Bretz 1 Kaitlyn Bretz Dr. Bert Ely BIO 303: Genetics 1 Nov 2013 Population genetics: the analysis of coral populations in various reef systems, and how genetics play a role in designing regional conservation programs Coral reefs are the ocean’s most diverse ecosystems; they harbor an enormous number of marine species, and are one of the most fragile environments on the planet. As marine scientists struggle to find ways to protect and conserve these valuable reefs from climate change and other anthropogenic impacts, several critical questions need to be addressed: what coral species are crucial to the survival of reefs, and how these species have spread across the ocean. These seemingly straight-forward questions have multiplied in their complexities as scientists have come to realize that today’s identified species may not be the true species delineation, that coral genetic migration is drastically affected by different modes of reproduction and larvae viability, as well as the effects of physical barriers in and around reef systems. A combination of multiple studies, centered on genetic determination of species and genetic flow and diversity for various populations, allows for scientists to begin generating tentative responses to the initially proposed questions. From those conclusions, scientists can create rudimentary guidelines to aid in international conservation efforts. The development of advanced technology has taken genetics and propelled it to the forefront of scientific research; new procedures, faster and smarter computers, and better technology have allowed scientists to collect and analyze more data than they had ever before. The analysis of organisms’ entire genomes, for instance, is now possible, and has been instrumental in the determination of species differentiation. Pinzón et al. (2013) designed a project to identify the coral species in the genus Pocillopora, a hard coral found throughout the Indo-Pacific region. This coral is “common, ecologically important, and widespread…but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution,” (Pinzón et al. 2013). Traditional morphological classifications are based on skeletal and colony features, however due to disparity in taxonomy, scientists have recognized anywhere from 17 species (Veron 2003) to 7 species (Cairns 1999) of this genus. Pocillopora corals are one of the most susceptible reef-building corals to rapid climate change and it is necessary to conserve its multiple species. Through the collection of samples and analysis of internal transcribed spacer 2 (ITS2), mitochondria open reading frame loci (ORF) and seven microsatellite loci, Bretz 2 Pinzón et al. (2013) were able to provide significant evidence that current special divisions are incorrect and that scientists need to redouble their efforts into classifying the natural world prior to conserving them. Samples of Pocillopora were collected from reefs all over the Indo-Pacific region, although some previously collected data from Pinzón and LaJeunesse (2011) were used. These collections were identified by their morphospecies using photographs and when possible, were verified with local experts. DNA was extracted from the skeleton and tissue samples and then the internal transcribed spacer 2 (ITS2) and mitochondrial loci open reading frame (ORF) were amplified with their respective primers. The resulting ITS2 and ORF data were sequenced, reviewed, edited and aligned by various programs. Two separate phylogenies were created for ORF and ITS2 to show possible Pocillopora speciation. Seven microsatellites for Pocillopora species were already described from prior research (Starger et al., 2008; Pinzóne & LaJeunesse, 2011), so Pinzón et al. (2013) identified the loci, marked them and ran them through PCR so they could analyze the data. Hardy-Weinberg equilibrium in each phylogenetic group was also analyzed. ORF sequencing resulted in the identification of 21 distinct haplotypes from the 906 samples collected. Eight well-differentiated groups were distinguished, and the haplotypes that differed by more than five or six base changes were assigned to types 1 to 8 (Figure 1). ITS2 analysis (Figure 2) was largely concordant with the ORF data, however ORF types 4 and 7 were unresolved and ITS2 type 8 could not be amplified. ORF type 1 was divided into 2 groupings, type 1 and type 9 because of a comparison with microsatellite data. The parallel between the ORF and ITS2 data indicated that each type/group represented “genetically isolated groupings or discrete species”; these results were tested by further analyzing the data from microsatellite markers. These markers held an entire data set of genotypes, comprised of 806 samples, which were used to identify populations that covered isolated gene pools. The seven loci “conservatively delimited at least five but no more than seven genetically cohesive Indo-Pacific populations” (Pinzón et al. 2013). Hybridization was also taken into account and the results obtained varied by geographic location: for example, samples collected in Hawaii showed five reproductively isolated lineages and with further analysis Pinzón et al. (2013) found that there was a 9.7% admixture among genotypes, a higher than normal hybridization, whereas