establishment and ex situ conservation of Hevea spp. germplasm collections is the last possibility to preserve their genetic diversity.In this work, 186 ex situ collection sites in different countries.The purpose of core collections is to facilitate the use, maintenance and management of the germplasm by providing a set of accessions that display most of the genetic diversity available in the larger collection with minimum redundancy . Such stHevea gene banks exist worldwide, mostly on the South American continent. However, the majority of these collections are composed of accessions from the 1981 IRRDB survey [Hevea germplasm. Moreover, we identified a large number of private alleles and high genetic variability in the accessions from the 1995 germplasm. Although the planted and recently domesticated populations exhibited greater genetic diversity, the wild populations have preserved the most private and rare alleles, causing these populations to be the most important reservoirs of genetic variation.Various B survey . None ofHevea core collection resulted in the selection of 99 accessions from the germplasm collection with 85% of the entire core collection represented by the rubber tree accessions grouped in cluster 2. The observed heterozygosity was slightly lower in cluster 2 than in cluster 1, but the number of private alleles was greater in cluster 2, as predicted. These observations can be explained by the greater diversity of the different species present in cluster 2 and the greater contribution to the core collection. A total of 32.3% of the accessions were from the Amazonas group, indicating the importance of the wild Hevea relatives collected in 1995 and confirming that these collection efforts were a worthwhile scientific activity to safeguard the most valuable genetic resources for future crop improvements of the Hevea species.The selection procedure for developing a Hevea breeding.The accessions of the proposed core collection comprise 85% wild material, and the collection would possess abundant genetic diversity and private alleles, an advantageous attribute for dissecting the genetic basis of QTL for immediate application in These investigations should include complementary criteria, such as phenotypic, agronomic and adaptive traits. A core collection would also provide a logical subset of germplasm for examination when the entire collection cannot be used.Finally, such core collections would also be useful for the development of new breeding strategies for adaptive and agronomic traits through genome-wide association studies.S1 Fig2 of rain forest had been cleared through 2003. Systematic cutting of forest vegetation starts along the roads and then fans out to create the "fishbone" pattern that begins to be visible in the eastern half of the 1986 image. The deforested land and urban areas appear lavender; healthy vegetation appears green. (http://earthshots.usgs.gov/earthshots/node/39#ad-image-0). Images courtesy of the Geological Survey (the USGS home page is: http://www.usgs.gov.)(A) June, 1975; (B) July, 1986; (C) August, 2001; (D) August, 2013; red dot–city of Ariquemes. As much as 67,764 km(TIFF)Click here for additional data file.S2 Fighttp://earthshots.usgs.gov/earthshots/node/39#ad-image-5). Images courtesy of the Geological Survey (the USGS home page is: http://www.usgs.gov.(A) June, 1975; (B) July 1986; (C) August, 2001; (D) August, 2013. The early images show main roads cutting through the forest. Highway 421 snakes through the forest south-southwest from the city of Ariquemes, and Highway 364 runs roughly north to south through Ariquemes. Additional roads branch out from the main roads to create the fishbone pattern. As time proceeds, a patchwork of cleared areas, forest remnants, and settlements are left behind. ((TIFF)Click here for additional data file.S3 FigBar plots from the CLUMPP results aligning 20 structure runs for K = 3 and K = 7.(TIFF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.


First, heritability for δ13C was estimated (0.29) using a 15-year-old progeny trial (Landes provenance), with no significant differences among three sites contrasting in water availability. High intersite correlations (0.63–0.91) and significant but low genotype–environment interactions were detected. Secondly, the genetic architectures of δ13C and growth were studied in a three-generation inbred pedigree, introducing the genetic background of a more-drought-adapted parent (Corsican provenance), at ages of 2 years (greenhouse) and 9 years (plantation). One of the quantitative trait loci (QTLs) identified in the field experiment, explaining 67% of the phenotypic variance, was also found among the QTLs detected in the greenhouse experiment, where it colocalized with QTLs for intrinsic WUE and stomatal conductance. This work was able to show that higher WUE was not genetically linked to less growth, allowing thus genetic improvement of water use. As far as is known, the heritability and QTL effects estimated here are based on the highest number of genotypes measured to date.To meet the increasing demand of wood biomass worldwide in the context of climate change, developing improved forest tree varieties for high productivity in water-limited conditions is becoming a major issue. This involves breeding for genotypes combining high growth and moderate water loss and thus high water-use efficiency (WUE). The present work provides original data about the genetics of intrinsic WUE (the ratio between net CO From 2000 to 2010, the world lost 130 million hectares of forest, corresponding to 3.2% of the total forest area, but on the other hand, it has gained 78 million hectares, mainly as planted forests and natural forest expansion . This in2 concentration are likely to increase growth  of plant organic material, such as needles or wood —and intrinsic water-use efficiency (Wi)—the ratio of net CO2 assimilation rate to stomatal conductance of water vapour . The direct estimation of WUE at the whole-tree level, for example by estimating time-integrated transpiration and biomass accumulation, is difficult  was used for several reasons. First, a breeding programme was launched in France in the 1960s to improve growth and straightness, and genetic resources are available to work both on genetic parameters and genetic architecture. Second, the planted forest in southwestern France, where this species spans over 1 million hectares, is expected to undergo reductions in water availability in the context of climate change, particularly during the growing season (Wi (as estimated from δ13C) correlated well to WUE at the whole-plant level  to compare the genetic architecture of δ13C and growth across different tree ages in a cross between a genotype from the breeding population and a genotype from a region with lower soil water availability. The rationale for the introduction of δ13C as new selection criteria for maritime pine breeding is discussed with the aim of providing improved varieties that maintain biomass production under water-shortage conditions.In this context, the specific objectives of this work were two-fold: (i) to estimate genetic parameters for δSupplementary Table S1 available at JXB online) were used to study the genetics of WUE and its relation to growth: (i) a progeny trial from the Landes breeding population to estimate genetic parameters; and (ii) two F2 quantitative trait loci (QTLs) mapping populations, using the same grandparental genotypes, with one from the Landes breeding population and one from a Corsican population, for dissecting the genetic architecture of the studied traits.Two types of plant material (–1 (4×2 m). A total of 196 (Escource), 156 (Lagnereau) and 174 (Cestas) half-sib families were planted in each site, in 35 randomized complete blocks with a single-tree plot design. Seedlings were sown in 1995 and raised for 1 year in a nursery before being transferred to the field. These sites are characterized by a sandy podzol. Following Erica cinerea and Calluna vulgaris, deep water table), mesophylous (semihumid) heathland , wet (humid) heathland . There are also differences in soil nutrients, with less nitrogen and carbon contents at Escource compared with the other two sites (Supplementary Table S2 available at JXB online).In the 1960s, ‘plus’ trees were selected in the Landes de Gascogne forest (southwest of France) to constitute the base breeding population of maritime pine (G0 generation). This study considered a half-sib genetic trial (HST) consisting of progenies from G1 mother trees selected for growth and stem straightness and crossed with a polymix (mix of pollen from 42 G1 trees). The HST was established in three sites  with a density of 1250 trees haSupplementary Fig. S1 available at JXB online). Between 10 and 13 trees per half-sib family and per site were phenotyped for WUE .From this progeny trial 50 half-sib families were chosen, present in all three sites and representing the diversity in growth observed at age 12 in the G1 population (–1 (4 m×2 m) and trees were 9 years old at the time of phenotyping (2008).A three-generation inbred mapping population (F2) was used to study the genetic architecture of quantitative traits. To generate the F2 population, selfed seeds were obtained from a single hybrid tree (accession H12) derived from a controlled cross between a Landes genotype  and a Corsican genotype . The closest meteorological stations (Meteo-France) were used to describe the climate for the origins of the parental trees: Sabres for the Landes genotype and Corte for the Corsican genotype. Based on data from 1995 to 2010, Sabres showed significantly higher annual precipitation (1108mm) compared with Corte (818mm), whereas monthly mean potential evapotranspiration (PET) was significantly higher in Corte (80mm) compared with Sabres (68mm), especially during the growth period (May to August). The whole mapping population was divided into two seed lots. The first population (F2 greenhouse) consisted of 200 genotypes raised in 1998 