@article{khurram_larawai_shalizi_akamani_groninger_2023, title={Assessing regeneration strategies for sustaining intensively used Chilgoza pine-dominated community forests in Afghanistan}, volume={14}, ISSN={["2666-7193"]}, DOI={10.1016/j.tfp.2023.100443}, abstractNote={Income from Chilgoza pine (Pinus gerardiana) nut harvests, grazing, and the collection of firewood support forest communities within Afghanistan's Eastern Forest Complex. Persistent instability, frequent incidence of armed conflict, limited capacity of Indigenous communities, and inaccessibility to scientific expertise on forest regeneration limit options for addressing forest degradation. Representatives from forest communities in 16 districts in Khost, Paktia, and Paktika Provinces were surveyed to assess community user perceptions of Chilgoza pine regeneration status, forest protection, and acceptability of potential regeneration strategies (rotational stand harvesting, group seed tree protection, individual seed tree protection, partial cone harvesting, and integrated method). Human activity management, primarily via fine systems and forest guards, was widely reported and was regarded as important in managed forests. Respondents who reported current implementation of regeneration methods were more likely to regard natural regeneration as important and most regarding natural regeneration as very important reported the use of partial cone crop harvest as the prevailing regeneration method. Among proposed strategies, partial cone harvesting was the most frequently chosen option where regeneration was regarded as very or somewhat important. In light of the previously reported decline of forests under prevailing management practices, these results indicate a general awareness of regeneration as a forest management issue but also a significant gap among forest users in identifying the limitations of partial cone crop harvesting without additional protection for seedlings, as a potential remedy. We offer integrated rotational harvesting and grazing management strategies as a means to promote sound silviculture practices and provide a next step for community-based forest management to sustain Chilgoza pine. The context of this work in a region where tribal politics has limited outsider input allows it to serve as a model to address natural resource management issues in similar conflict-prone settings.}, journal={TREES FORESTS AND PEOPLE}, author={Khurram, Safiullah and Larawai, Mohammad Ismael and Shalizi, Mohammad Nasir and Akamani, Kofi and Groninger, John W.}, year={2023}, month={Dec} }
 @article{khurram_shalizi_bashari_akamani_groninger_2023, title={Barriers and opportunities regarding community-based forest management in Afghanistan: considerations for fragile states}, ISSN={["1469-4387"]}, DOI={10.1017/S0376892923000280}, abstractNote={SummaryThe Government of the Islamic Republic of Afghanistan (GIRoA), in power during 2002–2021, initiated the process of instituting community-based forest governance and building local capacity for natural resource management. These efforts coincided with the presence of international security forces and the mobilization of civil society organizations, and they were in response to community aspirations to protect and restore often degraded local forests. Legislation was passed to enable forest protection and management, including a provision to encourage participatory management by local community user groups organized as Forest Management Associations (FMAs). By the end of the GIRoA era, c. 20 registered FMAs were operating with c. 400 others in various stages of development across Afghanistan. Our analysis of relevant policy documents revealed that the policy framework developed during the GIRoA era scores favourably on the ideal criteria for community-based resource management. Despite the change in political administration with the inception of the current Islamic Emirate of Afghanistan regime, the influence of the GIRoA era serves as a starting point and may have enduring influences on rural communities in Afghanistan and the natural resources that support them. Anecdotal evidence suggests that community-based forest management may persist under the current national leadership despite international isolation and funding constraints. The model developed in Afghanistan may be relevant to other fragile states, especially in contexts where rural forest-dependent communities have strong local institutions, such as shuras, and where forests are not prone to heavy extraction pressure.}, journal={ENVIRONMENTAL CONSERVATION}, author={Khurram, Safiullah and Shalizi, Mohammad Nasir and Bashari, Mujtaba and Akamani, Kofi and Groninger, John W.}, year={2023}, month={Nov} }
