Tubastraea coccinea and T. tagusensis, have been introduced by opportunistic colonization in 1980 and are now widespread along more than 3,500 km of coastline. To better understand the invasion process and the role of vectors in spreading these species, we sampled 306 and 173 colonies of T. coccinea and T. tagusensis from invaded sites, possible vectors and one native population. Analyses revealed a higher diversity of multi-locus genotypes (MLGs) on vectors, suggesting that they were contaminated prior to their arrival in the Southwestern Atlantic, and a high proportion of clones at invaded sites, with few genotypes spread over ~2,000 km. This broad distribution is most likely a result of secondary introductions through the transport of contaminated vectors. Results also suggest the occurrence of multiple invasions, mainly in the northernmost sites. In summary, clonality, secondary introductions, and multiple invasions are the main reasons for the broad spread and invasive success of Tubastraea spp. in the Southwestern Atlantic. Consequently, the correct control of vectors is the most effective approach for management and prevention of new invasions.Accidental introduction through ballast water and biofouling are currently the main factors responsible for spreading non-indigenous species in the marine realm. In the Southwestern Atlantic, two scleractinian corals,  Accidental introductions can occur through a number of ways, such as aquaculture, trade in ornamental species, canals linking previously unconnected waters, ballast water and biofouling, the last two being the main factors responsible for spreading non-indigenous species in the marine realm7. As a consequence of the increasing marine traffic, vessels  transport a large number of species , some of which will be able to establish and disperse, becoming invasive in the new environment8.Marine bioinvasion is reshaping the distribution and biogeographic patterns of species worldwide and is reaching unprecedented levels with hundreds of species being transported to new environments every yearTubastraea coccinea and T. tagusensis)9. T. coccinea was first reported in the Atlantic during the 1940’s in Curaçao and Puerto Rico, and was probably introduced as biofouling on ship hulls traveling from Indo-Pacific waters12. Further records of the genus were reported in the Northwestern Atlantic in 2004 (T. coccinea)13, Southwestern Atlantic in the 1980’s (T. coccinea and T. tagusensis)15 and Gulf of Mexico in 2010 (T. coccinea and T. micranthus)16. Given the pattern of sea surface currents and previous examples from other invasive species, the Gulf of Mexico and Florida could have been naturally invaded by Caribbean populations12. However, the occurrence of T. micranthus, a species not yet found in the Caribbean, on oil platforms at Gulf of Mexico indicates that human vectors have also been responsible for the introduction into this region17. In the Southwestern Atlantic, Tubastraea spp. were firstly reported as fouling on offshore oil platforms in Rio de Janeiro State14. The genus is now widespread on rocky shores and artificial substrates  along more than 3,500 km, from Ceará 18 to Santa Catarina 19, outcompeting native and endemic species24. Although there is no doubt that the introduction in the Southwestern Atlantic was through biofouling12: (1) the invasion history remains unclear; (2) there are no studies elucidating why these two species have been so successful in invading the Brazilian coast; and (3) the role of vectors in spreading them along the coast is unknown.Recently, a review listed 15 non-indigenous species causing major negative impacts in the South Atlantic, including two azooxanthellate corals , sexual and asexual reproduction, early maturity and phenotypic plasticity40. When founded by a small number of individuals, recently established populations can suffer a drastic reduction in genetic diversity as a consequence of genetic drift. Ultimately, genetic drift can have negative consequences such as the fixation of deleterious alleles and decrease of the species resilience45. On the other hand, multiple introduction events of non-indigenous species from more than one native population can lead to an increase in genetic diversity by mixing previously separated populations and increasing the propagule pressure, consequently reducing negative genetic outcomes of the invasion process and enhancing the possibility of a successful invasion47.The occurrence of multiple introductions has also been correlated with invasion success48. Here we use a set of microsatellite markers34 to: (1) investigate genetic diversity and clonality at invaded sites and on vectors along the Brazilian coast; (2) provide insights into the role of vectors at spreading these invasive corals in the Southwestern Atlantic; and (3) evaluate the population structure at invaded sites with regard to the possibility of multiple introduction events.A better understanding of the invasion process and the ways by which invasive species are spreading into new environments is essential for improving management effectiveness and control plans that ultimately reduce or prevent future invasionsT. coccinea and T. tagusensis with only 84  and 30  unique MLGs within all sampled sites. Similar proportion of clones were found when all indivuduals with missing data were removed . For T. coccinea, invaded sites had, in general, less MLGs when compared to vectors and native population, with five sites holding three or less MLGs  close to 1, Fig. T. tagusensis. Invaded sites and vectors had similar numbers of MLGs  and clonal richness was slightly lower on vectors, reaching 0.8 in the vector SBM-V  from T. tagusensis are shared with one or more sampled sites  from 2% from TPsex value higher than 0.01 (Table T. coccinea (3%) and 12 (7%) T. tagusensis had Psex value higher than 0.001, thus being considered products of distinct sexual reproduction events. Two loci from T. coccinea (Tco 1 and Tco 30) and two from T. tagusensis (Tco 4 and Tco 37) showed evidence of linkage disequilibrium with at least two other loci and were excluded from further genetic diversity analyses. There was no evidence of null alleles for T. coccinea, while for T. tagusensis three loci showed evidence of null alleles for one population each , two vectors (SBM-V Araça and FPSO Marlim Sul) and in the native population (Taiwan) (Table Fis) was negative for most invaded sites (except for AI and Alc) and P14, indicating an excess of heterozygotes (Table For n) Table . ObserveT. tagusensis, the number of alleles and allelic richness were similar among sampled sites, ranging from 13 to 20 and 1.6 to 2.2, respectively. Exclusive alleles were found at all but three invaded sites , with the highest number observed at the northernmost site, Petroleiro do Acaraú  was negative for all sites but SBM-V, indicating an excess of heterozygotes , while all remaining sites overlapped, indicating no clear difference in overall gentic variance amond them  that travel from offshore oil platforms to onshore localities are acting as vectors in spreading these species along the Brazilian coast.Forty years after its first record, the genus T. coccinea and T. tagusensis the Southwestern Atlantic invaded sites have a higher proportion of clones when compared to vectors, with sites dominated by a single genotype . Thus, their early reproductive age33 and ability to reproduce asexually are probably the main factors responsible for their success as invaders. When environmental conditions are suitable, such abilities enable large densities from a small starting number of individuals. Interestingly, although T. coccinea from Taiwan had fewer clones when compared to the majority of the Brazilian invaded sites, half of the examined samples were composed of clones of the same genet. This demonstrates that asexual reproduction also plays an important role in its native distribution range. As discussed by previous studies, asexual reproduction in Tubastraea occurs through the asexual production of larvae34, a strategy broadly used by anthozoans52, but to date only observed in three scleractinian species, T. coccinea, T. diaphana and Pocillopora damicornis54.For both T. coccinea and T. tagusensis had one dominant genotype each , showing an over-representation of few genotypes. This may be a consequence of the invasion process where only one or a few genotypes better fitted to the recently invaded environment were able to establish and disperse56. A similar pattern was previously observed for Pocillopora damicornis in Hawaii55 and Reunion Islands57, and also for Acropora palmata in the French Antilles58. Nevertheless, those studies analyzed samples collected over small geographic scales (less than 20 km), while the dominant genotype of T. coccinea and T. tagusensis in invaded sites were spread over 1,500 and 2,000 km, respectively . Nevertheless, due to the Brazilian surface currents regime, it would be oceanographically not probable that competent larvae would travel long distances. Furthermore, the gregarious settlement with high local clonality observed for Tubastraea follows the “strawberry-coral” model60, when organisms use sexual reproduction to disperse genotypically diverse individuals, while asexual reproduction helps to spread locally adapted genotypes. Interestingly, an opposite hypothesis of dispersal capability was proposed for P. damicornis, where the asexual larvae would be responsible for long-distance dispersal61. Indeed, studies showing evidence of local recruitment from sexual larvae with low clonality corroborate the hypothesis that asexually produced larvae of P. damicornis may travel further63. Future studies comparing the size and duration of sexual and asexual larvae of Tubastraea spp. in situ are recommended to test if they follow such pattern.Although possible for nearby localities, larval dispersal itself does not explain the broad distribution of clones at sites separated by more than 1,500 km. Tubastraea spp. in the Southwestern Atlantic was on offshore oil platforms from the Campos Basin, north of Rio de Janeiro State, in the late 1980s. In such context, oil platforms built by foreign companies abroad that were slow towed to the Southwestern Atlantic may have been colonized with local fauna that were further transported as biofouling. Thus, such structures are the most probable means of introduction of these species along the Brazilian waters12. Once the platforms started to operate, their associated structures (such as buoys) and the year around movement of associated platforms and offshore support fleet shorewards are the most probable vectors for spreading Tubastraea spp. along the Brazilian coast. Indeed, the distributional range of Tubastraea spp. in the Southwestern Atlantic appears to be directly associated to sites with intense ship traffic and waterway terminals. de Paula and Creed64 analyzed the distribution and expansion of Tubastraea spp. at Ilha Grande Bay and found that the Petrobras oil terminal or Verolme shipyard were likely points of introduction of these species at that locality. In addition, Ferreira at el.65 found 22 non-indigenous species when analyzing drill-ships, platforms and cargo ships in Arraial do Cabo, including T. coccinea, and other studies had demonstrated that artificial substrates facilitate invasion68. Tubastraea spp. seem to be opportunistic and have been reported on artificial substrates at both invaded65 and native localities69. To confirm the hypothesis of multiple introduction events from the same native population it is essential to know the origin of the vessels and when they first arrived in the Southwestern