in 4-l pots in a greenhouse and were subjected in their second year to a drying cycle by withholding watering for 6 weeks, after a last watering to field capacity. The second population (F2 plantation) consisted of 477 genotypes sown in 1998 and raised for 1 year in a nursery before being transferred to the field. This trial was located at Lacanau de Mios , a semihumid heathland, with a density of 1250 trees ha13C was measured on a set of three annual rings , which were extracted from increment cores. Extractives were removed by soaking the cores in pentane for 24h. Wood was cut by hand into small pieces, preground in a centrifugal mill  and milled to a fine powder in a ball mill . For the greenhouse population, δ13C was measured on bulk needle dry matter. Four pairs of needles were harvested from the upper third of the main stem for 200 genotypes before the drying cycle (δ13C_WW_stem) and after the drying cycle (δ13C_D_stem) for 189 genotypes. Four pairs of needles were also sampled from a lateral shoot for 107 genotypes before the drying cycle (δ13C_WW_shoot) and after the drying cycle (δ13C_D_shoot) for 105 genotypes. The needles were ground to a fine powder using a ball mill. For all analyses, a 1mg subsample of the plant material (wood or needle dry matter) was combusted in an elemental analyser . δ13C was determined with a coupled continuous-flow isotope ratio mass spectrometer . Carbon isotope composition (δ13C expressed in ‰) was calculated relative to the VPDB standard as  to stomatal conductance of water vapour . A and gs were assessed once before the drying cycle using a portable gas-exchange system with a cylindrical chamber  on one pair of 1-year-old needles per plant at a chamber CO2 concentration of 1200 µmol mol–1 and a saturating photosynthetic photon flux density (1500 μmol m–2 s–1). The elevated CO2 concentration during gas-exchange measurement does not affect gs in maritime pine compared with an ambient CO2 concentration  as described by Total height and circumference at breast height were also measured in 2008 at age 12 in the three sites of the HST. Woody biomass was evaluated in the greenhouse population based on weight of roots and primary and secondary axes without needles.13C, A, gs, and A/gs.For the greenhouse population, a linkage map (here referred as MapF2g) was built from DNA of 200 haploid megagametophytes with 235 amplified fragment length polymorphisms (AFLPs), 127 random amplified polymorphic DNA (RAPDs), and 32 protein markers resulting in 13 linkage groups   was established from the genotyping of 477 offspring with 248 single-nucleotide polymorphism (SNP) markers , resulting in 12 LGs corresponding to the haploid number of chromosomes of the pine genome. The length of the map was 1754 cM (146 cM per LG on average) with a density of one SNP every 7 cM. In this study, MapF2p was used to detect QTLs for δ13C and growth by Supplementary Table S3 available at JXB online.In order to compare QTLs detected for the greenhouse and plantation populations with QTLs detected by Analysis of phenotypic correlations among traits was carried out using linear regression analysis.Genetic parameters were first estimated from the HST within each site (model 1) using the following linear mixed model (interactions between block and family effects were not significant) for univariate or bivariate analyses:y is the vector of phenotypic individual observations, b is the vector of fixed block effects, f is the vector of random family effects, e is the residual, and X and Z are the incidence matrixes linking phenotypic observations to fixed and random effects.where Variances of random effects were defined as follows:σP2) and additive genetic (σA2) variances were obtained from the following equations:Phenotypic  were derived from these variances:Genetic and phenotypic coefficients of variation  was estimated as:Narrow-sense heritability (rP) and additive genetic (rA) correlations between two traits, y1 and y2, were estimated as follows:The phenotypic  in a similar linear mixed model as described previously, with specific family covariances fitted between each site (model 2). G and R matrices (the variance - covariance matrix of families’ effect (ie. genetic effect) and the variance - covariance matrix of the residual effect, respectively) can then be described as follows:Intersite genetic correlations were estimated as:Analyses were conducted with the restricted maximum-likelihood method using the software ASReml (The expected response (R) after a selection step can be expressed as :i=2.67 , σP is phenotypic standard deviation, and h2 is individual heritability.where 13C, gas-exchange data , ring width, and biomass were analysed. Data were not transformed despite slight deviations from normality because the interval mapping method is robust against this assumption (http://www.multiqtl.com) as described by δsumption . Moreovesumption . QTL detAs the maps of the hybrid tree were constructed using either megagametophytes (MapF2g) or needle DNA (MapF2p), QTL detection was carried out under a back-cross model and a classical F2 model, respectively.13C estimated from the two needle positions (stem or shoot) and sampling times before and after the drying cycle. As no needle growth had taken place during the drought stress and as there were strong positive correlations between δ13C_WW_stem, δ13C_D_stem, δ13C_WW_shoot, and δ13C_D_shoot, with slopes close to 1 (Supplementary Table S4 available at JXB online), these data were used as technical replicates in order to increase the statistical power of the QTL analysis. By reducing environmental variance, this method enhances the detection power of low-effect QTLs  and the greenhouse and plantation populations are presented in Supplementary Table S5 available at JXB online. δ13C was normally distributed except for the plantation population (Shapiro–Wilkinson test). In the HST populations, δ13C was higher at Escource (dry site) compared to the two other sites, but no differences were found in CVP. As expected due to similar experimental conditions , δ13C was comparable for the HST populations (mean of the three sites –26.1‰) and the plantation population (–26.4‰) but plants of the greenhouse population showed clearly lower δ13C (–28.3‰) which may be attributed to the lower δ13C of the atmospheric CO2 in the greenhouse (mixing of outside CO2 with 13C-depleted CO2 issued from plant and soil respiration). Both mapping populations clearly exhibited higher CVP for δ13C than the HST populations. The observed variance was higher in the greenhouse population compared with the plantation population (3.1 versus 2.6%) and the greenhouse population showed a clear bimodal distribution with a peak ratio of 4:1.At 12 years (2008), trees on the three sites showed significant differences for growth . The distribution of δ13C exhibited significant additive genetic variability in the three HST sites (Supplementary Table S5 available at JXB online). Heritability of δ13C was first estimated within each site (model 1): 0.23 at Escource, 0.41 at Lagnereau, and 0.34 at Cestas. These estimates  0.29±0.07 or 0.25±0.07, respectively, could be estimated (model 2). Based on these genetic parameters, if the best 1% of individuals were selected from the HST for δ13C, the expected response would be a shift of 0.4‰ for the δ13C population mean.δstimates  were hig13C between Escource, Lagnereau, and Cestas with model 2 were high  and Lagnereau . A highly significant positive correlation between δ13C and ring width  was also obtained at Escource.The intersite genetic correlations estimated for δere high : from 0.ach site  were eit13C in the greenhouse population, a large variation for Wi was also observed (CVP=31%). This variation was mainly determined by the variation of stomatal conductance (gs), which was shown by its equally high CVP of 31%, compared to the lower CVP for assimilation rate (A) of 14%. A and gs were significantly correlated , with a low correlation coefficient and a low slope . Further, the correlation between Wi and δ13C was significant, with a slope of 0.03, indicating a variation of 0.3 μmol mmol–1 per ‰ change. Correlation between δ13C_WW_shoot and A was negative and lower  than that between δ13C_WW_shoot and gs . The correlation between biomass and gs was higher  than with A .In addition to the large variation observed for δ13C (13C measurements (data not shown). One QTL was also detected for the A/gs ratio (Wi) and gs, whereas none was identified for A (Supplementary Table S7 available at JXB online). The QTLs for A/gs and gs were both located in the same region on LG 12, close to the QTL for δ13C . Working with a genetic map of the F2 population using codominant markers allowed to study the contribution of alleles at the two flanking SNP markers of this QTL. Homozygous genotypes for the Landes allele as well as the heterozygous genotypes presented a significant lower δ13C compared with the homozygous genotypes for the Corsican allele (Supplementary Table S8 available at JXB online). The differences between genotypes with one or two copies of the Landes allele versus the homozygous genotypes for the Corsican allele  was around 1‰. The interaction of these alleles showed that the Corsican allele was recessive.For the plantation population, the QTL analysis identified one large-effect QTL on LG 12, explaining 66.7% of PEV, as well as a minor QTL on LG 8. The QTL on LG 12 presented positive additive and dominant effects . Its con13C and ring width mean was not significant for the complete plantation population (R=–0.04) as well as when F2 offsprings of the three genotypes  were analysed separately (−0.01<R<–0.05).The phenotypic correlation between δ13C QTL  implies a large uncontrolled heterogeneity of the soil. This can have an effect on the phenotype and thus complicate the estimation of genetic parameters. However, the large families used in this study made it possible to establish trials consisting of blocks, which can be used to take this heterogeneity