 @article{lin_shalizi_walker_lauer_carrasco_gujjula_suren_isik_2023, title={Low-density AgriSeq targeted genotyping-by-sequencing markers are efficient for pedigree quality control in Pinus taeda L. breeding}, volume={19}, ISSN={["1614-2950"]}, url={https://doi.org/10.1007/s11295-023-01608-8}, DOI={10.1007/s11295-023-01608-8}, number={4}, journal={TREE GENETICS & GENOMES}, author={Lin, Yu-Ming and Shalizi, Mohammad Nasir and Walker, Trevor D. D. and Lauer, Edwin and Carrasco, Claudio D. D. and Gujjula, Krishna Reddy and Suren, Haktan and Isik, Fikret}, year={2023}, month={Aug} }
 @article{shalizi_walker_heine_payn_isik_bullock_mckeand_2023, title={Performance Based on Measurements from Individual-Tree Progeny Tests Strongly Predicts Early Stand Yield in Loblolly Pine}, volume={2}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxad002}, DOI={10.1093/forsci/fxad002}, abstractNote={Abstract
               To facilitate the utility of genetic improvement in loblolly pine, individual-tree volume (productivity) scores estimated from single-tree plot or row-plot progeny test designs were compared with stand-level volume per unit area from block plots. A large number of families representing a wide range of progeny test scores for volume were established in growth and yield trials to generalize the results to families created by the breeding program. Individual-tree volume scores from progeny tests strongly corresponded with stand-level volume from block plots, especially after accounting for site quality and the risk of fusiform rust disease. A ten-point increase in the volume score from progeny test data was estimated to increase stand-level volume by 3.9 m3 ha-1 at age 6 years. A prediction model is presented that includes a new statistic, rust risk index, which is the expected rust incidence for a family at a new site when the hazard of rust for a checklot can be estimated from historical data. The study results through age 6 years corroborate the Performance Rating System as effective in guiding family deployment decisions. The models presented are based on pre-crown closure data at 6 years and will be updated with older measurements as the study matures.
               Study Implications: The Performance Rating System (PRS™) has been a successful tool for presenting genetic merit of improved loblolly pine families for landowners and forest managers in a more coherent and standardized manner. This system can be easily applied in other forest tree improvement programs, because it makes genetic improvement user-friendly for silviculturists and forest managers. Landowners can use this system to make decisions for selecting improved families suited to their specific forest management objectives. Seed orchard and nursery managers also depend on the PRS to choose the families to produce and as a third-party verification to market their genetic merit to customers. This study demonstrates that higher stand-level volume per unit area can be achieved when forest managers plant fast growing families with low fusiform rust disease risk on productive sites. The combined effect of genetic improvement for productivity and fusiform rust disease resistance is significant on stand-level volume per unit area.}, journal={FOREST SCIENCE}, author={Shalizi, Mohammad Nasir and Walker, Trevor D. and Heine, Austin J. and Payn, Kitt G. and Isik, Fikret and Bullock, Bronson P. and McKeand, Steven E.}, year={2023}, month={Feb} }
 @article{shalizi_payn_isik_2022, title={Genetic linkage between the training and selection sets impacts the predictive ability of SNP markers in a cloned population of Pinus taeda L.}, volume={18}, ISSN={["1614-2950"]}, url={http://dx.doi.org/10.1007/s11295-021-01532-9}, DOI={10.1007/s11295-021-01532-9}, number={1}, journal={TREE GENETICS & GENOMES}, publisher={Springer Science and Business Media LLC}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Isik, Fikret}, year={2022}, month={Feb} }