Atlantic. However, this information is not easily traceable and could not be verified. Of the five vectors included in the present study, such information was traceable for two: P27 was brought from Singapore to Arraial do Cabo, Brazil, in 1998; and P14 was built in France in 1983, with no information of where or when it has first arrived in Brazil. Singapore is within the natural distributional range of Tubastraea spp.70 and it is highly possible that the platform P27 was infested before its arrival in the Atlantic. Indirect evidence supporting this assumption is the large size of colonies sampled on the platform and the first records of Tubastraea spp. in Arraial do Cabo only one-year after the arrival of P27 in the region12. Regarding the platform P14, it probably arrived free from Tubastraea, as there are no records of this genus in Europe yet. However, it was probably contaminated in Brazilian or Caribbean waters and then became a vector. Although we cannot confirm the origin of all vectors, the (i) occurrence of unique MLGs, (ii) exclusive alleles not found within invaded sites 12 of which we have analyzed samples from only five. It is highly possible that vectors not included in this study were the primary responsible for introductions along several localities in the Southwestern Atlantic. Recently, Petrobras (2016) reported that 78% of the 32 structures they operate in the Sergipe region of northeast Brazil were also contaminated with Tubastraea spp.The occurrence of secondary introduction from one invaded site to another is supported by information of vessels being transported along the Brazilian coast Table 12 and th34, with at least five genetic clusters with no geographic pattern for T. coccinea. The lack of geographic pattern is likely a result of the transport of infested vectors previously discussed. However, as the software Structure is not appropriate for organisms that reproduce mainly asexually71, results should be interpreted with caution. Sammarco et al.72 found similar results when analyzing invasive populations of T. micranthus at two oil platforms in the Gulf of Mexico, with four distinct genetic clusters observed on one single platform, likely resulting from multiple introductions from distinct source populations. In addition to increasing the propagule pressure, multiple introductions can lead to an increase in genetic diversity via the isolate breaking effect by creating new genotypes, potentially benefiting invasive populations and enhancing their chance of survival40. Patterns of high genetic diversity of invaded populations associated with multiple introductions have been observed for other marine organisms, such as the green crab Carcinus maenas73, the nassariid gastropod Cyclope neritea74, the caprellid Caprella scaura at the Iberian Peninsula75, and others77.Our results corroborate the hypothesis of multiple introduction eventsT. coccinea, showing that there is no specific structure in their distribution. Nevertheless, based on the distribution of MLG it is possible that the northern sites were invaded more than once, as they have higher genotypic diversity when compared to the southern sites. The later was invaded less than ten years ago mostly by the same genotypes, suggesting a single invasion event. For T. tagusensis, both Structure and NJ suggest that the Brazilian northernmost invaded site (Petroleiro do Acaraú) was colonized by a different population, not present at any other invaded site or vector analyzed herein, and is most probably the result from a single introduction event. This site is a shipwreck 1,500 km distant from Todos os Santos Bay, the closest recorded invaded site on the Brazilian coast, and the direction of sea surface currents are westward, which possibly prevents any gene flow between Petroleiro do Acaraú and the remaining Southwestern Atlantic invaded sites. Nevertheless, Mucuripe waterway terminal is ~200 km east from the shipwreck and it is possible that this invasion was also through biofouling on small or large vessels that used this terminal. The remaining invaded sites and vectors are likely derived from two different native populations. The native distribution of T. tagusensis is currently unknown and until an extensive revision of the genus is undertaken  further assumptions of the origins of the Southwestern Atlantic populations are challenging.NJ analyses had low support values for et al.34, we observed an excess of heterozygotes for T. coccinea and a higher genetic diversity on vectors when compared to invaded sites. Lineages where asexual reproduction predominates tend to have high levels of heterozygosity and negative FIS as a consequence of an independent evolution of loci (e.g. “Meselson effect”), accumulating divergence within alleles80 and a higher genetic diversity on vectors in comparison to invaded sites would be expected when only a few individuals are successufully established on invaded sites. In general, the observed genetic diversity for Tubastraea spp. in the Southwestern Atlantic may result from a combination of factors, such as reproductive strategy, high growth rate, high propagule pressure, occurrence of multiple invasions, and through their dissemination by oil platforms and other shipping.Supporting preliminary analyses showed by Capel Tubastraea spp. in the Southwestern Atlantic. High clonality capability is a common feature among successful invasive species, enabling invaders with low number of individuals/low genetic diversity to reach high densities and successfully dominate the invaded region56. We also suggest that the Atlantic population was invaded more than once by different populations from the native region and that the Indo-Pacific is a possible source of the Southwestern Atlantic populations of T. coccinea, although a more extensive sampling of native populations and other invaded sites, such as the Caribbean, are recommended to track the exact origin of the Southwestern Atlantic invaders. We observed that vectors still hold most of the genetic and genotypic diversity and new invasions can worsen the situation by enhancing the diversity and, consequently, increase the resilience of the populations along the coast. Local strategies have been taken to control the expansion of Tubastraea spp. in the Southwestern Atlantic coast81; however, controlling the vectors responsible for introduction and dispersion is the key procedure to turn management more effective and to prevent further invasions/population expansions82.Understanding the invasion processes and the identification of the vectors are primordial steps for improving management and control of this ever increasing problem. Our results show that clonality and dissemination through vectors are the main reasons for the fast spread and invasive success of T. coccinea and T. tagusensis, from 14 and nine sites respectively, were sampled by SCUBA diving between 2012 and 2017 , two oil platforms (P14 and P27) and one Floating Production Storage and Offloading Vessel (FPSO Marlim Sul). Additionally, a native population of T. coccinea (Taiwan) was sampled for comparison  for all individuals of T. coccinea and T. tagusensis, respectively. PCRs were performed in 10 μl reactions including 0.2 μM of forward primer with M13 tail at their 5′ end (TGT AAA ACG ACG GCC AGT), 0.4 μM of labeled primer 84, 0.8 μM of reverse primer, 1U GoTaq (Promega), 1X PCR Buffer (Promega), 0.20 mM dNTPs (Invitrogen), between 1.5 and 2.5 mM MgCl2 , 10 μg BSA (Invitrogen), and 5–10 ng of DNA. Cycling conditions were: 95 °C for 3 min followed by 5 cycles at 95 °C, 30 s; 52–62 °C, 30 s; 72 °C, 45 s; and 30 cycles at 92 °C, 30 s; 52–62 °C, 30 s; 72 °C, 55 s; with a final extension at 72 °C for 30 min85. Final concentration of MgCl2 and annealing temperature followed Capel et al.34. Amplification was verified in 2% agarose gel. PCR products were pooled with GS600-LIZ size standard (Applied Biosystems) and genotyped in the ABI 3500 genetic Analyzer (Applied Biosystems). Genotypes were determined using the program Geneious 7.1.986.Total DNA was extracted using the Phenol:Chloroform method described by Fukami 87 on R 3.2.388 was used to assess the clonal structure of each species on all sites. A total of eight samples from T. coccinea (3%) and six samples from T. tagusensis (4%) failed to amplify for more than one locus and were excluded from the analyses. Of the remaining samples (298 T. coccinea and 166 T. tagusensis), 48 (16%) and 10 (6%) individuals have missing data at one locus. All individuals with identical alleles at all loci (ramets) were assigned to the same multilocus genotype . To check if individuals with the same MLG are truly clones, the probability of finding identical MLGs resulting from distinct sexual reproductive events (Psex) was calculated for each population89. When Psex > 0.001, samples were considered product of distinct sexual reproduction events (not truly clones) and included in analyses of genetic diversity. Two indexes were used to describe the clonal diversity in each population, the clonal richness (R), taking into account the number of individuals sampled (R = (MLG − 1)/(N − 1), ranging from 0 to 1, when all samples analyzed correspond to a different MLG); and the genotypic evenness (V), calculated by the Simpson’s complement evenness index to evaluate equitability in the distribution of the MLG 90. For genetic diversity analyses, only unique MLGs per population were considered.The package ‘RClone’91 was used to test linkage disequilibrium among all pairs of loci. Subsequent analyses were done by removing loci in linkage disequilibrium with more than one other locus. The software INEst was used to evaluate the occurrence of null alleles using the individual inbreeding model (IIM) and taking into account intrapopulation inbreeding92. The presence of null alleles can bias several parameters usually measured in population analyses such as the inbreeding coefficient, the observed heterozigosity and fixation indexes92. To assess each population’s genetic diversity, the number of alleles (A), private alleles (Ap), allelic richness (Ar), observed (Ho) and expected heterozygosities (He) and were calculated using the package ‘diveRsity’93 in R 3.2.388. The inbreeding coefficient (FIS) and deviations from Hardy-Weinberg equilibrium were calculated with the software FSTAT91.The FSTAT program94, was constructed using the software Populations 1.2.3295 and the package ‘ape’96 in R 3.2.388. To visualize possible groups of sites, a Principal Components Analysis (PCA), using sampling sites as grouping factor, was performed using the package ‘Adegenet’97 in R 3.2.388.To explore the topology of phylogeographic relationships among sampling sites, a neighbor-joining (NJ) tree based on Cavalli-Sforza’s and Edwards chord distance, suitable for microsatellite dataT. coccinea and T. tagusensis, respectively. A Bayesian analysis was performed in the new data set using the software Structure v. 2.3.498 with the admixture ancestry model, correlated allele frequency and no sampling locations as prior. The analysis was performed with an initial burn-in of 500,000 cycles followed by 500,000 additional cycles and the number of clusters (K) tested varied from 1 to 14 for T. coccinea and 1 to 9 for T. tagusensis with 15 iterations for each K-value. The most likely K-value was estimated by estimating the “log probability of data” for each value of K (mean LnP(K)) and ΔK criterion98 using Structure Harvester99.To estimate the number of genetic clusters in the dataset, repeated MLGs were removed from the data set, leaving 84 and 30 individuals for Supplementary File