into account.Supplementary Fig. S3 available at JXB online).Many tree species cannot be easily propagated vegetatively (including maritime pine), therefore QTL studies in these species are based on a single-tree plot design without ‘clonal’ replicates. Consequently, environmental heterogeneity, especially of the soil, cannot be controlled by introducing blocks into the experimental design. Spatial variation of soil properties could therefore have an impact on the estimation of the phenotype and thus result in less statistical power to detect low-effect QTLs. Therefore, before the data analysis, this work verified for the QTL field experiment, using a spatial analysis of the phenotype of the measured trees, that no spatial pattern was detectable  often represent an integration over several growing seasons, which will average out annual environmental variation when the genotype×environment interaction is not particularly strong and thus result in a more robust estimation of phenotypic values for each genotype.13C heritability measured across different environments was moderate (0.29±0.07) and did not vary significantly among sites. It was similar to that found for ring width growth (0.25±0.07) evaluated for the same years but slightly higher than for total height and circumference at the age of 12. The genetic parameters of δ13C were accurately estimated in this study due to the presence of a large genetic variability in the G1 breeding population on the one hand and the analysis of the same genetic material in three sites contrasting in water availability on the other. Thus, this robust estimation of δ13C heritability was obtained using a wider genetic background within the breeding population compared to the first estimation of 0.17±0.06 provided by 13C was as large as the one found across the natural range of the species  and by Picea mariana (0.54), whereas very low values (<0.1) were observed for Pinus taeda  that was also detected in the greenhouse population. This QTL had not been detected in the intra-Landes pedigree used by Supplementary Table S9 available at JXB online). This suggests that the underlying genetic factors are different between the pedigrees. Compared to the geographical origin of the Landes parent, the original population of the Corsican parent is subjected to higher annual potential evapotranspiration, especially in the summer. This results probably in a higher summer water deficit, which might have caused specific strategies (therefore different genetic mechanisms) to cope with soil water deficit.In the plantation population, a major QTL region linked to δ13C located on LG 12 in the plantation population: (i) colocalized with the QTL detected in the greenhouse population; and (ii) colocalized with a QTL for a direct measurement of Wi and with a QTL for gs. Similarly to the Quercus robur L., the colocalization of the QTL as well as the positive phenotypic correlation between δ13C and A/gs confirmed the major QTL for δ13C as a QTL for WUE rather than for one of the 2). Further, the colocalization with a QTL for gs suggests an introduction of alleles by the Corsican, supposedly more drought adapted parent, which might be related to stomatal responses, resulting in genotypes that are more efficient in water use. The correlations between gas exchange related traits and δ13C suggest that the variability of WUE in this cross was probably driven by variation in gs rather than A. The coefficients of variations of A and gs suggest a larger diversity of the latter in the greenhouse population. Additionally, the significant correlation between the two traits had a low slope, suggesting only a relatively low impact of gs on A. Thus, within this family, a lower gs effectively reduced water consumption, increasing WUE with only a low impact on aboveground biomass growth. It is worth noting that the impact of this genomic region on LG 12, which controlled the variability of δ13C, became much stronger in the field plantation (8–67%), even though these trees were much older than the seedlings in the greenhouse, and measurements were done on wood samples in the field, which integrated whole-canopy WUE as well as post-photosynthetic discrimination  have only been detected in recombinant inbred lines on Arabidopsis thaliana  for δ13C has also been detected with a multiyear QTL analysis , as did At the interprovenance level, several studies have analysed the correlation between δ13C but this correlation appears not significant at the genetic level. Enlarging the literature review to other forest trees evaluated in field after the juvenile age, no general trend could be highlighted. Some authors found negative correlations, such as Pinus elliottii × Pinus caribaea, Picea mariana, and C. sativa, while others showed positive correlations, such as Araucaria cunninghamii or nonsignificant correlations as Quercus petraea. These results can be first explained by a poor estimation of the genetic correlation due to limited sampling, as δ13C measurements are cost and time demanding. This discrepancy also suggests that the direction of this correlation is driven by different physiological mechanisms depending on the species and even ecotype considered. A positive correlation between WUE and growth could suggest that WUE is primarily determined by leaf assimilation, which would impact variability of biomass accumulation. On the other hand, a negative correlation could indicate that WUE is primarily determined by stomatal conductance, having little impact on biomass accumulation.At the within-provenance level, 13C and growth traits. Thus, it appears possible to select maritime pine for δ13C without counter selection for growth within the Landes genepool. Moreover, highly significant positive (favourable) correlations were estimated from the dry site (Escource), suggesting that the acclimation to this site resulted in an increased WUE that was genetically linked with an increase of growth.No significant unfavourable genetic correlations were found between δ13C. Disentangling the effect of both factors will require further investigation.As all three planting sites are within a small region in the southwest of France, the overall climate is similar and the differences in soil water content are mainly dependent on the soil type. The driest soil at Escource, which contained the highest proportion of sand, also showed relatively low nitrogen and phosphorous contents. The resulting nutrient limitation was therefore probably higher in the dry site due to reduced nitrogen mineralization compared to the other sites . Thus, i13C and growth traits. In addition, there was no phenotypic correlation  between these two traits. Additionally, the test of the homogeneous group at the closest markers from the QTLs did not show the same pattern of significant differences between the homozygous and heterozygous groups (Supplementary Table S8 available at JXB online), suggesting no common genetic regulation between growth and δ13C. These results therefore suggest that the genetic determinisms of δ13C and ring width are independent. The absence of relationships between growth and δ13C has also been found in Populus interspecific families , established in sites contrasting in water availability, showed medium heritability for δ13C in the Landes breeding population was rather low (shift of 0.4‰ if the best 1% of genotypes are selected). However, the Corsican genetic background, which brings a recessive allele improving WUE greatly by decreasing stomatal conductance with only little effect on assimilation rate and growth, could be used in controlled crosses with the Landes genetic background. More generally, it seems interesting to explore the genetic diversity for WUE within the Corsican gene pool for implementation in the maritime pine breeding programme. The usefulness of WUE, estimated by δ13C, is under debate in breeding of annual crops for higher yield under drought conditions (The expected genetic gain for a selection for δnditions , with thThe genetic improvement of the Landes breeding population in itself for WUE might not be a major aim. Rather, more research is needed to support the interest of the Corsican genetic background in hybrid combination with the Landes provenance, which is well adapted to the Aquitaine region, especially in terms of frost resistance. To gain more insights into the functional background of observed variability in WUE, an approach of choosing specific genotypes for detailed studies, as has been done for pedonculate oak (JXB online.Supplementary data are available at Supplementary Table S1. Main characteristics of the studied trials and associated annual measurements.Supplementary Table S2. Soil composition in the three HST sites.Supplementary Table S3. Main characteristics of the four genetic linkage maps used in this study.Supplementary Table S4. Pearson’s correlation coefficients between water-use efficiency estimated by δ13C for the F2 greenhouse populationSupplementary Table S5. Means, phenotypic coefficients of variation, and additive coefficients of variation for δ13C in the HST and mapping populations.Supplementary Table S6. Pearson’s correlation coefficients and linear correlation slopes between A, gs, A/gs, δ13C, and woody biomass for the F2 greenhouse population.Supplementary Table S7. Significant QTLs for WUE estimated by A/gs and for each component of the previous ratio for the F2 greenhouse population.Supplementary Table S8. Effect of the Corsican recessive allele on WUE estimated by δ13C and mean ring width in the F2 plantation population.Supplementary Table S9. Correspondence between linkage groups of the different genetic maps used in this study.Supplementary Fig. S1. Distribution of breeding values for height at 12 years in the G1 population and the sampled G1 population.Supplementary Fig. S2. Relationship between stomatal conductance of water vapour and net CO2 assimilation rate.Supplementary Fig. S3. Individual measurements of δ13C for the F2 plantation population.