 @article{shalizi_payn_walker_isik_heine_mckeand_2022, title={Long-term evaluation of intra- and inter-provenance hybrids of loblolly pine in the Piedmont region of the southeastern United States}, volume={522}, ISSN={["1872-7042"]}, url={http://dx.doi.org/10.1016/j.foreco.2022.120469}, DOI={10.1016/j.foreco.2022.120469}, abstractNote={Long-term response of two intra- and two inter-provenance populations of loblolly pine (Pinus taeda L.) were evaluated in the Piedmont region of the southeastern United States. In total, 82 polycross families of the Atlantic Coastal (C) and Piedmont (P) provenances (C×C, P×P) and their hybrids (C×P, P×C) were field tested for growth, sawtimber potential, and survival through age 19 years. The Coastal pure (C×C) families were the tallest, and the hybrid populations (C×P, P×C) were intermediate for height. The four populations did not differ for diameter at breast height. The hybrid C×P population, followed by the C×C population, showed significantly higher stand volumes per hectare. These two populations maintained higher survival and stand density compared to the Piedmont pure populations. Sawtimber potential was significantly higher in the Piedmont pure families at the coldest study sites, presumably due to defect in the C×C and C×P from cold damage. No significant genotype-by-environment interactions were detected for any traits. The genetic gain for height, stand volume, and survival was considerable in the C×C and C×P over the Piedmont source, suggesting potential for benefiting from the faster growth of the Coastal material in the Piedmont region. The performance of the Coastal intra- and inter-provenance populations was marginally affected by the minimum winter temperatures (MWT). These results indicate that the Coastal and the hybrid families can be planted in the Piedmont region with MWT’s of −13 °C or greater and where the difference in MWT between the origin of the Coastal parents and the test sites was not extreme (e.g., the difference did not exceed 2.8 °C). These MWT limits encompass the southern Piedmont of North Carolina (<35.615 °N) and the Piedmont of South Carolina, Georgia, and Alabama.}, journal={FOREST ECOLOGY AND MANAGEMENT}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Walker, Trevor D. and Isik, Fikret and Heine, Austin J. and McKeand, Steven E.}, year={2022}, month={Oct} }
 @article{shalizi_cumbie_isik_2021, title={Genomic prediction for fusiform rust disease incidence in a large cloned population of Pinus taeda}, volume={11}, ISSN={["2160-1836"]}, url={http://dx.doi.org/10.1093/g3journal/jkab235}, DOI={10.1093/g3journal/jkab235}, abstractNote={Abstract
               In this study, 723 Pinus taeda L. (loblolly pine) clonal varieties genotyped with 16920 SNP markers were used to evaluate genomic selection for fusiform rust disease caused by the fungus Cronartium quercuum f. sp. fusiforme. The 723 clonal varieties were from five full-sib families. They were a subset of a larger population (1831 clonal varieties), field-tested across 26 locations in the southeast US. Ridge regression, Bayes B, and Bayes Cπ models were implemented to study marker-trait associations and estimate predictive ability for selection. A cross-validation scenario based on a random sampling of 80% of the clonal varieties for the model building had higher (0.71–0.76) prediction accuracies of genomic estimated breeding values compared with family and within-family cross-validation scenarios. Random sampling within families for model training to predict genomic estimated breeding values of the remaining progenies within each family produced accuracies between 0.38 and 0.66. Using four families out of five for model training was not successful. The results showed the importance of genetic relatedness between the training and validation sets. Bayesian whole-genome regression models detected three QTL with large effects on the disease outcome, explaining 54% of the genetic variation in the trait. The significance of QTL was validated with GWAS while accounting for the population structure and polygenic effect. The odds of disease incidence for heterozygous AB genotypes were 10.7 and 12.1 times greater than the homozygous AA genotypes for SNP11965 and SNP6347 loci, respectively. Genomic selection for fusiform rust disease incidence could be effective in P. taeda breeding. Markers with large effects could be fit as fixed covariates to increase the prediction accuracies, provided that their effects are validated further.}, number={9}, journal={G3-GENES GENOMES GENETICS}, publisher={Oxford University Press (OUP)}, author={Shalizi, Mohammad Nasir and Cumbie, W. Patrick and Isik, Fikret}, year={2021}, month={Sep} }