Modelling of internal migration to new cities is challenging, yet necessary to ensure that these newly established urban areas will be populated and function as intended. In the State of Kuwait, there is a unique set of push and pull factors: government subsidised housing for citizens, the existence of a single urban area, and the initiation of a new and ambitious master plan for the construction of 12 new cities, which are expected to attract not only locals, but also international residents and businesses. On top of these factors, there is an unusual demographic situation, as non-citizens outnumber Kuwaiti citizens by a factor of 2.3, with these groups having widely different preferences in terms of housing. Currently, there is no plan to take these resident groups’ opinions into consideration for the new cities project. Besides, the current study simulates the impacts of the involvement of residents in urban planning. Samples from resident groups (citizens and non-citizens) participated in targeted surveys and useful answers were extracted in relation to the migration likelihood, push and pull factors that may affect their decisions, spatial preferences for new cities and their opinions on segregation by nationality. Specifically, the survey results showed significant interest of residents in moving to the new cities. For citizens, the most important factors in deciding whether to move or not were proximity to their close family and housing availability, while for non-citizens the most important factor was the creation of new employment opportunities. Both survey groups agreed that existing city property prices are too high and make the prospect of moving to a new city more attractive. The responses were transferred in an Agent Based Model, and the simulations showed certain differences to the official projections for 2050 without the public responses, in regards to the geographical distribution of the most desirable suburbs. Furthermore, the simulations showed that in the new cities, nationality segregation levels are expected to drop by at least 15% compared to the 2015 levels. The findings may be utilised by the authorities to modify the master plan accordingly. Kuwait is an Arabian Gulf country that has experienced a rapid population growth in the last decades mainly driven by international migration . This haPredicting migration and future population distribution are essential for the successful development of new urban areas, the provision of affordable housing and creation of new job opportunities . The majIn Arabian Gulf countries and specifically in Kuwait, economic-driven migration may not be significant due to its plentiful resources  and relatively small size leading to relatively uniform distribution of wealth. In fact, the drivers behind internal migration in Kuwait and similar Arabian Gulf countries as a geographical phenomenon are largely unknown. The reason for this is mainly the lack of data about internal migration. In the past, urban growth in Gulf cities was mainly driven by city expansion and intensification and no independent cities were developed , 9, whicRecently however, and as many new cities are planned to be constructed in Arabian Gulf countries , 11, thePush-Pull theory of migration is used to identify the factors driving migration at origins and destinations . TraditiIn modern industrialised societies, it is common for government planning authorities to regulate push and pull factors, for instance by offering new public sector jobs or subsidising housing markets in new planned cities in order to achieve a balanced population distribution , 16. In Urban planning that does not thoroughly consider the drivers of internal migration may result in costly and unsuccessful urbanisation policies. Generally, this is not an issue in cases where development planning is transparent and conducted in harmony with the market trends and community participation , 19. HowLack of sufficient number of people migrating to new cities and hence resulting in uninhabited cities, orStagnated growth for new cities if a lower than expected numbers of people settle in the new cities.One notable example of the risks of excluding the public opinion in planning is the construction of Ghost Cities in China; complete cities established with full infrastructure, but without any residents . It can The Kuwait government is launching a project for developing new cities for its current and future residents . This stWill future planned city areas attract sufficient population for settlement?Do people’s preferences on migration and future cities differ from the government plans, and potentially avoid problems of creating ghost cities?Will removing land use policies that separate Kuwaitis and non-Kuwaitis change future settlement patterns?This will be done by simulating the migration to new cities in Kuwait under different scenarios, including scenarios where public opinion for urban development is considered. The preferences and responses of the two resident groups (citizens and non-citizens) in Kuwait in relation to housing and migration obtained via an online survey and are integrated as behaviours in a simulation model. Finally, simulation outcomes are assessed in terms of their effectiveness in addressing a key urban issue in Kuwait, namely the level of residential segregation.Among the most important issues in urban planning is failing to meet project goals due to differences between community stakeholders’ perspectives, especially when resident opinions are not included in planning . In ordeThe aforementioned methods are part of a planning school referred to as participatory or comprehensive planning. Comprehensive planning, as the name implies, involves a holistic view on urban planning that accounts for the needs of broad demographic groups as a whole, rather than just planning for individual and/or localised urban systems, like residential zones or motor networks. Decisions for the medium and long term in comprehensive plans are made with consideration of multiple factors at the same time, ranging from land use to infrastructure and transportation networks and how these factors interact with each other. In comprehensive planning, community participation in decision making is vital to ensure that the needs of all resident groups and urban stakeholders are considered. Participatory planning involves the residents in the decision making processes in an attempt to develop successful urban development . The benSeveral internal migration models have been proposed in recent decades based on the individual migrants’ behaviours and decision making. Some models attempt to simulate migration based upon theorised human-economic behaviour, while others are more empirical and rely on direct observation or collected data from key stakeholders and demographics . In thisModelling internal migration to evaluate and check the validity of future development decisions can be done through simulating future locational patterns of migrant destinations . The majABM has been widely used for modelling urban planning and future development assessment around the world –41. The Scheduling agent behaviours and decisions may take place over a period of time that could range from seconds to decades. The environment within agents live, commute and interact can also be simulated at various spatial and temporal scales . The advSpatial modelling with ABM’s is important in urban planning for understanding the way cities grow with internal urban intensification or outward expansion, and for assessing potential negative impacts such as traffic congestion and housing shortage , 45_4i7oGovernment scenario: Simulates the urban development of new cities based on the government’s plans alone (without any public participation). Segregation is simulated according to the business as usual approach.Resident scenario: Simulates urban development of new cities based on the resident preferences as extracted from the online survey. Segregation is simulated according to the resident responses.Global Cities scenario: Simulates urban development of new cities based on the resident preferences as extracted from the online survey. Segregation is simulated according to the Global Cities plan .For each of the above scenarios, nationality segregation levels and the potential of limited internal migration to new cities will be assessed. The outputs are expected to help in evaluating the new master plan and understanding the future internal migration trends in Kuwait.Kuwait is used as case study in this paper. Kuwait has a population of 4.5 million living in an area of 17,818 km2 and the non-citizens make up for 70% of the total population . It shouThe government plans to establish 12 new urban centres independent from the sole existing urban area of Kuwait City, but as of the date of this paper none as yet have been implemented . In 2007The most important issues identified for developing the new plan according to Kuwait government were housing shortages and traffic congestion . AccordiThe government policy of offering free dwellings to citizens in specific residential districts.The right to own a house is limited to Kuwaitis and Arabian Gulf citizens only Non-citizens may only rent or share a house and cannot legally own any property in the country .The differences in district type and dwelling type preference between citizens and non-citizens: Kuwaitis prefer residential districts and large plot size houses; whereas, non-Kuwaitis prefer mixed use districts and apartments , 53, 54.The population proportion in mixed districts is 9% Kuwaitis and 91% non-Kuwaitis. In residential districts, non-citizen numbers are still notable, but the majority is living in their employers’ (citizens) dwellings as servants. The high levels of segregation can be seen in Due to the relatively small area and population of Kuwait, the high ratio of non-citizens and the existence of a single urban area, the drivers of internal migration are not clearly understood. Furthermore, there is a lack of data to understand the future of internal migration to the new cities, as there has been no significant internal migration occurrence in the past in Kuwait as explained earlier.A strong pull factor to attract citizens to move to the new cities in Kuwait is supported via government policy by the provision of housing welfare  . As of 2Cultural diversity is a rather controversial topic with a range of political and social dimensions. In a country with a high number of foreign residents like Kuwait, even internal migration is likely to trigger unpredictable effects and may undermine social solidarity in previously culturally uniform regions. For instance, non-Kuwaitis (South Asians or Egyptians) often concentrate in one district and so do Kuwaitis from the same tribe , 58. GenWith the above points, the research considered the following influences for modelling outcomes of new cities:Push-pull factors at the origin (existing urban areas) and destination (new cities).Resident willingness to move to new cities.Effects of nationality segregation.New master plan approval by the public.This paper is part of a larger project that contains two additional scenarios  , 50, 60.Due to the lack of data about internal migration and its drivers in Kuwait, it was necessary to conduct a survey for residents to obtain primary data. According to Brown and Robinson , data coThe survey invitations were sent via social media such as Twitter, Instagram and WhatsApp, as these applications are the most commonly used in Kuwait . The samThe survey was online and stayed open for collecting responses for 2 months. 