We review current phylogeographic knowledge from across the Antarctic terrestrial landscape with a focus on springtail taxa. We describe consistent patterns of high genetic diversity and structure among populations which have persisted in glacial refugia across Antarctica over both short (<2 Mya) and long (>10 Mya) timescales. Despite a general concordance of results among species, we explain why location is important in determining population genetic patterns within bioregions. We complete our review by drawing attention to the main limitations in the field of Antarctic phylogeography, namely that the scope of geographic focus is often lacking within studies, and that large gaps remain in our phylogeographic knowledge for most terrestrial groups. With appropriate sampling of genes and individuals, phylogeographers can test biogeographic hypotheses, infer processes underlying the origin, distribution and maintenance of biodiversity, and evaluate a population's demographic history )All of the sub-Antarctic islands are characterized by two major biotopes . These cet al. examined mtDNA (COI) genetic substructure in two indigenous and two introduced springtails on Marion Island [Cryptopygus antarcticus travei Deharveng and Tullbergia bisetosa Börner, respectively) and no structure  in both of the introduced species , compared to introduced species whose residency time has been shorter. One study employing haplotype distribution analysis looked at this in detail and found exactly this pattern . Myburghn Island . They fo species . For theC. a. travei from Marion Island [C. a. travei [Eupodes minutus [C. a. travei [This result was supported by a second haplotype distribution analysis of n Island . This wo. travei . Analysi. travei , and als minutus  supporte. travei . This fiThus, a diverse genealogical history impacted strongly upon by events resulting in isolation of populations in refugia, is a pattern not only common to the deeper continental Antarctic, but also prevalent at its most northern (sub-Antarctic) locations.3.While a large proportion of Antarctic terrestrial biota remains understudied ,33,103, First, Antarctic springtail populations, regardless of their zonal location, are characterized by high genetic diversity and strong genetic structure. This fragmentation is represented by the presence of unique haplotypes within populations and a very low degree of haplotype sharing between populations. It is generally maintained by the isolating nature of Antarctic terrestrial habitats—each population is an island—over both contemporary and historical timescales. In some cases, this isolation has led to incipient e.g., ,62–64) o–64 o62–64.Go. hodgsoni from continental southern Victoria Land is the only species for which we can reliably say this level of sampling has been achieved  woulIn addition to ‘more locations’, we can give more confidence to studies showing concordant patterns across taxa as this often reveals a concerted response of species and communities to the historical environmental changes that have shaped their present distributions. Hence, ‘more species’ are a second required future directive.Finally, analysis of ‘more genes’, especially combining the use of both nuclear and mitochondrial sequence data, is an optimal future strategy for phylogeographic studies. This approach can provide information over different temporal scales, accommodate coalescent stochasticity and improve the accuracy of inferences about past demography and divergence times ,106–109.While this review highlights the ‘work in progress’ nature of the field currently , the promise of such future approaches shows that the outlook for Antarctic phylogeography is an exciting one. There is much to be gained from Antarctic studies—particularly how populations have responded and may respond to long-term environmental changes. Previous phylogeographic research, reviewed here, will provide a valuable platform from which to expand this knowledge in the years to come.


Fusarium head blight (FHB) and Septoria tritici blotch (STB) severely impair wheat production. With the aim to further elucidate the genetic architecture underlying FHB and STB resistance, we phenotyped 1604 European wheat hybrids and their 135 parental lines for FHB and STB disease severities and determined genotypes at 17,372 single-nucleotide polymorphic loci.Cross-validated association mapping revealed the absence of large effect QTL for both traits. Genomic selection showed a three times higher prediction accuracy for FHB than STB disease severity for test sets largely unrelated to the training sets.Our findings suggest that the genetic architecture is less complex and, hence, can be more properly tackled to perform accurate prediction for FHB than STB disease severity. Consequently, FHB disease severity is an interesting model trait to fine-tune genomic selection models exploiting beyond relatedness also knowledge of the genetic architecture.The online version of this article (doi:10.1186/s12864-015-1628-8) contains supplementary material, which is available to authorized users. Wheat improvement is characterized by the need to control a high-dimensional trait space comprising grain yield and its components, quality traits, as well as abiotic and biotic stress resistances . As a coIn marker-assisted selection, a small number of predefined functional markers is used to predict the performance of genotyped material for a trait . This stFusarium graminearum, F. culmorum and other Fusarium species severely impacts wheat production worldwide [Mycosphaerella graminicola (anamorph Septoria tritici) has become one of the most devastating leaf diseases in Central European winter wheat [Fusarium head blight (FHB) caused by orldwide . Septorier wheat . Accurater wheat . Especiaer wheat , 13. ConThe relative relevance of linkage disequilibrium in comparison to relatedness for genomic selection is trait specific. It is challenging to differentiate both sources contributing to the accuracy of genomic selection as their effects are intermingled . Using mStb1 originating from a Bulgarian landrace [The genetic architecture of STB resistance has been recently analyzed based on a mapping population of approximately 1000 European wheat hybrids that were phenotyped in two environments . The rellandrace  in this landrace . The potlandrace . The acclandrace . VerificFhb1 from line Sumai 3 or QTL Fhb5 from line CM82036 [Major QTL for FHB resistance have been identified in populations derived from crosses with exotic donor lines. Examples comprise QTL  CM82036 . Despite CM82036 . As alte CM82036 , 23, 24  CM82036 –27. The  CM82036 . NeverthBased on phenotypic data obtained from multi-environment field trials and genotypic data generated using a wheat 90 k SNP array for a large collection of 1604 F1 elite winter wheat hybrids and their 135 parental inbred lines, we contrasted the genetic architecture of FHB and STB disease severities applying association mapping and genomic selection in combination with a cross-validation approach. The objectives of our study were to (1) examine the correlations among FHB and STB disease severities, (2) investigate the genetic architecture of both traits, and (3) assess the potential of marker-assisted and genomic selection for improving FHB and STB disease resistance.In the three environments Harzhof 2012, Harzhof 2013 and Rosenthal 2013 FHB and STB disease severities were scored on the same plots, but we observed no significant correlations between FHB and STB disease severity values for all three environments  larger than zero observed for all environments . These levels of Pearson moment correlation are characteristic for diseases where susceptibility is controlled by multiple gene loci. Consequently, multi-location field trials are needed to precisely estimate the genotypic value for FHB and STB disease severity.FHB and STB disease pressures were high in all environments as reflected by the wide range of phenotypic values and genotypic variances significantly (P < 0.01) larger than zero. Heritability estimates for lines and hybrids were high and similar for both traits  were low to moderate and amounted to 0.58 for FHB and for 0.23 STB  between both disease severities was detected  lines were crossed as males in a factorial scheme with 120 female lines by the use of chemical hybridization agents, yielding sufficient seed for field trials from 1604 F1 hybrids [Fifteen European winter wheat  to 9 (fully susceptible).The population of 1749 genotypes was also evaluated for STB disease severity at three locations in the year 2012 and at five locations in the year 2013  separately for the two environments with replicated data. In the next step, we used these BLUEs along with the raw data from the other five environments without replications and carried out an analysis of variance across environments as outlined in detail in . In addiDNA was extracted according to standard procedures from all genotypes and fingerprinting was performed with a 90 k SNP array based on an Illumina Infinium assay . All marData from each environment were used in association mapping scans correcting for population stratification with a kinship matrix . Kinshipπ [Based on the adjusted entry means of all genotypes, we applied Ridge Regression Best Linear Unbiased Prediction (RR-BLUP)  and Bayeπ , 44 consπ . All staπ .π using cross validations. In this work, we sampled 100 times 600 hybrids, 10 of their male, and 80 of their female parental lines as the training set, and estimated the additive and dominance effects applying the genomic selection as well as the association mapping models outlined above. For the association mapping approach, we corrected for population stratification with a kinship matrix and identified significant marker-trait associations. The implementation of the two genomic selection models was based on estimates of the genetic variances and the broad-sense heritability on an entry-mean basis of the full population. We tested the accuracies of prediction for three types of test sets with gradually decreasing degrees of relatedness to the training set. The most closely related test set T2 included different hybrids derived from the same parental lines as the hybrids evaluated in the training set, while the less related test set T1 included hybrids sharing one parental line with the hybrids in the training set and the least related test set T0 included only hybrids having no parental lines common with the hybrids in the training set [We evaluated the accuracy of prediction of FHB and STB disease severities by association mapping and two genomic selection approaches RR-BLUP and BayesC ning set . Predict2 values classes: 0.2–0.4, 0.4–0.6, 0.6–0.8, 0.8–1.0).We performed a simulation study to examine the power to detect QTL in our association mapping approach using our 90 k SNP array data. Following , we simuThe data is stored under Dryad Digital Repository: doi:10.5061/dryad.461nc.This study did not involve taking actual samples from humans or animals.