 @article{mahmoodi_shalizi_groninger_akamani_khurram_2021, title={Stand Characteristics and Perceptions of Local Communities on the Management of Pistachio (Pistacia vera L.) Forests in an Unstable Region of Afghanistan}, volume={9}, ISSN={["1540-756X"]}, url={http://dx.doi.org/10.1080/10549811.2021.1978097}, DOI={10.1080/10549811.2021.1978097}, abstractNote={ABSTRACT Pistachio (Pistacia vera L.) forests support livelihoods in communities within Afghanistan’s Pistachio Belt, a region characterized by extreme poverty and chronic insecurity. In this study, we used ecological data, as well as survey data to characterize standing attributes and resource user perceptions about local pistachio forests and their management. The survey questionnaire was verbally administered to 507 household representatives in remote communities that were chosen from eight districts in northern and northwestern Afghanistan based on accessibility and their location within the Pistachio Belt. Stand density and tree form varied widely between sites and as a function of elevation. Partial harvesting for fuelwood collection was positively correlated with stand density. The survey data also showed that pistachio forests support a variety of livelihood activities among respondents and their households. However, suboptimal nut collection timing and use of damaging nut harvesting methods were widespread with little effort to accommodate natural regeneration. Forest users typically recognized the degraded condition of the pistachio forest and the negative impacts of grazing and fuelwood collection on forest density. Respondents also recognized the impacts of nut collection practices, fuelwood collection, and grazing on forest regeneration status. These results suggest that efforts to sustainably manage pistachio forests must recognize considerable variation within and between communities regarding forest physical condition, accustomed uses by associated communities, and existing or potential mechanisms regulating forest uses. All of these necessitate context-specific forest management planning. We discuss challenges inherent to collecting baseline data needed for planning multiple-use community-based natural resources management in highly insecure environments.}, journal={JOURNAL OF SUSTAINABLE FORESTRY}, publisher={Informa UK Limited}, author={Mahmoodi, Mohammad Bashir and Shalizi, Mohammad Nasir and Groninger, John W. and Akamani, Kofi and Khurram, Safiullah}, year={2021}, month={Sep} }
 @article{shalizi_gezan_mckeand_sherrill_cumbie_whetten_isik_2020, title={Correspondence between Breeding Values of the Same Pinus taeda L. Genotypes from Clonal Trials and Half-Sib Seedling Progeny Trials}, volume={66}, ISSN={0015-749X 1938-3738}, url={http://dx.doi.org/10.1093/forsci/fxaa016}, DOI={10.1093/forsci/fxaa016}, abstractNote={AbstractThe correspondence between breeding values of 65 loblolly pine (Pinus taeda L.) genotypes from clonal genetic tests and half-sib seedling progeny tests was studied in the southern United States. The two experiments were established separately, 10 years apart. Additive genetic variance estimates from clonal tests were larger compared with the estimates from the half-sib progeny tests, regardless of the covariance structure used in the statistical models and the traits. However, clone-mean and half-sib family-mean heritability estimates were comparable for all traits, ranging between 0.88 and 0.99. Based on the independent analysis, the correlation between the breeding values of the same genotypes from two propagule types was moderate (0.59) for tree height and stem volume. The combined analysis resulted in a strong genetic correlation (>0.93) between the breeding values of two propagule types. Herein the large discrepancy is mainly the outcome of different data analytical approaches. Conclusively, selecting genotypes for deployment based on clonal testing may not be optimal, but forest tree breeders can use the results from clonal tests to make some informed decisions.}, number={5}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Shalizi, Mohammad Nasir and Gezan, Salvador Alejandro and McKeand, Steven E and Sherrill, Joshua R and Cumbie, W Patrick and Whetten, Ross W and Isik, Fikret}, year={2020}, month={Sep}, pages={600–611} }