879 responses were collected from Kuwaitis, which represent a 3% of Margin of error, whereas 406 responses were collected from non-Kuwaitis, which represent a 5% of Margin of error .According to Klabunde and Willekens , push anIt should be noted that this research’s surveys were approved as complying with the Australian National Statement on Ethical Conduct in Human Research Regulations and University of Queensland- Human Research Ethics Committee has approved it in 16/2/2016. Besides, eleven questions were developed related to internal migration decisions and locational preferences. These questions relate to the theoretical model of push and pull factors. Question 1 was developed to extract the residents’ decisions about migration. The locations of the new cities were shown to the survey respondents on a map . QuestioThe survey data was firstly disaggregated in different age and nationality categories. A separate category for servants was implemented, as they live in their employers’ dwellings and do not have the ability to make any decision for migration.The agent groups formed and used in the ABM were:Kuwaitis- teenagers (<18).Kuwaitis- young adults (18–34).Kuwaitis- middle aged (35–49).Kuwaitis- seniors (>50).Non-Kuwaitis- teenagers (<18).Non-Kuwaitis- young adults (18–34).Non-Kuwaitis- middle aged (35–49).Non-Kuwaitis- seniors (50->60).Servants (non-Kuwaitis).These population categories were assigned to actual agents in the ABM, the details of which are presented in section 3.2.1. A possible sampling problem of bias may arise as it is expected that more young adults will be attracted to participate rather than seniors. To make sure this statistical bias is avoided, a correction technique called post-stratification weighting adjustment  was usedThere are several tools available for ABM that describe simulation models in terms of agents, environment, scheduling, interacting and rules and behaviours –69. InteThe model involves two types of agents:Decision agents (government planning authorities).Resident agents (mobile agents able to migrate from existing urban areas to the new cities).The resident agents are divided into two categories (citizens and non-citizens). These categories were further classified into 9 classes, according to the factors discussed in 3.1.2. Each of the nine resident agents was represented as resident agent locations (point features in GIS) for spatial visualization of migration in the model (each point = 100 persons). The environment was represented as a polygon feature class that includes the land use as districts. The decision-making process in modelling typically involves two steps: firstly, an assessment of the choices about migration and secondly the transformation of the assessment results into an action . HoweverThe first step is about establishing or not establishing new cities according to the number of people willing to move, as derived from the surveys. The threshold percentage of residents willing to move, above which new cities are established is 50% of the new city establishment capacity . The secThere are vacant lots in the district.Migration may be only towards the new cities (old districts can be occupied by residents in infilling step).The residents that would want to migrate to the new city exceed the aforementioned threshold percentage.Certain assumptions had to be made during the model design, due to lack of data and to promote realistic representation of the urban development in Kuwait. These assumptions are summarized in The model uses two types of spatial and population data to simulate population migration: 1) locational suitability parameters and 2) model demographic variables.Near tool in ArcGIS and according to existing and future infrastructure. Costs were calculated with the help of real estate annual reports ..73].Results shown in this section are the average or mode values out of 35 runs of the model. The results section will present the model’s results for the different scenarios in three different outcomes: a) future migration, distribution and densities in 2050, b) the order of establishing the new cities and c) the future nationality segregation levels. Therefore, According to the survey responses, the South region ranked higher in preference, however simulation results showed that the North region will host more residents. This is due to the suitability weights of the North region that are higher than the South region cities and the fact that North region cities have higher capacities and hence may host more residents. The West region does not appear to be in the top 3 regions for any group, due to its high distance to the current urban area and the coast. The Middle region is the second most preferred in most cases, most likely due to its closeness to the existing urban area and existing public services. Finally, the existing urban area is still predicted to be the most highly preferred region for all the residents even by 2050. Based on the future resident distribution in The simulation period is not long enough for the new city pull factors to reach high level of desirability.The residents are concerned about delays in new cities projectsThe residents prefer to be stay close to their current work places and current public services.Survey data or simulation such as:Senior citizens who own a dwelling do not desire to move.Young citizens who live in their parents’ dwellings are content with their current situation.Push factors of the existing urban area affect only young and middle aged residents.Real world reasons such as:Although the population is expected to be higher in 2050 compared to 2015, the urban density will drop by more than 50%. Figs It can be seen that the order based on citizen responses is different than the master plan proposed order, which highlights the importance of participatory planning.The diagram in In all scenarios the segregation ratios will be lower compared to the current situation and the Global cities scenario will present the lowest segregation ratio between residents. Figs In all scenarios the segregation levels will be lower across all new regions compared to the existing urban area. This trend is mainly due to the allocation of residents being only in the new cities.Three scenarios were developed and simulated with Agent Based Modelling (ABM) as a purely empirical model, to address a series of research questions in relation to the nationality segregation levels and the desirability of Kuwait’s new cities in terms of internal migration by 2050. The simulation outcomes signify the importance of public participation in urban planning. While this is not considered by the government in Kuwait or countries with similar conditions at present, the model of this paper may form a basis for integrating resident opinions in the design and evaluation of construction projects in the future.The online survey used in this research succeeded as a participatory planning approach to involve residents in land use decisions, and the results used in an agent-based migration model to assess outcomes of future plans. The survey allowed extracting residents’ choices, demands, needs and preferences. These were in turn used in the model as inputs and behaviours for the agents. The results showed that the new master plan of Kuwait will most likely not create ghost cities, as there is interest and sufficient number of residents willing to move to the planned new cities.From the survey it was clear that the main drivers of internal migration were related to housing and new employment opportunities. However, it was also noted that there were some differences between citizens and non-citizens in their needs and preferences. The results of the survey and the outcomes of the model suggested that there were no significant differences in terms of deciding whether to migrate or not. However, the preferred new settlement regions and district types were different between the two groups. In addition, economic and social reasons behind the decision of not moving to the new cities (pull factors at origin) are similar; whereas, the pull factors (at destination) that new cities offer to attract residents are different. This was the main factor used to distinguish agent groups based upon citizens and non-citizens in the model.It was no surprise that young and middle aged Kuwaitis had the highest desire to migrate to the new cities, as these age groups are the primary recipients of the welfare housing. However, it was surprising that non-Kuwaiti seniors are the keenest on migration. This could be explained because many non-Kuwaitis are nearing retirement age and they may have to migrate back to their home countries if they are not employed. Non-citizens typically work under contracts of various lengths, so retirement age may actually be relatively early. The new cities may offer new employment opportunities and entice them to stay in Kuwait instead of terminating their stay in the country after their contract expires. This is a particularly attractive prospect to most non-Kuwaitis, as leaving Kuwait would mean they lose their high salaries and social benefits  relative to their home countries.Furthermore, this illustrates how the push-pull drivers behind migration are different between citizens and non-citizens in Kuwait. The major pull factor at the destination for Kuwaitis and for non-Kuwaitis is housing, and employment opportunities respectively. Push factors at the origin were found to be similar: high pressure on land and property values and long commuting times in the existing urban area.The results showed that the nationality segregation levels will be lower in the future compared to 2015 level. In the scenarios based on government’s plans and resident preferences segregation is higher by 15% than in the third “Global Cities” scenario. The main reason for this is that citizens prefer to settle in purely residential districts, while non-citizens prefer mixed districts and this preferred settlement trend appears to persist by 2050 in the new cities. Furthermore, the government supports this trend by offering welfare housing only in residential districts. As seen from the Global Cities scenario, which does not include any purely residential districts, but establishes mixed districts with housing, public services and business activities instead, nationality segregation may be drastically reduced. Lower segregation levels will in turn attract more investors and should contribute in transforming Kuwait into a regional trade centre according to the government’s new vision for the future.The model results confirm that the resident responses are mostly aligned to the government’s development plans. Importantly, there are a sufficient number of people willing to migrate to the new cities. It can be concluded that establishing new cities is an effective plan as it will mitigate the traffic congestion, solve the housing shortage problems  and decrA major limitation of this study was that current resident preferences and responses were applied in the model as inputs for all time steps, which assumes that the responses will not change in the future. However, it was beyond the scope of research to predict and model future generation’s needs as there is a multitude of non-linear and unpredictable factors that may affect them. Future work can focus on predicting future political, social and economic conditions and integrate them in the ABM for future time steps for enhanced result reliability. In addition, further investigation about the minimum number of cities needed to reduce the negative impacts of urban growth in Kuwait can be carried out through new simulations.S1 File(DOCX)Click here for additional data file.S2 File(DOCX)Click here for additional data file.