samples collected in California contained only one single genetic lineage, with no population subdivision or hybridization (Figure 3). Overall, hybridization was inconsequential at many locations. Bretz Figure 1: Mitochondrial ORF unrooted parsimony tree 3 Bretz 4 Figure 2: ITS2 ribosomal DNA rooted parsimony tree and geographical distributions observed for rare or less common Pocillopora types. With a more in-depth comparison of ORF, ITS2, and microsatellites, there were some difficulties discovered, mainly in differing resolutions of the data: differences in sibling lineages, the possibility of haplotypes 3h-j and 7 belonging to a single homologous species, and the disparity between types 2 and 6 as separate lineages or one type. Major groupings defined with a large resolution were usually agreeable, yet the smaller divisions between populations and close-related sibling lineages were difficult to differentiate and weren’t always accurate. This incongruence could be corrected by an increase in sample size, finer statistical resolution, or further development and application of additional and variable microsatellite loci. Pocillipora has relatively low species diversity compared to other widespread genera. This could be explained by the lack of hybridization and a temporal difference in spawning, which minimizes the Bretz 5 chances of recombination between species. Also, “high connectivity that persists over time ultimately minimizes the potential for allopatric speciation, and may further explain why species diversity…is low,” (Pinzón et al., 2013). Thus, low hybridization has allowed several species to spread throughout the IndoPacific region; however interspecific recombination doesn’t occur frequently enough to break down genetic differentiation that occurs between widespread types. On this note, low species diversity means a small number of species present in the Pacific, and this does not correlate with the current number of accepted morphospecies. This frequent “discordance between morphology and genetics over broad geographic scales could lead to incorrect inferences about connectivity and hybridization,” (Pinzón et al., 2013). Such inferences in the past have led to incorrect classification of endemic versus widespread species, a key example being the disparity in species classification between Hawaii and California (Figure 3). Widespread species are more prevalent in Pocillopora than initially realized, as types 1, 3, 5 and 9 were all found to be homogenous over thousands of kilometers. Continental landmasses often restrict major ocean currents, limit genetic connectivity, and maintain “zoogeographical breaks” between oceans, and can also further separate species through ocean basins (i.e., the Arabian Peninsula and the Red Sea). Geographical factors may explain why several species were highly divergent, such as types 2 and 6, which were found only at Clipperton Atoll and O’ahu, Hawaii, respectively. The variances in geographic spread among Pocillopora could be accounted for by the different species’ reproduction methods: broadcast and brooding. Explained further in Underwood et al. (2009), Pinzón et al. (2013) determined that types 1, 3, 7 and 9 were broadcast spawners, while the brooders were types 4 and 5. The reproductive modes of types 2 and 6 were not available, but Pinzón et al. (2013) inferred from the coral’s phylogenetic placement and small geographical distribution that they were brooders. While hard corals (Scleractinia) are often broadcast spawners, Pocillopora corals use both broadcast and brooding modes of reproduction, which may explain why Pocillopora corals are less diverse, have low levels of hybridization and are found in certain geographical regions. Bretz 6 Figure 3: A comparison of Pocillopora morphospecies in Hawaii and California, and the results of genetic analysis from Pinzón et al. (2013) Out of the initial estimation of 21 species of Pocillopora, Pinzón et al. (2013) determined there to be anywhere between five and eight genetically distinct lineages in the Indo-Pacific region. Colony morphology was not an accurate indicator for true species differentiation, which resulted in Pinzón et al. (2013) determining that the general delineation of species diversity through genetics needs to take precedence over the taxonomic division based on morphology. Genetic identification of organism speciation will advance the general understanding of any species’ geographical distribution, ecology and evolution; the conclusions reached by Pinzón et al. (2013) concurred with many other studies completed prior to 2013, and all called for a larger reliance on genetic research for future ecological and experimental work. Corals have the ability to sexually reproduce in two ways: brooding or broadcast spawning. Spawning corals release eggs and sperm which then fertilize one another and leave developing zygotes to settle on a reef; broadcast corals become fertilized and then harbor the developing zygote until larvae is released to settle on a reef and develop into coral. Genetic variation is heavily affected by the different reproductive methods; scientists recognize that “long distance dispersal has…been associated with the production by outcrossed sexual reproduction