 @article{shalizi_khurram_groninger_akamani_morrissey_2020, title={Redbud woodlands conservation status in Afghanistan: Implications for sustaining vulnerable ecosystems under multiple drivers of change}, volume={22}, ISSN={["2351-9894"]}, url={http://dx.doi.org/10.1016/j.gecco.2020.e00942}, DOI={10.1016/j.gecco.2020.e00942}, abstractNote={Afghan redbud (Cercis griffithii Boiss.) woodlands near Kabul, Afghanistan face continued impacts from multiple drivers of change, including urban expansion, grazing, illegal cutting, and the implementation of forest policies. In this study, we collected ecological and social data from three sites to assess stand characteristics, as well as community perceptions on the drivers of change impacting them. A survey of community perceptions revealed that while only 24% of respondents perceived that natural regeneration was occurring on redbud forests, only 25% perceived that the forests were declining in status. Respondents perceived that Afghan redbud stands were exposed to multiple proximate and underlying drivers of change, although these perceptions differed across the three sites. Ecological surveys of stand conditions indicated that although all three study sites were exposed to the pressures of urbanization, the intensity of wood collection differed among the sites. Differences in contextual factors, such as the availability of effective traditional institutions, socio-demographic characteristics of residents, and the availability of alternative sources of fuel seem to explain the differences in fuelwood collection among the sites. Following the collapse of the Taliban regime, the heaviest cutting was associated with stands where unauthorized construction of new houses by repatriated populations from Pakistan and Iran was most prevalent, while impacts were lower where alternative fuel sources were available and local institutions were effective. Given the challenges entailed in the enforcement of recent forest protection policies in Afghanistan, our findings suggest that a promising starting point for the sustainable management of Afghan redbud forests is the initiation of a community-based natural resource management approach that addresses local socio-economic concerns while engaging local communities in the decision-making process. Conservation programs in conflict-impacted environments should consider local government capacity and stakeholder motivations to propose practical alternatives to strict forest protection policies. Training local policing authorities to differentiate between destructive and sustainable natural resource management practices and educating local populations on sustainable use could catalyze improved environmental engagement.}, journal={GLOBAL ECOLOGY AND CONSERVATION}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Khurram, Safiullah and Groninger, John W. and Akamani, Kofi and Morrissey, Robert C.}, year={2020}, month={Jun} }
 @article{shalizi_goldfarb_burney_shear_2019, title={Effects of Five Growing Media and Two Fertilizer Levels on Polybag-Raised Camden Whitegum (Eucalyptus benthamii Maiden & Cambage) Seedling Morphology and Drought Hardiness}, volume={10}, ISSN={["1999-4907"]}, url={http://dx.doi.org/10.3390/f10070543}, DOI={10.3390/f10070543}, abstractNote={In developing countries, tree seedlings are often produced in polybags filled with mixtures of locally available materials. Seedling growth and quality can be affected by the type and amount of these substrates used in the mixture. Differences in seedling growth and quality can also be significantly affected when fertilization is employed during the nursery growing period. In this study, we assessed the effects of five different growing media and two fertilization regimes on nursery growth, seedling morphology and early post-planting response to drought of Eucalyptus benthamii (Maiden & Cambage) seedlings. First, we evaluated the effects of each media by fertilizer treatment combination on morphological attributes during a nursery growing period. Seedlings raised in fertilized media without rice hulls yielded higher growth, root dry mass, shoot dry mass, total dry mass, Dickson quality index (DQI) scores, and number of first order lateral roots (FOLRs). Root to shoot ratio (R:S ratio) was, however, greater in non-fertilized media that contained rice hulls. We then conducted a simulated outplanting and drought hardiness experiment, in which seedlings were planted in 13.2 L containers and irrigated for one month, followed by the imposition of drought stress. Seedlings in fertilized media composed of sand, topsoil and compost showed greater growth than those in rice hull-containing media, during the irrigation phase. With the discontinuation of irrigation and prevention of precipitation reaching the seedlings, seedlings grown in non-fertilized media containing rice hulls survived longer than those in other media. There were no large differences in survival among other media or between fertilized and other non-fertilized seedlings. Seedling total size and shoot height at the time of planting played a major role in survival. Smaller seedlings with smaller shoot sizes and greater R:S ratios survived longer. This study demonstrates that growing media and fertilization can be manipulated to affect seedling morphology in the nursery and, ultimately, seedling performance and survival under water stressed conditions.}, number={7}, journal={FORESTS}, publisher={MDPI AG}, author={Shalizi, Mohammad Nasir and Goldfarb, Barry and Burney, Owen Thomas and Shear, Theodore Henry}, year={2019}, month={Jul} }