Glycine max (L.) Merr.) is one of major food and feed crops. It is the world’s most cultivated annual herbaceous legume. Constructing a core collection for soybean could play a pivotal role in conserving and utilizing its genetic variability for research and breeding programs. To construct and evaluate a Korean soybean core collection, genotypic and phenotypic data as well as population structure, were analyzed. The Korean soybean core collection consisted of 430 accessions selected from 2,872 collections based on Affymetrix Axiom® 180k SoyaSNP array data. The core collection represented 99% of genotypic diversity of the total collection. Analysis of population structure clustered the core collection into five subpopulations. Accessions from South Korea and North Korea were distributed across five subpopulations. Analysis of molecular variance indicated that only 2.01% of genetic variation could be explained by geographic origins while 16.18% of genetic variation was accounted for by subpopulations. Genome-wide association study (GWAS) for days to flowering, flower color, pubescent color, and growth habit confirmed that the core collection had the same genetic diversity for tested traits as the total collection. The Korean soybean core collection was constructed based on genotypic information of the 180k SNP data. Size and phenotypic diversity of the core collection accounted for approximately 14.9% and 18.1% of the total collection, respectively. GWAS of core and total collections successfully confirmed loci associated with tested traits. Consequently, the present study showed that the Korean soybean core collection could provide fundamental and practical material and information for both soybean genetic research and breeding programs.A core collection is a subset that represents genetic diversity of the total collection. Soybean ( Genetic diversity is fundamental in crop breeding and research programs. Although genetic diversity could be a barrier to progress, it is essential for crop improvement. Monoculture of a few improved cultivars has decreased the genetic diversity across crop species . One of Oryza sativa L.) [Triticum aestivum L.) [Gossypiumbar badense L.) [Arachis hypogea L.) [Capsicum spp.) [Ziziphus jujube Mill.) [Cucumis melo L.) [Medicago spp.) [Glycine max L. Merr.) [Across the world, germplasm conservation centers have been established to preserve genetic diversity of target crop species. Although large numbers of collections are desirable to preserve genetic variability, their usefulness and accessibility might be inversely related to their size . An incrtiva L.) , wheat (ivum L.) , cotton ense L.) , peanut ogea L.) , pepper um spp.) , jujube e Mill.) , melon (melo L.) , medicaggo spp.) , and soy. Merr.) .http://genebank.rda.go.kr/). China has the largest soybean collection. There are approximately 26,000 accessions in the Institute of Crop Germplasm Resources of the Chinese Academy of Agricultural Science [Soybean is one of the most important crop species as both food and feed sources in the world. Soybean genetic resources are largely preserved in China, the USA, Japan, and Korea , 19, 20. Science .Many studies have evaluated various strategies to construct core collections of many crop species , 21, 22.Although a core collection of soybean was first constructed in 1987 , no follThe objectives of this study were to: 1) construct a Korean soybean core collection from 2,872 soybean collections, 2) evaluate genetic and phenotypic diversity of core and total collections, and 3) conduct genome-wide association studies (GWAS) for several important phenotypic traits in both core and total collections and compare GWAS results.A total of 2,872 soybean collections  maintained in the National Agrobiodiversity Center in the Rural Development Administration  were used for this study. These soybean collections originated from China, Japan, the USA, N. Korea, S. Korea, and other countries . Among these collections, 2,872 cultivated soybeans originated from China, Japan, the USA, N. Korea, S. Korea, and others .® 180k  SoyaSNP array was used for SNP genotyping [® Genotyping Solution Data Analysis User Guide [Young trifoliate leaves from a single plant of each collection were collected for DNA extraction. Genomic DNA was isolated using the CTAB (cetyltrimethylammonium bromide) method  with a mnotyping . Genomicer Guide .® 180k SoyaSNP array. Phylogenetic tree and principal component analysis (PCA) were conducted by using APE R package [Phylogenetic analysis of the total collection was performed using genotype data from the Axiom package . A dista package  was used package , 39. SNP package  program  package , 42.To select accessions for a core collection, genotype data of the total collection were analyzed using GenoCore , a fast Five qualitative traits and two quantitative traits were evaluated for both core and total collections in field tests. The total collection was tested in an experimental field at the National Institute of Crop Science  in 2013 and the core collection was grown in an experimental field at the National Institute of Crop Science  in 2016. The experimental design was a randomized block design (RBD) with two replicates. The field plot was 3 m long with 0.75 m of row spacing and plant spacing within rows of 0.15 m. Two seeds were sown per spot (or hole).Five qualitative traits, including hypocotyl color, leaflet shape, flower color, growth habit, and pubescent color, were investigated at V1, R1, R2, R3, and R7 stages, respectively. Flower color was recorded as purple or white. Hypocotyl color was purple or green. Pubescent color was tan or gray. Growth habit was recorded as either determinate or indeterminate type. Leaflet shape was classified as ovate or narrow. In the case of quantitative traits, days to flowering (R1) were recorded as numbers of days from planting to beginning to bloom. Each accession was individually bulk-harvested after its full maturity stage (R8). A sample of 100 cleaned seeds from each collection was randomly selected and weighed.http://www.r-project.org/). GWAS was conducted for both core and total collections to compare their genetic diversities for tested phenotypic traits.To evaluate whether the core collection could sufficiently represent genetic diversity of the total collection, four phenotypic traits  with known controlling genes were tested through GWAS. After filtration of SNPs with < 1% minor allele frequency (MAF) and > 5% heterozygosity, 131,620 SNPs were selected and used for GWAS using a compressed mixed linear model . All anaE1, E2, and E3, have been genetically mapped to chromosome 6, 10, and 19 in soybean, respectively [Genes controlling flower color (W1), pubescent color (T), and growth habit (TFL1) of soybean have been mapped to chromosome 13, 6, and 19, respectively , 48, 49.ectively , 52, 53.® 180k SoyaSNP array were used. In the total collection, average sample call rate, homozygosity rate, and heterozygosity rate were 99.41%, 98.82%, and 0.59%, respectively. In the core collection, average sample call rate, homozygosity rate, and heterozygosity rate were 98.83%, 97.21%, and 1.62%, respectively .To identify genetic diversity in the total collection, 170,223 high-quality SNPs from the Axiomectively . SoybeanThe 170,223 high-quality SNPs were also used to construct the core collection from the total collection . Based oWe first selected 407 accessions reflecting 99% of genetic diversity of total accessions. Second, as additional sources of genetic variations, 24 cultivated soybeans used for whole-genome re-sequencing were included with the first selection. This addition produced a core collection consisting of 431 soybean accessions. However, we found that one collection (Danbaek) was included in both the first selection and the re-sequencing accessions. Finally, a Korean soybean core collection consisting of 430 accessions was constructed .PCA was conducted to confirm whether the core collection represented the genetic diversity of the total soybean collection. Results showed that the distribution of collections by genetic diversity showed similar trends for both core and total accessions . As showSNP information was used to evaluate the population structure of the core collection. Marginal likelihood was found to be the highest when K was 5 . The numThe population structure of the core collection was doubled-checked using both phylogenetic tree and PCA. In the phylogenetic tree, most accessions with more than 50% admixture fractions for a genome were distributed over the five subpopulations while admixed accessions were placed between subpopulation clades . Scree pImportant phenotypic traits of soybean in both core and total collections were evaluated. In the core collection, days to flowering ranged from 27 to 68 days . Two hunIn the present study, we investigated and compared five phenotypes in core and total collections. The proportion of each trait  in the core collection to that in the total collection was approximately 18.1%. Specifically, proportions of these qualitative traits in the core collection to that in the total collection were around 15.8% in South Korea, 38% in North Korea, 51.4% in China, 27.7% in Japan, 16.6% in the USA, and 20.2% in other countries . These rIn the case of quantitative traits, the proportion of days to flowering in the core collection to that in the total collection was around 26.1%. The proportion of days to flowering in the core collection to that in the total collection was around 12.1% in S. Korea, 48.9% in N. Korea, 68.6% in China, 47.8% in Japan, 19.7% in the USA, and 39.3% in other countries . The proWe also compared the distribution of accessions between total and core collections by their origins  Figs. ThE1, E2, and E3 were positioned on the same chromosomes in both core and total collections , pubescent color (T), and growth habit (TFL1), GWAS confirmed that both collections had significant SNPs at gene regions of the same positions. QTLs associated with days to flowering genes lections .® 180k SoyaSNP array. Genotypic, phenotypic diversity, and population structure of the population were then analyzed. As mentioned previously, earlier studies have tested various selection methods to construct core collections in diverse crop species. To date, most of core collections for crop species have been developed based on geographic origin, morphological, and phenotypic traits. Ultimate goals of a core collection are not only to have the maximum possible genetic diversity of the total collection, but also to have minimum repetition. However, it has been reported that phenotypic data cannot perfectly reflect the genetic diversity of the total collection since most of quantitative agronomic traits are easily affected by environmental factors [In the present study, a Korean soybean core collection was constructed based on SNP information from the Axiom factors . In cont factors .Ziziphus jujube Mill) core collection. For Capsicum germplasm, Lee et al. [Although several studies have previously established core collections based on genotypic data, relatively few molecular markers have been used to determine genetic diversity in total collections and select core collections. Kuroda et al.  have usee et al.  have conCompared to STRUCTURE analysis, the phylogenetic tree did not present clear separation according to geographical origin. In particular, most of the Chinese collections belonged to subpopulation V . HoweverW1), pubescent color (T), and growth habit (TFL1) were identically detected in both collections. However, the GWAS for polygenic traits presented different results for the two collections. In the case of E1 (major gene for days to flowering), GWAS results were identical for the two collections. The p-value of the SNP associated with E1 was highly significant in the two collections: p = 1.83E-08 in the core collection and p = 1.21E-11 in the total collection. In the case of minor genes (E2 and E3), GWAS results for E3 were similar for the two collections. The p-value of the SNP representing E3 was also highly significant in the two populations: p = 3.67E-07 in the core collection and p = 5.40E-10 in the total collection. However, the p-value of the SNP representing E2 was found to be highly significant (p = 3.81E-12) in the total collection, but less significant (p = 0.0021) in the core collection Click here for additional data file.S2 Fig(TIF)Click here for additional data file.S3 Fig(TIF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 TableTested traits included flower color, hypocotyl color, pubescent color, growth habit, and leaflet shape.(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(XLSX)Click here for additional data file.