We develop a framework to consistently define cities, using commuting to work and population density thresholds, and construct thousands of realizations of systems of cities with different boundaries for England and Wales. These serve as a laboratory for the scaling analysis of a large set of urban indicators. The analysis shows that population size alone does not provide us enough information to describe or predict the state of a city as previously proposed, indicating that the expected scaling laws are not corroborated. We found that most urban indicators scale linearly with city size, regardless of the definition of the urban boundaries. However, when nonlinear correlations are present, the exponent fluctuates considerably.Cities can be characterized and modelled through different urban measures. Consistency within these observables is crucial in order to advance towards a science of cities. Bettencourt  There is however little understanding on how all the different features interweave and co-evolve. Certain properties such as morphological attributes, e.g. fractality of cities ,2, Zipf Y(t) and N(t) represent the urban indicator and the population size of a city at time t respectively, and Y0(t) is a time-dependent normalization constant. It is conjectured that the nature of the urban observable will unequivocally define one of the three universal categories to which the scaling exponent β belongs: (i) β < 1, a sublinear regime given by economies of scale associated with infrastructure and services, e.g. road surface area; (ii) β ≈ 1, a linear regime associated with individual human needs, e.g. housing and household electrical consumption and (iii) β > 1, a superlinear regime associated with outcomes from social interactions, e.g. number of patents and income  persons per hectare. For each integer threshold ρ0 in the interval, we cluster all adjacent wards with density ρw such that ρw≥ρ0. If a ward k has a density ρk < ρ0 but is surrounded by wards such that for each ward w, ρw ≥ ρ0, then the ward k is also included in the cluster. The resulting city area is hence a continuous surface. We obtain 40 different realizations of systems of cities for E&W, varying from very large clusters containing various settlements, to clusters containing only the core of cities for the highest density values . We define the parameter for population density y values .Figure a), and the jump corresponds to the merging of Liverpool and Manchester. Given that these two cities are very close, we select the density threshold ρc = 14 prs ha−1, which is near the transition and before the joining takes place. It is important to note that this choice is not unique, and the properties and results that we will show below hold for a range of choices of ρ. The system of cities defined at ρc has a Zipf distribution of city sizes2, figure 3b, and the boundaries, displayed as black contours in figure 3c, show an excellent overlap with the built areas (red clusters in the map) derived from remote sensing [ρc = 14 prs ha−1 are therefore a good proxy for a definition of cities vis à vis of their morphology, i.e. the urbanized space.For a range of densities, the algorithm produces realizations that are in very good agreement with the identified urbanized areas. One of many possible good realizations can be determined by looking at transitions in the cluster sizes resulting from the change in density from high to low values. The largest cluster exhibiting a sharp transition is the third biggest one rank 3; a, and th sensing . Cities 4.Metropolitan areas correspond to urban agglomerations linked together through socio-economic functionalities. We construct such areas by considering the density-based cities as destinations of commuter flows. For each city, we add the areas that are the origins of its commuter flows.In order to include small settlements as origins rather than destinations of commuting flows, we impose a minimum population size on the initial clusters, such that only the larger settlements are considered commuting hubs. The data on commuter flows at the ward level are taken from the 2001 census of the UK .ρ0 ∈ {1, 2, … , 40} prs ha−1, we impose a minimum population size cut-off N ≥ N0 for each of the clusters, where N0 ∈ {0, 104, 5 × 104, 105, 1.5 × 105} individuals.3 We remove smaller clusters to allow their constituting wards to be part of larger clusters, as is the case of satellite settlements around London. For every given ward, we compute the percentage of individuals commuting to each of the clusters out of the total number of commuters from the ward. The ward is added to the cluster that receives the largest flow if the flow is above a threshold4τ0. We investigate all the different realizations for τ0 ∈ {0, 5, … , 100}% individuals commuting from a ward to a cluster. The extreme value of τ0 = 100% reproduces the original system without commuting as the percentage of commuters from a given ward cannot exceed 100%. The other extreme value of τ0 = 0% in which a ward is added to a cluster if a single individual commutes to it, leads to an almost full coverage of E&W, where nearly every ward belongs to a cluster.In detail, this second algorithm works as follows. For each density realization ρc = 14 prs ha−1, a minimum population size of N = 5 × 104 individuals and different flow thresholds τ, are pictured in 4 realizations of systems of cities that serve as a laboratory to assess the behaviour of the scaling exponent in equation (1.1).Specific realizations for the density cut-off of 5.ρc = 14 prs ha−1 , whereas for the cut-off of 5 × 104 individuals, linearity cannot be rejected. The absence of robustness for the scaling exponent for these two cases suggests that there is a lack of self-similarity for the full range of scales examined. This brings into question whether a minimum population size for settlements should or not be considered. Such a behaviour is often observed in systems that present power laws only for the tail of their distribution. Nevertheless, in this case, this variable has zero values for many of the clusters, leading to a substantial amount of zero counts, including cities as large as of the order of 105 individuals. These are given in the form of percentages in the plot.Scatter plots of patents and city size are shown in The sensitivity of the scaling exponent to the population size cut-off indicates, on the one hand, that the value of the exponent can bear no real significance on the behaviour of the system. On the other hand, this urban indicator is unable to present a quantifiable measure over 10 years for some large cities. This suggests that such a measure might be inadequate to properly quantify innovation.In addition, the plots indicate that the most productive cities relative to size are not the biggest ones, but places that are highly rooted in education, such as Cambridge and Guildford or places corresponding to technological and business hubs. The latter are strategically located in the M4 corridor: e.g. Newbury (headquarters of Vodafone) and Slough , or are equally well connected to other strategic transport links within the Greater South East , such as7.