 @article{shalizi_isik_2019, title={Genetic parameter estimates and GxE interaction in a large cloned population of Pinus taeda L.}, volume={15}, ISSN={["1614-2950"]}, url={http://dx.doi.org/10.1007/s11295-019-1352-7}, DOI={10.1007/s11295-019-1352-7}, number={3}, journal={TREE GENETICS & GENOMES}, publisher={Springer Science and Business Media LLC}, author={Shalizi, Mohammad Nasir and Isik, Fikret}, year={2019}, month={Jun} }
 @article{shalizi_groninger_khurram_ruffner_burney_2018, title={Data on ecological associations and stand structure of chilgoza pine (Pinus gerardiana Wall. ex D. Don) in Afghanistan}, volume={18}, ISSN={["2352-3409"]}, url={http://dx.doi.org/10.1016/j.dib.2018.03.118}, DOI={10.1016/j.dib.2018.03.118}, abstractNote={Reported here are original data related to the article “Indigenous knowledge and stand characteristics of a threatened tree species in a highly insecure area: Chilgoza pine in Afghanistan” (Shalizi et al., 2018) [1]. A dendrochronological summary of all known chilgoza pine tree growth increment cores collected in Afghanistan is presented in this data in brief article. Chilgoza pine trees and regeneration density profiles are reported for four provinces of eastern Afghanistan. In addition, images depicting chilgoza pine forest structure, stand conditions, and utilization impacts are presented.}, journal={DATA IN BRIEF}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Groninger, John W. and Khurram, Safiullah and Ruffner, Charles M. and Burney, Owen T.}, year={2018}, month={Jun}, pages={939–946} }
 @article{shalizi_khurram_groninger_ruffner_burney_2018, title={Indigenous knowledge and stand characteristics of a threatened tree species in a highly insecure area: Chilgoza pine in Afghanistan}, volume={413}, url={http://dx.doi.org/10.1016/j.foreco.2018.01.053}, DOI={10.1016/j.foreco.2018.01.053}, abstractNote={Chilgoza pine (Pinus gerardiana) is an important source of income in forested eastern Afghanistan through the harvest of edible seeds. Since the late 1970s, the resource has been largely inaccessible to researchers and government personnel from outside the region, except for the years 2002–2015, roughly coinciding with Operation Enduring Freedom. We assessed physical and social attributes of chilgoza pine forests and the management capacity of indigenous communities. We employed interviews/questionnaires and field measurements performed by Afghan forest scientists from Kabul, trained local residents, and U.S. forest scientists associated with military operations to examine stakeholder perceptions of chilgoza pine forest resilience, assess forest health, stand structure and natural regeneration status. Intensive cone collection, tree damage caused by cone harvesting, grazing, fuelwood collection, and other biotic/abiotic factors (insects, diseases, and drought) were associated with chilgoza forest degradation. Most interviewees observed natural regeneration in the understory layer of chilgoza forest stands, but perceived the overall rate of natural regeneration to be insufficient. Respondents from villages prohibiting grazing and fuelwood collection reported the greatest regeneration while the converse was associated with the lowest levels of regeneration. Field measurements confirmed the scarcity of natural regeneration of chilgoza pine, portending the further decline of this species in Afghanistan. Field surveys indicated diverse stand conditions, age class structures and land use practices employed by local stakeholders, suggesting the need for situation-specific forest management recommendations. We discuss the opportunities and limitations for forest resources data collection in highly insecure environments.}, journal={Forest Ecology and Management}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Khurram, Safiullah and Groninger, John W. and Ruffner, Charles M. and Burney, Owen T.}, year={2018}, month={Apr}, pages={1–8} }