A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, STF was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and STF mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations’ ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda–Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population STF among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while STF between Egyptian and Rwanda–Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa , and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom E. tenella infection (coccidiosis)  . The Danidiosis) .1, the 30-year averages for the major meteorological parameters for the capital of each country are as follows: Egypt has the hottest and driest weather with larger diurnal variation. Average temperatures ranged between 18.9 and 34.7°C and 2.47 ml of average annual precipitation rate. In Rwanda, average temperatures ranged from 25.9 to 28.2°C with an average annual precipitation rate of 79.24 ml, while Ugandan average temperatures ranged between 26.9 and 29.3°C with a precipitation rate of 105.24 ml. Altitude averages are, respectively, 75, 1,497 and 1,155 m in Egypt, Rwanda, and Uganda. For climatic variation among sampling locations of indigenous Egyptian chicken populations, 2/year, and accordingly, Egypt was classified into 12 belts (zones). The Nile delta  is located in a solar radiation belt that receives between 5.5 and 6.6 kWh/m2/day, while Fayoum (Mid-Egypt) receives 7.0–7.3 kWh/m2/day and Qena (Southern Egypt and source of Dandarawi) receives 8.3–8.5 kWh/m2/day. For solar radiation estimates in Rwanda, 2/day in Kayonza district and 5.28 kWh/m2/day in Bugesera district. While annual ETo (mm/day) varied between 4.49 in Kayonza and 4.9 in Bugesera districts. In Uganda, average solar radiation ranged between 17.2 MJ/m2 (4.78 kW/m2/day) in Kabale and 21.5 NJ/m2 (5.97 kWh/m2/day) in Soroti . ROH exist when identical haplotypes are inherited from each parent. ROH analysis indicated the population history and trait architecture  and the allele-frequency-based inter-population genetic differentiation (itecture . The lenitecture . It was itecture . Therefoting FST . With thn = 25), Kicukiro, Kirehe, Musanze, Nyagatare, and Rubavu (n = 15 for each) districts. Ugandan samples were collected from three districts; Kamuli, Masaka, and Luweero . For more details on Ugandan and Rwandan samples see A total of 268 blood samples were collected on FTA cards from birds of East Africa , and North Africa . Samples were collected by local veterinarians following the approved country standards of animal care practices. A total of 172 samples were collected in EA: 100 Rwandan and 72 Ugandan ecotypes. Rwandan samples were collected from the Huye  using the Affymetrix Axiom0k Array . A total0k Array . The rawk < 10, where k is the number of expected subpopulations, and the best k was determined based on the cross-validation error for different numbers of ancestral genetic backgrounds.PLINK 1.9  was usedRuns of homozygosity analyses were carried out for both individual populations and combined EA and NA breeds/ecotypes using PLINK 1.9 to examine overlapping genomic regions that harbored alleles driven to fixation within each population or group of populations using a SNP based sliding window approach. ROH requirements were defined as ≥300 SNPs, a minimum SNP density per ROH was set to one SNP per 50 kb, a maximum gap permitted between consecutive homozygous SNPs was set to 10 kb, three heterozygous calls were allowed within a run to account for genotyping errors and/or hitch-hiking events, and allelic match threshold of 0.95 identity and >20 SNPs. The overlapping ROH was considered as those overlapped across all populations, regardless their length, and consensus ROHs are those reached a consensus in either >50% of the individuals of an ecotype or in >75% of a breed, except for the Rwanda and Uganda ecotypes where a 40% consensus threshold was accepted. A gene ontology (GO) enrichment analysis was conducted for the list of genes located at the identified ROH consensus regions.STF analysis was calculated according to STF window consisted of 500 kb with a step size of 250 kb. Only windows with ≥20 SNP were considered. Candidate genomic regions under selection were defined by a cutoff STF value >0.30, that exceeds the value of 0.25 defined as very great genetic differentiation according to STF windows.To identify the regions under selection that are differentiated among breeds or ecotypes, an overlapping sliding window-based STF analyses were identified using the software bedtools v2.26.0 using the  annotation genome2. GO for molecular function and biological processes for the identified genes were determined by PANTHER using the Gallus gallus reference genome3 and enriched genes were identified using Enrichr  was determined based on the cross-validation error for different numbers of ancestral genetic backgrounds. Admixture analysis ; tolerance to solar radiation (melanogenesis); ion binding and transport ; immunity and defense response ; oxygen-heme binding and transport; angiogenesis; apoptosis; tissue morphogenesis ; and tolerating acute heat stress (heat shock protein transcription factor).A total of 153 within-population consensuses ROH were detected with 41, 49, 35, and 28 in Baladi, Dandarawi, Fayoumi, and Rwanda–Uganda populations, respectively. Consensus ROHs were found on Chromosomes 3, 5, and 8 in Rwanda–Uganda; 2, 3, 4, 8, and 11 in Fayoumi; 1, 4, and 8 in Dandarawi; and 2, 3, 8, and 11 in Baladi . The numThe total 196 genes located on the consensus 153 ROH regions were used for detecting over-enriched GO terms. Enriched GO terms indicated biological processes and molecular functions promoting different mechanisms for adaptation to various cellular and environmental stressors .AMY2A  gene (located on Chromosome 8) was annotated in the three African populations  was commonly enriched in the same three populations. The annotated SLC25A24 , Chromosome 8, in both Rwanda–Uganda and Dandarawi  and North-African (Fayoumi and Dandarawi) chicken populations studied. The (GO:0004556); molecular function of alpha-amylase activity was enriched and the ulations . AMY2A iandarawi  is involVASH1) and neuroglobin (NGB). VASH1 gene is involved in the biological processes of angiogenesis (GO:0001525), response to wounding (GO:0009611) and regulation of lymphangiogenesis (GO:1901491). Neuroglobin (NGB) gene is associated with molecular functions of oxygen binding to heme (GO:0019825) and transport (GO:0015671) which contributes to the adaptation to high altitude and lack of oxygen stresses.According to the environmental conditions of the two East-African countries studied (Rwanda and Uganda), the major stresses on the local chicken populations were oxidative stress, which is a common denominator for other stresses; high-altitude accompanied with lower oxygen availability; and lack of vaccination and poor health care. GO terms for molecular function of Oxygen binding (GO:0019825) and heme binding (GO:0020037); and physiological process of angiogenesis (GO:0001525), and oxygen transport (GO:0015671), S-transferase zeta 1 (GSTZ1) increases the glutathione-S-transferase activity (GO:0004364) and the molecular functions of glutathione metabolic process (GO:0006749), and therefore decreases lipid oxidation products  gene, Chromosome 8, was annotated in both GO terms in Dandarawi and Fayoumi , Golgi apparatus, and nucleus in testis, spleen, liver, kidney, heart, brain, and lungs (CLCC1 leads to disruption of chloride anion homeostasis in the ER and therefore disruption of protein-folding capacity and ER stress (Two GO terms associated with chloride transport were enriched being the chloride channel activities (GO:0005254) and the chloride transmembrane transport (GO:1902476). The chloride channel CLIC like 1 , Chromosome 11, was annotated (SLC6A2 is involved in NE transport and is associated with the pathophysiology of attention-deficit/hyperactivity disorder (ADHD) in children , Chromosome 11, annotated for the oxidoreductase activity (GO:0016491) is a microsomal enzyme complex that oxidizes the glucocorticoid cortisol to the inactive metabolite cortisone. This activity limits the impact of cortisol and would support immunity and defense response of Fayoumi and Baladi populations.Gene ontology terms for biological processes of NE transport (GO:0015874) and dopamine uptake involved in synaptic transmission (GO:0051583); and molecular function of oxidoreductase activity (GO:0016491) were commonly enriched . For botnnotated . SLC6A2 children . Dopaminchildren . SLC6A2 +-Cl- cotransporter solute carrier family 12 member 3 (SLC12A3) and the K+-Cl- cotransporter (SLC12A4), Chromosome 11. SLC12A3 is a cotransporter in the kidney that is involved in sodium ion transport and chloride transmembrane transport. It re-absorbs sodium and chloride ions from the tubular fluid into the distal convoluted tubule cells of the nephron. SLC12A4 exhibits chloride symporter activity, playing key roles in electrolyte movement across epithelia and in intracellular chloride homeostasis of neurons and muscle cells  and anion transmembrane transport (GO:0098656) were enriched. Common putative