of genotypically diverse propagules, which maintain genetic homogeneity of interconnected local populations…in contrast, restricted dispersal of propagules Bretz 7 is…associated with inbreeding, loss of heterozygosity, and increased genetic subdivision due to drift and site specific selection,” (Ayre et al., 2000). While this pattern is not guaranteed to match all marine organisms, Underwood et al. (2009), with their research on two reproductively different corals in northwest Australia, Acropora tenuis and Seriatopora hystrix, discovered that “levels of genetic subdivision among populations were markedly higher in the brooder than in the broadcast spawner…[which was] congruent with expectations based on life histories.” Beyond just reproductive methods, Underwood et al. (2009) also used high-resolution genetic markers to investigate temporal effects on reproduction, and their results have led to a conservation plan focused on the development of coral reef protection areas based around “routine dispersal distances” for key coral species. Underwood et al. (2009) collected samples from three locations in northwest Australia: Rowley Shoals, Scott Reef systems, and Browse Island systems. In total, 576 colonies of broadcast-spawning Acropora tenuis from the Rowley Shoals and Scott Reef systems, and 476 colonies of brooding coral Seriatopora hystrix were collected. GPS coordinates of each sample were recorded for the development of an x and y coordinate map. Corals which were likely to have been produced via asexual reproduction were avoided, and Underwood et al. (2009) came up with 98% of samples having unique multi-locus genotypes caused by sexual derivation. Final sample sizes averaged about 21 and 50 individuals being analyzed at each site. DNA was extracted from the samples, then separate genotyping procedures were used for each coral: eight microsatellite loci from Seriatopora hystrix and seven microsatellite loci from Acropora tenuis were analyzed. Two multiplex PCR were conducted using fluorescently labeled primers and then the products were analyzed. Genotyping errors were minimized by manually checking the PCR results and any uncertainties in the data were re-amplified and compared once more. Several tests were subsequently conducted, including Hardy-Weinberg equilibrium and FST approximations. HardyWeinberg estimates revealed that significant heterozygote deficits were detected at all sites for both species, meaning that these deficits were “common features of these populations…[and likely attributed]…to biological factors associated with spatial and/or temporal admixture and nonrandom mating within sites,” (Underwood et al., 2009). FST values were calculated to quantify the geographic genetic variation at different alleles, and represented three relationships between sites: system to system, reef to reef and site to site. The genotype likelihood ratio distance (DLR) is the “mean genotype loglikelihood ratio across individuals from the two populations,” (Underwood et al., 2009), and was calculated for pairs of sites for both species. A Principle Coordinate Analysis (PCA) allowed Underwood et al. (2009) to create a coordinate graph from the DLR genetic distance matrix (Fig 4). A spatial autocorrelation analysis was also conducted, which uses spatial positioning of the genetic identity of individuals as data, rather than a summary of statistics that FST and DLR rely on. The resulting data is then displayed as a ‘correlogram’; in effect, the data (Fig 5) can be interpreted by looking at two points: the x- Bretz intercept of the graph, the estimated distance where random effects of genetic drift are primary determinates of genetic composition, and where r begins to decline after an initial plateau, which is the limit of mixed genetic neighborhood and the distance past which the gene flow is limited. Finally, coral samples were tested to predict the likelihood of an individual belonging to a particular population (Bayesian analysis). This final test was where long-distance migrants were identified. Figure 4: Genetic differentiation between Rowley Shoals, Scott Reef System and Browse Island System (Underwood et al., 2013) 8 Bretz 9 Figure 5: Spatial autocorrelation analyses of the genetic correlation coefficient (r) as a function for distance for A. tenuis and S. hystrix gene flow/migration On a broad scale, there was a “clear lack of panmixis across…the study, with significant subdivision detected between systems, between reefs, and even within some reefs” (Underwood et al., 2009). There were also major differences in subdivisions between S. hystrix and A. tenuis and differences in genetic distance between the two species. FST values for the brooding coral (FST [excluding Browse Island]=0.191) were far higher when compared with the broadcast spawner (FST [excluding Browse Island]=0.034) indicating that the brooding coral has higher genetic diversity than the broadcast spawner; this pattern remained when Underwood et al. (2009) adjusted for null alleles. The genetic distances between the species (DLR) were similarly differentiated, as S. hystrix DLR(avg)=6.34 and A. tenuis DLR(avg)=0.06. These patterns displayed in the Principle Coordinate Analysis (PCA) plots (Fig 4) show the clear