β, to the different boundaries of cities and metropolitan areas. We make use of heat maps to illustrate the value of β, where the horizontal axis represents the parameter for the density threshold, and the vertical axis the parameter for the percentage of commuters in the clustering algorithms.In this section, we look at the sensitivity analysis of the scaling exponent a clearly shows that for total income, population size does not convey any information on agglomeration effects, showing homogeneity throughout the map for all the different city demarcations. The same results were found for many other variables where superlinear exponents were expected, such as employment categories reflecting economic activity or requiring highly skilled individuals . On the other hand, the heat map in figure 7b shows that for variables that present nonlinear dependencies, such as patents, the scaling exponent is sensitive to boundary definitions.The heat map in figure 78.dragon-kings. A statistical test showing that London can be classified as such can be found in the electronic supplementary material. A two-system theory of cities might then emerge: a regime for cities driving international dynamics, the dragon-kings, and a regime for the remaining cities composing a country.We showed that for all the different definitions of cities and metropolitan areas devised with our methodology, population size does not fully grasp the economic intricacies that constitute a system of cities in E&W. Looking at possible causes of discrepancy between our results and those previously found, it is evident that London plays a special role within the urban system of the UK. Its strong role as an information and economic hub suggests that the urban system is highly integrated and that it is difficult to partition the system into individual cities that capture these social interaction effects. On the other hand, if these economic functional areas are integrated following our methodology, we observe that for most urban indicators, London overperforms with respect to all other places in E&W. Its position as a primate city , but mosIn addition to economic hubs, one also encounters knowledge hubs, which also present dragon-king-like qualities and which are not necessarily correlated with size. These hubs are the outcome of path-dependencies that give rise to emergent properties that are not present in all cities as is the case of patents. This is most dramatically demonstrated by the dominance of patent production in Cambridge, UK.2 emissions, present conflicting results. Some studies have found a sublinear relationship, whereas others have found a superlinear relationship between CO2 emissions and city size [There are many difficulties in measuring the performance of a city through scaling laws. As discussed, there are problems in defining innovation in terms of patent counts, and this is not a unique case, other variables, such as COity size –37. SuchAll this indicates that a theory of cities cannot rest simply on a relationship like equation (1.1), because relevant patterns pertaining to social behaviour, such as the well-known Pareto distribution of wealth, cannot be grasped if only aggregated values are considered. A theory of cities needs therefore to reproduce the main relevant emergent behaviours that are encoded in the diversity and heterogeneities of cities. It is only through this perspective that city planning and policy making can be effective.


Relictus solitarius, is a Great Basin endemic cyprinid with a native range that is restricted to four valleys in eastern Nevada. Relictus solitarius now occupies spring systems that are the remnants of Pleistocene-era pluvial lakes, although it may have occurred in the area for much longer. Here we use mitochondrial DNA sequence data to assess range-wide genetic diversity of R. solitarius, and to estimate divergence times to determine whether pluvial drainages played an important role in shaping intraspecific genetic diversity. Genetic diversification within R. solitarius began during the early to mid-Pleistocene, separating populations within two sets of valleys (Butte/Ruby and Goshute/Steptoe). Additional diversification in each of the two sets of valleys occurred more recently, in the mid- to late-Pleistocene. Holocene desiccation has further isolated populations, and each population sampled contains unique mtDNA haplotypes. Pluvial drainage patterns did contribute to the genetic structure observed within R. solitarius, but most of the intraspecific diversification does not appear to be associated with the Last Glacial Maximum. Holocene desiccation has also contributed to the observed genetic structure. The relict dace populations we sampled are all unique, and we recommend that future management efforts should strive to preserve as much of the genetic diversity as possible.Changing drainage patterns have played a significant role in the evolution of western North American aquatic taxa. Relict dace,  Western North American drainage patterns have been dramatically altered throughout the Cenozoic as a result of a myriad of geological processes and global climate shifts. The modern Great Basin comprises a series of endorheic hydrological basins (closed drainages with no outlet to the ocean). These basins formed as a result of the uplift and episodic extension of western North America, beginning in the Eocene. The westward extension of the Great Basin continued through the Miocene, and is still underway ,2. TheseClimatic oscillations during the Pleistocene also played a significant role in the evolution of the western North American biota by forcing organisms through a series of range contractions, expansions, and shifts as glacial ice sheets expanded and retracted . The incRelictus solitarius, is a narrowly distributed Great Basin endemic cyprinid [R. solitarius is confined to four closed basins in the north-central Great Basin: Butte Valley, Goshute Valley, Ruby Valley, and Steptoe Valley in eastern Nevada  and Lake Waring  likely occurred, although they did not speculate on the direction of this postulated dispersal event. No clear overflow connections exist between the two pairs of valleys (Butte/Ruby vs. Goshute/Steptoe), as satellite imagery does not show any signs of scarring similar to the aforementioned connections between the other valleys. However, other biogeographic signals demonstrate western North American aquatic connections for which there is little to no geological evidence [Geomorphological evidence shows inter-basin spillover connections between Butte Valley and Ruby Valley ,38, thusevidence ,10,12,34R. solitarius currently resides. Hubbs et al. [R. solitarius was in just one valley (but did not speculate about which one) and dispersed among pluvial drainages through these aquatic connections in a short period of time. It was long thought that R. solitarius populations within these four valleys had not differentiated based on lack of morphological differences across the species’ range [R. solitarius populations has yet to be determined.The postulated connection between Lake Franklin  and Lake Waring  would have provided a Pleistocene-aged aquatic connection between the four valleys where s et al.  hypothess’ range ,36. Howes’ range , althougR. solitarius and determine the timing of Pleistocene and Holocene impacts on that structure. Any inter-basin gene flow that occurred during the Wisconsin glaciation would have ceased as pluvial drainages dried with the onset of Holocene desiccation. If so, divergence times may correspond to a late-Pleistocene/early-Holocene time frame. Alternatively, it is plausible that diversification within R. solitarius occurred earlier in the Pleistocene, as pluvial lake levels fluctuated with glacial and inter-glacial cycles. Another alternative is that R. solitarius divergence times pre-date the Pleistocene, corresponding to ancient changes to the landscape and they did not disperse through pluvial drainage connections . The latter alternative is plausible given divergence times between Relictus and other genera that are Pliocene in age with confidence intervals spanning from late-Miocene to mid-Pleistocene [In this study, we used mtDNA sequence data to assess the range-wide genetic structure of istocene , and thaR. solitarius, we generated phylogenies using Bayesian inference and maximum likelihood. We also constructed a haplotype network to better visualize the finer-scale phylogeographic structure. We estimated divergence times among major clades within R. solitarius to determine whether splits were Pleistocene in age and, if so, whether they were in the early, middle or late-Pleistocene. We also explored genetic variation at hierarchical geographic levels to determine which level best explains the observed variation.To assess the evolutionary relationships among populations of b sequences  ND2 sequence (GenBank: EU158191) and amino acid sequence as references. We concatenated both mtDNA genes prior to performing phylogenetic analyses after a likelihood ratio test showed no significant difference between models selected for each gene separately (p > 0.05). Sequences from northern pikeminnow (Ptychocheilus oregonensis) and hardhead  were included in the alignment as outgroup taxa because they are closely related to relict dace [We used purified PCR products as templates for cycle-sequencing reactions, and carried out Sanger sequencing according to methods described by Houston et al. , the onln et al. . We aligict dace ,13,41, aWe performed analysis of molecular variance (AMOVA) using Arlequin v.3.11 . SamplesWe used jModeltest2 v.2.1.4  as impleWe performed Bayesian analysis using MrBayes v.3.2  employinTo better visualize intraspecific mtDNA genetic diversity, we generated a haplotype network using TCS v.1.2.1 , using tWe generated molecular dating estimates using the uncorrelated lognormal relaxed clock in the program BEAST 1.7.5 . We usedb (previously published) from 79 relict dace individuals representing 8 populations. There were 2187 total characters in the final alignment, 458 of which were variable. All DNA sequences have been made publicly available in GenBank .Pluvial drainage patterns shaped the early genetic diversification among populations of istocene . It is wR. solitarius. The results of AMOVA indicate that the majority of the genetic diversity within the species (~82%) is explained by within population variation . BYU accession numbers, the number of individuals sampled from each populations, and GenBank accession numbers for both the cyt (DOCX)Click here for additional data file.


Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.Descendants from the extinct aurochs (We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources. Thus, AAiming at an unbiased view of genetic structure and differentiation between taurine and zebu cattle breeds from distinct continental areas, we compiled a worldwide multi-breed AFLP dataset. We do not intend to suggest the use of sparse panels of molecular markers over the present portfolio of high-density SNP arrays, or to interrogate their legitimacy for diversity research in cattle. Instead, we intend to propose an unbiased model of cattle differentiation which complements the assessment of genetic distance estimates obtained from molecular markers that are likely to suffer from ascertainment bias.et al. [A total of 1,593 individuals were genotyped for 135 AFLP markers, representing 13 zebu and 58 taurine breeds. The presence (genotype ‘1’) or absence (genotype ‘0’) of a band was scored considering AFLP as dominant markers, and occasional faint bands were considered as missing data. These samples were obtained from 23 countries from 9 distinct continental areas: Southern Asia (3 zebu breeds), Southwestern Asia (2 taurine breeds), Eastern Europe (3 taurine breeds), Central Europe (24 taurine breeds), Northern Europe (10 taurine breeds), Southern Europe (10 taurine breeds), Western Europe (8 taurine breeds), Western Africa (7 zebu breeds and 1 taurine breed), and South America (3 zebu breeds). This dataset builds on the data reported by Negrini et al.  by incluAFLPsurv v1.0[ST[base package in R v2.15.0[n-1 dimensional spaces of n observations (eigenvectors), where n is the number of groups, via classical multi-dimensional scaling (CMDS) [SPLITSTREE v4.13.1[We used surv v1.0 to calcuv v1.0[ST, Nei’s Dv v1.0[ST and Reynv v1.0[ST. We grouR v2.15.0 to perfog (CMDS) . The proE v4.13.1.AFLPsurv v1.0[ad hoc statistic to identify taurine and zebu ancestry informative markers . For each AFLP marker, we computed the band presence frequency across all breeds, and then calculated the mean for the pool of taurine and zebu breeds. We then calculated the difference in band presence frequency as Δf = ftaurine − fzebu. Positive and negative values indicate markers that are informative of taurine or zebu ancestry, respectively. We used thresholds of +0.55 and −0.55 to identify taurine and zebu ancestry informative AFLP markers, respectively. Finally, the average of band presence frequency of informative markers was computed for each breed in order to assess the relative level of taurine/zebu introgression across the investigated breeds.With the particular interest of identifying geographical patterns in the extent of genetic diversity in the cattle breeds analyzed, we used surv v1.0 to calcuSTRUCTURE v2.2[K ancestral populations, and the proportion of the individuals’ ancestry from each one of these populations is estimated via a Markov chain Monte Carlo algorithm. The assumption that the alleles are independent (i.e. linkage equilibrium) is reasonable in the present study, as the AFLP panel used is sparse and the markers are unlikely to be closely located on the genome. We applied this model from K = 1 to K = 60, and ran 5 replicates of 150,000 iterations for each analysis after a burn-in of 100,000 iterations [We estimated individual ancestry coefficients as parameters of a statistical model, following the Bayesian approach implemented in TURE v2.2. This isTURE v2.2,30 for derations .K statistic described by Evanno et al. [K values. The second method was abstracted from the approaches for model selection reviewed by Johnson & Omland [AIC) is calculated for each model, from K = 1 to K = 60, as follows: AIC = 2p − 2 ln(L), where p and 1n(L) are the number of parameters and the log-likelihood of the estimated model, respectively. Next, AIC differences are calculated for each model i as Δi = AICi − AICmin, where AICmin corresponds to the lowest AIC among all models; and relative likelihoods are computed as K models to produce Akaike weights K.We applied two methods to identify the most likely number of ancestral populations underlying the observed data. The first method uses the ∆o et al. , which i& Omland , and is After the exclusion of individuals exhibiting 5% or more missing genotypes, 1,470 animals remained from the initial set of 1,593 (see Table Different genetic distances were highly correlated (data not shown) and yielded consistent results . In contrast, in spite of a possible contribution of Spanish ancestry to Brazilian cattle, Brazilian and Spanish breeds are well separated with the largest distance between Nellore and the inbred Betizu (Reynolds’ distance = 0.656).The first two eigenvectors of the CMDS analysis of continental groups of cattle Figure B explainK = 1 to K = 60, were compared using ∆K and AIC weights in order to identify the most likely number of ancestral populations underlying the samples. Both ∆K and AIC weights selected the model with K = 2 as the most likely among all competing models . This indicates that models with K > 2 were susceptible to stochastic errors and represented poorly the underlying ancestry components of our samples. This may be due to model overfitting, by estimation of more parameters than allowed by the observed data. Hence, for our dataset, the model-based clustering analysis was limited to K = 2 due to the low number of dominant markers and estimation of unobserved genotypes.Higher f, and calculated the average band presence frequency for these markers across all breeds .Click here for fileBar plot of expected heterozygosities for each continental area. Error bars represent standard errors. Abbreviations as for Additional file Click here for file


Picoides borealis) creates opportunities to achieve financial and conservation goals simultaneously. Reversing the effects of habitat fragmentation is one of the main reasons for developing markets. I include uncertainty in habitat fragmentation effects by evaluating market transactions using five alternative dispersal models that were able to approximate observed patterns of occupancy and movement. Further, because dispersal habitat is often not included in market transactions, I contrast how changes in breeding versus dispersal habitat affect credit values. I use an individually-based, spatially-explicit population model for the Red-cockaded Woodpecker  to predict spatial- and temporal- influences of landscape change on species occurrence and genetic diversity. Results indicated that the probability of no net loss of abundance and genetic diversity responded differently to the transient dynamics in breeding and dispersal habitat. Trades that do not violate the abundance cap may simultaneously violate the cap for the erosion of genetic diversity. To highlight how economic incentives may help reduce uncertainty, I demonstrate tradeoffs between the value of tradable credits and the value of information needed to predict the influence of habitat trades on population viability. For the trade with the greatest uncertainty regarding the change in habitat fragmentation, I estimate that the value of using 13-years of data to reduce uncertainty in dispersal behaviors is $6.2 million. Future guidance for biodiversity markets should at least encourage the use of spatially- and temporally-explicit techniques that include population genetic estimates and the influence of uncertainty.Markets for biodiversity have generated much controversy because of the often unstated and untested assumptions included in transactions rules. Simple trading rules are favored to reduce transaction costs, but others have argued that this leads to markets that favor development and erode biodiversity. Here, I describe how embracing complexity and uncertainty within a tradable credit system for the Red-cockaded Woodpecker ( Homo sapiens, which may have flourished thanks to trade  − EV[Tp|M]). If EVPI is positive then reducing uncertainty, through further data collection, may lead to a different trade that provides greater conservation benefits.The expected value of learning the true dispersal behaviors can now be estimated as the expected value of perfect information (DSS) for the trade providing the highest EVPI for abundance credits [DSS was simply estimated as EV[M|T] − EV[Tp|DSS], where EV[M|T] is the expected value of knowing the true dispersal model included in the POM set, as estimated above.To value the new information acquired by POM relative to the old information provided by model 6(DSS), I calculated EVPI relative to model 6(DSS)  plus 8% profit .Given the strong impact that habitat fragmentation, independent of habitat amount, has on genetic diversity, and strong impact of habitat area, independent of habitat fragmentation, has on abundance , I assumThe total revenue expected by the banker to offset costs to restore and maintain 25 territories plus 8% profit would be $22,342,733 . CreditsAbundance credits available in the bank  were morFor abundance, there was a net decrease in the number of credits in the bank due to the loss of habitat in areas A and B, regardless of whether takes occurred individually or in series, or whether matrix habitat