annotated genes for those GO terms were the Nale cells . AnnotatHSD11B2 was the commonly gene annotated on Chromosome 11  and both physiological processes of glucocorticoid biosynthesis (GO:0006704) and response to glucocorticoid (GO:0051384). The osome 11 , in the MMP2) gene (Chromosome 11), annotated in this GO terms, contributes to the biological process of tissue morphogenesis; e.g., collagen catabolism and bone trabecula formation. MMP2 may therefore, contribute to the distinctive morphogenesis characteristics of Fayoumi. Both GO terms of growth factor activity (GO:0008083) and regulation of apoptotic process (GO:0043065) were enriched in Fayoumi and the OSGIN1 (oxidative stress-induced growth inhibitor 1), Chromosome 11  is involved in Fayoumi bone and ligaments morphogenesis . The Matosome 11  was annochondria . OSGIN1 Mel1c), 2/day  was annotated . SFRP2 is involved in chicken embryogenesis; development of the neural system (brain tissue), muscles (myogenesis), and developing eyes particularly the pigmented layer of the retina and photoreceptors , and response to radiation (GO:0009314). Expression of the annotated melatonin receptor type 1C , 2/day , the soueceptors . SFRP2 sHSF4 exhibits tissue-specific expression with preferential expression in heart, brain, skeletal muscle, and pancreas, with two alternatively spliced isoform HSF4a and HSF4b. HSF4a acts as an inhibitor, while HSF4b as an activator of tissue specific heat shock gene expression.The Baladi is the only naked neck population (ecotype) in this study. The physiological process of protein homotrimerization (GO:0070207) enriched in this breed reflected the homotrimerization of heat shock protein factor. Heat shock factor proteins 1, 2, 3, and 4 were annotated on Baladi Chromosome 11 , reflectSTF) analysis: (1) Dandarawi, (2) Baladi and Fayoumi (1 and 2 represent North-African populations), and (3) Rwanda and Uganda (East-African). Two comparisons were conducted; East-African vs. North-African and Baladi and Fayoumi vs. Dandarawi populations.Population stratification analyses  and ROH STF indicated one selection sweep on Chromosomes 4 (20.2–20.3 Mb), STF regions, on Chromosome 4, indicated several genes playing roles in cell cycle, differentiation and proliferation, i.e., SFRP2, FGA, FGB and FGG  and PLRG1 (pleiotropic regulator 1). GO enrichment analysis indicated the GO term for physiological process of cell differentiation (GO:0030154). Within this enriched GO term, annotated genes were found to be contributing to the development of muscular and neural systems . Myogenin (MYOG) acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. MYOG induces myogenesis (fibroblasts to differentiate into myoblasts), in a variety of cells and tissues. The SFRP2, as previously indicated, is involved in chicken embryogenesis; development of the neural system (brain tissue), muscles (myogenesis), and developing eyes particularly the pigmented layer of the retina and photoreceptors  vs. Dandarawi (Southern Egypt) F (ypt) FST  revealedGABARAPL2), Atg8 (autophagy-related protein 8) family that contributes to the formation of autophagosomes. This indicated genetic variation in autophagy process between the two genetic groups. For the cell cycle and bird aging associated gens, the TERF2IP  gene (GO:0032204 and GO:0032205) encodes a protein that is part of a complex involved in the biological processes of telomere length and protection .The annotated putative genes also reflected the similar mechanisms of adaptation. For the immunity-relevant genes, the annotated GABA type A receptor associated protein like 2 (AP1G1 (adaptor related protein complex 1 gamma 1 subunit) gene that was annotated in the two GO terms (GO:0035646 and GO:0032438) plays a major role in Dandarawi feather pigmentation (melanosome organization and transport). AP1G1 could reflect the sex-linked variation in feather coloring  and Dandarawi tolerance to intensive solar radiation in Southern Egypt. AP1G1 was also annotated in the GO:0045954 , ZFHX3 (zinc finger homeobox 3) gene affects the regulation of myoblast differentiation and fiber development .The SOD1, superoxide dismutase [Cu–Zn] contributes to the biological processes of cellular response to Oxygen radicals (GO:0071450), and Superoxide metabolic process (GO:0006801), SOD1 role, as an anti-oxidizing enzyme, is to converts harmful superoxide radicals into less reactive oxygen species (ROS) and hydrogen peroxide, H2O2 (NQO1  is a major quinone reductases, that is highly inducible and plays multiple roles in cellular adaptation to stress. Reported roles of NQO1 included its ability for quinone detoxification, to function as a component of the plasma membrane redox system generating antioxidant forms of ubiquinone and vitamin E, and its function as a superoxide reductase  contributes to the molecular function of nitric-oxide synthase activity (GO:0004517) and the nitric oxide biosynthetic process (GO:0006809). P < 0.05) during summer and winter peaks, in goats, as compared to moderate season. Authors, therefore, indicated the possible involvement of the NOS family genes in ameliorating thermal stress and to maintain cellular integrity and homeostasis.Concerning the adaptation to thermal stress, the annotated In African developing countries that lack genetic improvement schemes applied to indigenous chicken genetic resources, the major forces driving genetic diversity are natural biotic/abiotic stresses, including flock management. In this study, the MDS reflected genetic divergence between the smallest Egyptian breed, Dandarawi, adapted to Southern Egypt’s extreme heat and solar radiation conditions, from the other two populations belonging to a less stressful environment of Delta and Mid-Egypt. Both MDS and admixture analyses confirmed the genetic similarity between the Rwandan and Ugandan ecotypes that has been reported by A total of 153 within-population consensuses ROH were detected; 41, 49, 35, and 28 in Baladi, Dandarawi, Fayoumi, and Rwanda–Uganda populations, respectively. Chromosomal distribution of the within-population consensus ROH varied among the five populations studied, i.e., the highest ROH signals were found on Chromosomes 2, 3, 8 and 11 in Baladi; 2, 3, 4, 8, and 11 in Fayoumi; 1, 4, and 8 in Dandarawi; and 3, 5, and 8 in Rwanda–Uganda populations. Chromosome 8 was common among all studied populations in bearing signatures of selection. AMY2A  gene, in Rwanda–Uganda, Fayoumi and Dandarawi populations suggested the signatures of selection forces of carbohydrates and glycogen metabolism, and response to thermal stress and unbalanced feeding. On the same chromosome, the SLC25A24  was annotated in both Rwanda–Uganda and Dandarawi populations. SLC25A24 is involved in calcium ion binding (GO:0005509) and cellular response to oxidative stress (GO:0034599) , household waste and some grain supplementation. Therefore, carbohydrates metabolism, energy generation and transport are important traits for adaptation. The enriched GO term  and the annotated 0034599) . SLC25A2 demands  and suppVASH1) gene is involved in angiogenesis, regulation of endothelial cell proliferation in response to wounding (GO:0009611), and regulation of lymphangiogenesis (GO:1901491)  annotated in Rwanda–Uganda, enables the molecular functions of glutathione transferase and peroxidase activities in response to oxidative stress. 2+ is a part of the trade-off in Ca2+ usage between the calcium needed for eggshell formation and that stored in the ER. Maize contamination with the feed-borne mycotoxin aflatoxin B1 (AFB1) is a common problem in East-African humid environment. Meleagris gallopavo) was very susceptible to the AFB1 because it lacks a functional hepatic GST-mediated detoxification of AFBO , while the wild turkey (Meleagris silvestris) was resistant due to its hepatic ability for GST-mediated AFBO detoxification , oxygen transport (GO:0015671); and molecular function of heme binding (GO:0020037), and oxygen binding (GO:0019825). Annotated genes within detected ROH in the Rwanda–Uganda populations reflected the effects of high altitude and management forces, e.g., feeding quality, on shaping genetic divergence. Vasohibin-1 (1901491) . Fleming binding . This refication . AnnotatCLCC1), annotated in Fayoumi and Dandarawi; the Na+-Cl- co-transporter solute carrier family 12 member 3 (SLC12A3) and the K+-Cl- co-transporter solute carrier family 12 member 4 (SLC12A4) annotated in Fayoumi. CLCC1 was reported by CLCC1 and disruption of chloride homeostasis in the ER disrupted the protein-folding capacity of the ER and resulted in ER stress, misfolded protein accumulation, and neurodegeneration. SLC12A3 is a cotransporter in the kidney that re-absorbs sodium and chloride ions from the tubular fluid into the distal convoluted tubule cells of the nephron. SLC12A4 plays key roles in electrolyte movement across epithelia and in intracellular chloride homeostasis of neurons and muscle cells  was annotated in both Fayoumi and Baladi, while 11β-hydroxysteroid dehydrogenase type 2 (HSD11B2) was annotated in Fayoumi. SLC6A2 is involved in NE transport and availability, while HSD11B2 oxidizes the glucocorticoid cortisol to the inactive metabolite cortisone, preventing