definition between systems: each reef is generally in a different quadrant of the graph and similar sites are relatively crowded together. Each graph also represents one species and comparisons of the site clusters show that S.hystrix (brooding) have more defined subdivisions between systems than A. tenuis (broadcast) does, indicating higher diversity, and there is also larger genetic distances between pairs of populations. On a more local scale, Underwood et al. (2009) discovered that S. hystrix has a smaller ‘genetic neighborhood’, meaning that “larvae are routinely [recruited] over much smaller distances in the brooder corals compared with the broadcast spawner.” Spatial autocorrelation analyses of the genetic correlation coefficient (r) shows the distances the two species were most likely to be recruited from certain systems: the r-values of S. hystrix cross the axis before A. tenuis at the Scott Reef system and Rowley Shoals (Fig. 5), indicating the brooder had more local recruitment. The Bayesian analysis, where Bretz 10 “no [S. hystrix] colonies were assigned to sites from different systems,” (Underwood et al., 2009), provides further evidence for the local recruitment hypothesis. On the basis of the their results, Underwood et al. (2009) summed up their conclusions with three broad conclusions: differences in the reproductive mode of coral species influence levels of genetic subdivision; many coral reefs are genetically differentiated; and panmixia is only generally observed over scales of tens of kilometers or less. Brooder corals generally had higher genetic subdivision than broadcast corals, and most brooder corals settled relatively close to their parent colony. S. hytrix, the representative brooder coral, had larvae that settled “within 100 meters of their parent colony, while most A. tenuis larvae…dispersed within reefs over distances of kilometers to a few tens of kilometers,” (Underwood et al., 2009). Observations of life histories for the coral larvae reflect and reaffirm these results. Studies conducted in laboratory conditions show that S. hystrix larvae “are competent to settle within six hours of release,” (Isomura and Nishihira, 2001), while the broadcast coral A. tenuis “are competent after 3-4 days,” (Nishikawa et al., 2003); these temporal differences in biological behavior provide further evidence for the pattern of more local dispersal for brooding corals when compared to dispersal of broadcast corals. However, there were some instances of rare longer-distance dispersal from both species. Several samples that had very little differentiation between sites demonstrate that once larvae drift beyond local influences they are able to disperse between reefs. These anomalies in the general pattern of the data allow for populations to stay relatively homogenized and to keep the species from completely differentiating, potentially saving environments from collapse by allowing other populations in separate reefs to restore dying populations. Overall, coral larvae had much more local recruitment than originally hypothesized and the relationship between close reefs remains an important subject of study. Studies on cross-ocean dispersal and genetic connectivity that also support the importance of reef self-recruitment of coral larvae are all developed from studies of sexually-reproduced propagules. However, “asexual reproduction is commonly regarded as important for local proliferation, whereas sexually derived propagules are thought to be important for larger-scale dispersal,” (Whitaker, 2006). Asexual recruitment can occur in two ways: clonal production of larvae or colony fragmentation. Understanding the importance of asexual reproduction and local recruitment is imperative for colony conservation, especially if scientists have been overestimating the importance of sexual reproduction in gene flow. The purpose of the Whitaker (2006) study was to examine genetic mixing of the hard coral Pocillopora damicornus between and within reefs, to quantify the level of asexual versus sexual reproduction, and to validate the importance of independent recruitment for genetic diversity. Bretz 11 Pocillopora damicornus samples were taken from 10 sites at two separate locations: the Ningaloo Reef (8 sites) and Houtman Abrolhos Islands (2 sites). 644 Growing tips from phenotypically-consistent P. damicornus were collected, frozen, and then had allozymes extracted and subsequently run through electrophoresis, where ‘six consistently scorable polymorphic loci were found after preliminary screening of 30 enzymes encoding 37 loci on 6 buffer systems,” (Whitaker, 2006). Hardy-Weinberg deviations were calculated at individual loci, and then two methods were used to estimate the extent of asexual reproduction: one test to estimate the maximum proportion of the sample that could be produced by sexual reproduction (N*:Ni), and another to observe multi-locus genotype diversity by comparing expected conditions assuming panmixis to the observed condition (GO:GE). For allelic variation, FST tests were conducted on two different sample groups: one with all individuals irrespective of the reproductive origin and the other with only individuals from sexual reproduction. The results of the Hardy-Weinberg