was static or decreasing . Though When considering two takes occurring in series separated by five years, assuming a static matrix , the median credits remaining for abundance were close to zero for all models selected by POM, and less than zero for model 6(DSS). Allowing more time between takes  increased the number of abundance credits remaining for all models. Therefore, landscape transient dynamics affect abundance credits. The influence of transient dynamics on abundance indicates why basing trades on geometric indices indicative of the relationship between landscape and biodiversity patterns at one moment in time will be unable to predict the influence of landscape change in the future . However, bootstrapped distributions of remaining credit values were often similar regardless of whether take A proceeded B, or vice versa, though allowing more time between trades led to greater differences between the AB and BA treatments. Whether the remaining credits increased, decreased, or stayed about the same due to declining matrix habitat varied by dispersal model.Whether a take resulted in a net decrease or increase in credits for genetic diversity, relative to the number of credits available in the bank , often varied by take and dispersal parameterization Figs  and 4. OWhen takes A and B occurred in series, a median net increase in credits for Dst was often observed when A was taken before B, and no change or a slight decrease in credits was often observed when B preceded A. In contrast, credits for Hs often indicated a net decline in median credits relative to the number of credits available in the bank regardless of whether A preceded B or vice versa. It was surprising to see that the time interval between takes differing by as a little as five years or as much as 20 years did not strongly affect the magnitude of network externality. The order of trades had a more important impact on network externalities, determining whether network externalities are positive or negative. Therefore, the order of takes affects conservation value of connectivity. These results agree with a recent study of tiger salamanders in which wetland area and connectivity had a bigger influence on genetic divergence among breeding populations than wetland age or hydroperiod .The presence of a declining habitat matrix affected genetic credit values more under some dispersal models than others. For model 3 and trade B under a declining matrix , an increase in fragmentation effect was observed, as estimated by median credit values for Hs < 0, and yet a positive balance for abundance credits remained. Therefore, if median values for genetic credits were used to assess if the cap on network externalities was violated, then trade B would not be a viable trade if the habitat matrix were expected to decline. Therefore, the loss of unregulated dispersal habitat may prevent mitigation banking from protecting conservation values.Results for genetic credits indicated that network externalities may be positive or negative depending on the order in which the trades occur. Large dimensionality of spatial problems is often the barrier to applying spatially- and temporally-explicit techniques , 31, butDecision analysis indicated that when comparing treatments assuming static matrix habitat, that the EVPI was often zero for abundance credits . The excThe value of learning the true dispersal model , based on abundance credits, was greatest when contrasting take A or B in static versus a declining matrix. Given the price of credits, this leads to the estimated value of learning the correct dispersal behaviors to be $467k to $987k, with the greatest value observed when contrasting take B in static versus declining matrix. Thus, differences in landscape change  affect EVPI. In other words, the magnitude with which dispersal models disagree regarding which is the best trade will vary by the landscape change being compared. It is important to note that the an EVPI of $877k (Bmatrix vs B), does not mean that if we spent that sum on collecting more data that we are guaranteed to save $877k by making smarter trades thanks to a more certain model. EVPI represents the amount of money that could be saved if further research indicated that the dispersal model leading to the greatest LSYs remaining under each trade is indeed the true model. From this perspective it is more compelling that the comparison of most trades indicated an EVPI of zero, indicating the usefulness of POM and contradicting the early criticisms of IB-SEPMs , 58.For genetic credits, EVPI was greatest when comparing take A assuming a static versus a declining matrix. In fact, results indicated that EVPI, measured in LSYs, was greater for genetic credits than abundance credits. Therefore, there is greater disagreement among dispersal models regarding the impact a declining matrix would have on the retention of genetic diversity within and among breeding groups for take A.Interestingly, EVPI for Hs credits were greater than zero when determining whether it would be better to separate take B followed by A by five or 20 years . Therefore, while it is clearly best for abundance to allow for more time between trades, we are uncertain if allowing more time would lead to a greater retention of average expected heterozygosity within breeding groups.If the revenues from EV[T|M] are sufficient and the probability of no net loss of abundance and genetic diversity are high , bankers might decide to forego data collection, even if EVPI>0, and implement trades. After all, bankers will want to sell as many credits as they can, as fast as they can. Alternatively, if EVPI were high and the probability of no net loss of abundance or genetic diversity were low , the present analysis provides economic and ecological justification to forego a trade and collect more data.DSS. The greatest EVPI for abundance was observed for Bmatrix vs B. Therefore, I calculated EVPIDSS based on the comparison of these trades. EVPIDSS was 0.989 LSYs N (EV[M|T](2.16) − EV[B|DSS](1.17)), which is seven times greater than EVPI estimated using current information (0.137 LSYs N) for trades Bmatrix vs B. Using the banker’s current estimate of prices for abundance credits that would be a potential savings of $7.15 million. This value represents the cost of making a decision while ignoring uncertainty and lacking perfect knowledge [The value of applying 13-years of monitoring data within an IB-SEPM using POM relative to making decisions using past knowledge (DSS) was assessed by the estimate for EVPInowledge . Therefonowledge  were colnowledge .These results indicate the importance of spatial-, temporal-dynamics for conservation banking markets. To the best of my knowledge this represents the first comparison of changes in abundance and genetic diversity assuming dynamic breeding and dispersal habitat, and including spatial-, temporal- feedback mechanisms. It would be best to revise the conservation banking guidance to, at a minimum, encourage the use of spatially- and temporally-explicit techniques that estimate changes in population genetic metrics at a landscape-scale.While it has long been recognized that establishment of a bank can lead to habitat defragmentation, we have shown here that habitat trades themselves  can lead to habitat defragmentation estimated using population genetic theory. This poses policy challenges on four fronts. First, traditional interpretations of take and jeopardy do not include changes in network externalities . Second,No requirement for validation is included when determining if science is “available” under the ESA, so tradable credit systems could be developed using methods that have not been shown to be predictive of habitat occupancy or genetic diversity in dynamic landscapes. If we are willing to exchange habitat for such populations then we should also be willing to test our assumptions about how land use change affects population viability. If available data are excluded when evaluating trades due to administrative constraints, then an understanding of the potential conservation cost of using simple metrics should at least be expressed.Mitigation banking trades uncertain benefits for certain losses . TherefoOthers have contrasted the ability of IB-SEPMs to inform landscape management decisions with more simple landscape models, some have found important differences  while otGranted, RCW management has benefited from the availability of an IB-SEPM constructed with 15-years of monitoring data , which iThe integration of POM and LEA outlined here would be useful in passive adaptive management. Adaptive management is a method of incorporating the role of uncertainty in decision-making by treating decisions as hypotheses regarding the system’s response to management actions . PassiveWhen working to ensure trades do not decrease population viability at a landscape scale, our ability to monitor and detect changes in rates of migration, drift, inbreeding, and local extinction will be limited, a problem referred to as partial observability . Recall Walker et al.  argued tS1 Appendix(DOC)Click here for additional data file.S1 Table(DOC)Click here for additional data file.