illicit activation of the mineralocorticoid receptor. HSD11B2 is expressed in aldosterone-sensitive neurons and responsible for promoting appetite for sodium (feeding behavior), independently of thirst or hunger , results indicated that the adrenaline and noradrenaline play roles in their adaptation profiles, as both the biological processes of NE transport (GO:0015874) and dopamine uptake (GO:0051583) were enriched. Dopamine is a neurotransmitter and a precursor of adrenaline. Stress activates the hypothalamus–pituitary–adrenal (HPA) axis, which increases the release of glucocorticoids from the adrenal glands that in concert with other neuro-modulators, e.g., noradrenaline, promote cognitive adaptation to stressful conditions . Sodium-r hunger . Inhibiteceptors . HSD11B2 Fayoumi .MMP2  annotated in Fayoumi contributes to the biological process of tissue morphogenesis, collagen catabolism and bone trabecula formation (spongy bone that contains the red bone-marrow). The annotated TNFRSF11B, is a member of the TNF-receptor superfamily, which is responsible for the production of an osteoblast-secreted decoy receptor that functions as a negative regulator of bone resorption. Both annotated MMP2 and TNFRSF11B may be related to distinctive morphogenesis characteristic of mineral density and ability to fly in Fayoumi  and regulation of bone remodeling (GO:0046850) were enriched in Fayoumi.  Fayoumi .+ levels. Multiple genes contributing to oxidative stress reduction were annotated; OSGIN1 and HSD11B2 (hydroxysteroid 11-beta dehydrogenase 2) in Fayoumi. OSGIN1 encodes an oxidative stress response protein that regulates cell death and apoptosis by inducing cytochrome c release from mitochondria , is activated by monochromic light (green light) in several organs, and subsequently, activates several immune- and developmental-related processes within these organs. For instance, Mel1c activates B-lymphocyte proliferation in broiler bursa  and the biological process of response to radiation (GO:0009314) were enriched. Expression of melatonin receptor type 1C  revealed the population adaptation to the Egyptian heat condition. The heat shock proteins are chaperone proteins that effectively protect several proteins and cell organelles from stressors’ negative effects, mainly heat. Heat shock transcription factors, e.g., HSF4 exhibits tissue-specific expression with two alternatively spliced isoforms; HSF4a and HSF4b. HSF4a acts as an inhibitor, while HSF4b as an activator of tissue specific heat shock gene expression  and the annotated heat shock transcription factors 1, 2, 3, and 4 . The annotated SFRP2, as previously indicated, stimulates melanogenesis through microphthalmia-associated transcription factor and/or tyrosinase upregulation via β-catenin signaling (MAPK9 (mitogen-activated protein kinase 9) is involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. It targets specific transcription factors and mediates immediate-early gene expression in response to various cell stimuli, and is involved in UV radiation-induced apoptosis. Annotated SFRP2 and MAPK9 reflected selection footprints for the high-intensity of solar radiation in Southern Egypt governorate; Qena (source of Dandarawi), that receives 8.3–8.5 kWh/m2/day of solar radiation , and East-African (Rwanda and Uganda) populations were reflected in the annotated myogenin gene. Myogenin (MYOG) induces myogenesis (fibroblasts to differentiate into myoblasts), in a variety of cells and tissues, through its actions as a transcriptional activator that promotes transcription of muscle-specific target genes. Both NRP1 and NGF genes play role in neuron development. The NRP1 is involved in the development of the cardiovascular system, angiogenesis, the formation of certain neuronal circuits and in organogenesis outside the nervous system. NGF is a neurotrophic factor and neuropeptide primarily involved in the regulation of growth, maintenance, proliferation, and survival of certain neurons. Alteration in incubation conditions of developing chicks might change the developmental trajectories of some physiological regulation systems and may affect the quality of the young check during the first few days’ post-hatching  was enriched. Multiple genes contributing to the development of muscular and neural systems were annotated  and the Southern Egypt (Dandarawi) revealed genetic variation resulting from the different environmental stresses and breeding practices in Southern Egypt. Atg8 contributes to the formation of autophagosomes (GABARAPL2) , is a member of this family. STF results could reflect the variation between Fayoumi and Dandarawi in autophagy, which indicated variation in their resistance to NDV.agosomes . The annTERF2IP gene, annotated in the two GO terms, encodes a protein that is part of a complex involved in telomere length and protection  is practiced and birds are prone to extended production life, associated with an extended number of cell cycles, which could promote a signature of selection for telomere length and stability. otection . It is l2/day; Fayoum (Mid-Egypt and source of Fayoumi population) receives 7.0–7.3 kWh/m2/day; and Qena (Southern Egypt and source of Dandarawi) receives 8.3–8.5 kWh/m2/day. With absence of structural breeding plans, we speculated that Egyptian rural chicken populations, in the study, are under different selection pressures driven by variations in solar radiation. The enriched GO terms for biological processes of endosome to melanosome transport (GO:0035646) and melanosome organization (GO:0032438) could emphasizes variation between Dandarawi and both Baladi and Fayoumi in their tolerance to solar radiation stress. The AP1G1 (adaptor related protein complex 1 gamma 1 subunit) gene, annotated in both GO terms, plays a major role in feather pigmentation (melanosome organization and transport). AP1G1 could reflect both the sex-linked variation in feather coloring , and tolerance to intensive solar radiation in Dandarawi under Southern Egypt stressful environment. Climatic variation among sampling locations of indigenous Egyptian chicken populations had been reported. Egypt was classified into 12 zones according to the solar Atlas of Egypt . The NilIn conclusion, results of this study indicated that environmental stresses played major roles in shaping genomic variation of African chicken populations. In Egypt, Baladi and Fayoumi were genetically closer to each other than the Southern-Egypt Dandarawi population, while Rwanda and Uganda chickens showed clear overlap in their genomic structure, being under very similar environmental conditions. Although, no genetic exchange was reported between Egyptian populations (Fayoumi and Dandarawi) and East-African ecotypes (Rwanda and Uganda), the existence of some common ancestral genetic backgrounds among the two groups of populations could be due to the ancestral part of the genome, according to the hypothesis that ancient chickens were first introduced to Egypt, from Asia through the Cinnamon trade and then transported to other parts of the African continent including Rwanda and Uganda.STF mapping revealed selection footprints of possible environmental stresses, breed characteristics and management. ROH of all native African populations showed selection footprints for energy transport, calcium ion binding, and reduction of oxidative stress. North-African (Egyptian) populations, under hot desert environment, showed likely selection footprints for adaptation to heat, solar radiation, ion transport and immunity. East-African populations, under tropical savanna and higher altitude conditions, showed a signatures of selection for oxygen-heme binding and transport, and reduction of oxidative stress. Behavior and phenotypic characteristics were reflected by ROH mapping in the study. Genes associated with availability and transport of corticosteroid and NE could reflect the active behavior of the Fayoumi breed. STF mapping and its annotated genes emphasized the genetic variations likely generated by natural selective forces. Egyptian Fayoumi showed distinctive genetic mechanisms for their resistant to the endemic diseases, e.g., NDV. Management issues of chicken flocks, including extended bird longevity in the Southern-Egypt households was also reflected in terms of genes associated with telomere maintenance. These results enhance our understanding of the role of natural selection forces in shaping genomic variation, and genes contributing to adaptation under stressful African conditions.Intra-population ROH and inter-population The study presented in the manuscript involve blood sample collection from rural chicken in some Egyptian, Rwandan and Ugandan villages. Samples were collected by local villages veterinarians following the approved country standards for minimizing any probable bird uncomfortability.AE, FB, and MR conceptualized and designed the work. DF, AVG, and DK collected the sample and data. AE, FB, SL, and MR analyzed and interpreted the data. AE drafted the manuscript. FB, DF, AVG, CA, CS, DK, SL, and MR made a critical revision of the manuscript. All authors have approved the final version of manuscript to be published.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.