estimations varied greatly from site to site. Out of the 10 sites tested, only two sites (3 and 8) matched Hardy-Weinberg expectations, and the other 8 sites varied even further by different amounts of heterozygous excess and deficits. Pairwise comparisons showed strong genetic subdivision at nearly all of the sites, despite having some evidence of sexual reproduction; the maximum proportion for sexual representation (N*:Ni) varied from 4% (site 10 ) to 100% (site 2) (Fig. 6). The ratio test (GO:GE) illustrating the relative importance of sexual versus asexual production revealed significant variation between sites as well: only sites 3 (0.770) and 8 (0.725) showed levels of genetic diversity which are similar to those under conditions with sexual reproduction (Fig. 6). Allelic variation from site to site didn’t vary however, as “samples from the Houtman Abrolhos Islands shared just as many genotypes with Ningaloo as did samples within Ningaloo,” (Whitaker, 2006). Figure 6: results from the ratio tests concerned with identifying the importance of sexual reproduction and multi-locus genotypic diversity Bretz 12 Reproduction methods of Pocillopora damicornis at the tested locations, Ningaloo Reef and Houtman Abrolhos Islands, showed that populations have dual modes of reproduction (asexual and sexual), “but that there is considerable variation in the relative contribution of each to those populations sampled,” (Whitaker, 2006). Of the 644 individuals sampled, only 96 (15%) were from ‘apparent sexual origin’; but note that this number may be biased due to inadequate quantification of asexual propagule dispersal, or to the limited number of loci sampled. The disparity between reproductive modes from siteto-site can be seen in a comparison of sites 1 and 4 with sites 3 and 8. Sites 1 and 4 were highly impacted by asexual reproduction, while there was little to no evidence of asexual recruitment from the latter sites. Asexual reproduction had been formally reported in populations around the Pacific, and evidence suggests that the majority of asexual recruitment is from brooded ameiotic planulae and coral fragments following storm activity. Scientists have not been able to determine if certain conditions favor one mode of reproduction over the other since no consistent pattern has been discerned, as the variation in importance of sexual and asexual reproduction fluctuates from population to population and differs from study to study. The high diversity of Pocillopora damicornis creates a complex population structure, especially since “most sites share less than half their genotypes” (Whitaker, 2006). The combined results of genetic diversity between sites and the low percentage of sexual reproduction provide evidence that “asexual reproduction contributes substantially to local abundance, making an otherwise relatively rare organism common,” (Whitaker, 2006); however, the results vary depending on the study, so “the inference of restricted gene flow and asexual reproduction and inbreeding among some sexually reproducing colonies should be treated as a working hypothesis,” (Whitaker, 2006). The precise reproductive modes of coral populations need to be identified by more ‘sophisticated markers’ than allozymes. Until this time, the conclusions from this study and all other studies are still tentative. While biological factors greatly influence the genetic diversity and gene flow of coral species, scientists cannot forget the physical side of the equation. The structures of the reefs, systems, and islands themselves have an impact on genetic flow, not to mention the additional influence of ocean and air currents and local weather; these factors greatly influence coral genetic diversity, especially “following gamete release or in the early stages of larval life when behavioral capabilities are poorly developed,” (Underwood et al., 2012). The effects of ocean and air currents and local weather have not been sufficiently quantified to produce reliable results explaining their effects on the genetic dispersal of marine species. The location and shape of various geological structures, however, are generally static and relatively easy for scientists to compare and conjecture how they affect coral populations. Underwood et al. (2009) demonstrated the genetic difference between Scott Reef and Rowley Shoals through special autocorrelation analysis and hypothesize that the shape of Scott Reef and the effects this surface has on Bretz 13 other oceanic factors has a clear role in altering how coral populations can disperse between sites and broad versus local recruitment. Using the data previously discussed, Underwood et al. (2009) concluded that there were differences in gene flow and larvae recruitment between Rowley Shoals and Scott Reefs in both A. tenuis and S. hystrix. A close examination of the special autocorrelation analysis revealed that the two reef systems had varying dispersal distances and different x-intercepts. The corals at Scott reef had a much smaller x-intercept than the corals from Rowley Shoals: S. hystrix is 10 times greater at Rowley Shoals than Scott Shoals, and A. tenuis is nearly two times greater (note the logarithmic distance scale for Fig. 5). Rowley Shoals recruits larvae from a much larger distance than Scott Reef, meaning that gene flow is less restricted at Rowley Shoals. The difference between Rowley Shoals and Scott reefs can be found in the different levels of gene flow: Rowley shoals had limitations at the reef-to-reef scale, but Scott Reef had limitations within the reefs, from site-to-site. Scott reef is south of Rowley Shoals and is larger and of a semicircular structure (Fig. 7). The unique shape of this reef “is likely to modify water circulation patterns by increasing friction and therefore reducing circulation on the northern side of the reef and creating recirculating flows and eddies,” (Underwood et al., 2009). This modification of water circulation could result in a higher retention rate of larvae to their parent reefs, which could cause significant genetic differences between sites in the same reef. Note that the data for the hypothesis is resolved from this one study and that the authors acknowledge that further studies on local circulation patterns and temporal genetic data are required to test and verify the hypothesis. The conclusion that the shape of the island and the location of reefs relative among other systems is critical in developing Marine Protection Areas (MPA), a conservation effort to maintain diverse fisheries and protect important marine species. By knowing the relationship between the shape and location of different reefs, better designed MPAs may be established and help further the conservation effort. Bretz 14 Fig. 7: the location of the 3 systems from Underwood et al. (2009). Scott Reef is in the upper left quadrant The purpose of coral population studies is not to only genetically analyze coral speciation and gene flow, but to gather data about these important organisms to improve conservation efforts and to design more effective plans to protect and rehabilitate reefs. Today’s conservation efforts have shifted with the times, as illustrated by Pinzón et al. (2013), with their results comparing morphological and genetic species classification. Improved conservation efforts fueled by studies like Underwood et al. (2012) and Whitaker (2006), which focus on genetic dispersal and local recruitment, have also caused a modification in MPAs. Through a combination of the aforementioned studies and other similar publications, scientists have come to identify a general pattern in coral and other marine organisms’ gene flow through their respective species differentiation and larvae dispersal. Preserving the most threatened species and those vital to gene flow and genetic diversity is a vital step to rehabilitating and protecting marine environments; however, scientists need to continue studying marine organism classification, to verify and align morphological and genetic identities prior to advocating conservation efforts for certain organisms. Comparisons of larvae recruitment between reef systems has also helped scientists identify how nature maintains genetic diversity and by identifying key systems, scientists may help advance the recovery of reefs that rely on local recruitment. Knowing the importance of local recruitment via sexual and asexual reproduction is critical as Whitaker (2006) proved in her study when she found a significant number of corals maintain genetic diversity through asexual reproduction. The geographical effects of reef systems and oceanographic factors are also subjects that need to be further investigated, as Bretz 15 Underwood et al. (2009) mentioned in their study whilst comparing genetic diversity between Rowley Shoals and Scott Reefs. The combination of these results points to the implementation of Marine Protected Areas (MPAs) as being one of the most promising conservation techniques. The summative case study, Underwood et al. (2012), affirms that “Marine Protected Area planners must seek to protect the reproductive capacity of populations within each system…[and] that networks designed for the smaller scale dispersers should provide adequate protection for the larger scale dispersers.” While MPAs and no-take zones may protect certain locations, these are in no way applicable to all environments around the world. The research that was conducted to gather data which helped designed MPAs is very particular (i.e., Pinzón et al. (2013), Underwood et al. (2009), and Whitaker (2006) all involve regions in and around the coast of NW Australia); the findings in one location can vary rarely be transferred to another location. Underwood et al. (2012) recognized this, and purported that “depending on the taxa studied in the first location, basic information from one study, such as mean dispersal distances, may be used to model another region, however, this model will still need to be ground truthed and this requires the methods such as hydrodynamic modeling and genetic analysis described above.” In conclusion, the results of studies on population genetics are promising when applied to conservation efforts, however these results cannot be used on a global scale and take a lot of time and effort to conduct, assimilate with other studies, and then to be applied to the environment as conservation programs. Bretz 16 Works Cited Ayre, D.J., & Hughes, T.P. (2000). 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