Introduction:Camellia, the largest genus of Theaceae, is well-known for having high economic values. Camellia granthamiana demonstrates large beautiful flowers with some primitive characters, such as multiple large and persistent bracteoles and sepals, was listed as Vulnerable species on the IUCN Red List.Methods: In this study, we investigated all possible records of the species, and sampled four natural populations and five cultivated individuals. By applying shallow-genome sequencing for nine individuals and RAD-seq sequencing for all the sampled 77 individuals, we investigated population genetic diversity and population structure of the species.Results and discussion: The results showed that the population sampled from Fengkai, previously identified as C. albogigias, possessed different plastid genome from other species possibly due to plastid capture; the species possesses strong population structure possibly due to the effect of isolation by distance, habitat fragmentation, and self-crossing tendency of the species, whose effective population size declined quickly in the past 4,000 years. Nevertheless, C. granthamiana maintains a medium level of genetic diversity within population, and significant differentiation was observed among the four investigated populations, it is anticipated that more populations are expected to be found and all these extant populations should be taken into instant protection. Camellia, the largest genus of Theaceae, contains approximately 280 species distributed near the Tropic of Cancer in East Asia, and 238 species were recorded in China, which are mainly distributed in Yunnan, Guangxi, Guangdong, and Sichuan provinces  Kuntze, known as China tea, and C. oleifera C. Abel, as an important source of oil) and ornamental values .rovinces . CamelliCamellia  and C. vietnamensis and C. grandiflora (2n = 8x = 120). Both C. granthamiana and C. albogigas were ascribed to the sect. Archecamellia Sealy of subgen. Protocamellia Chang in Flora Reipublicae Popularis Sinicae, as they demonstrate some primitive characters, such as multiple large and persistent bracteoles and sepals .Karyotypic studies on Camellia  showed td sepals . Geograpof China  and C. ghttps://www.cvh.ac.cn/) and the online Flora of China (http://www.iplant.cn/). We have successfully collected three populations of C. granthamiana and one population of C. albogigas in Guangdong, China. Furthermore, we utilized the shallow-genome sequencing method to de novo assemble the chloroplast genomes and construct a plastid phylogenetic tree. At the same time, we performed the restriction-site-associated DNA sequencing method on all the sampled populations. Through these efforts, we endeavored to investigate whether C. albogigas and C. granthamiana constitute one species or two, assess the population structure and genetic diversity of these species, and eventually provide some valuable information for their conservation.For the better understanding of threats to endangered species, phylogenetics and population genetics have been widely used in conservation genetics and (or) conservation biology to investigate the causes of species decline, such as habitat fragmentation, genetic drift, and barriers to gene flow, and identify counteracting measures and conservation units. However, recent advancements in genomic tools have further enabled the utilization of vastly expanded datasets of single-nucleotide polymorphisms (SNPs), providing unprecedented insights into the importance of genetic diversity in conservation . CurrentC. granthamiana and one population of C. albogigas. For each population, geographical information was recorded using a Garmin GPS unit , and the others were transplanted from Fengkai, Guangdong, China . As it is difficult to make clear which individual was transplanted from Hong Kong, China, we sampled fresh leaves from all five individuals  for DNA extraction, library preparation, and Illumina sequencing.Briefly, genomic DNA for each sample was extracted using the modified CTAB method  and puriC. granthamiana (NC_038181.1) was used as a reference and its rbcL gene was used as a seed. Furthermore, plastid genomes for 111 samples of Camellia and one sample of Polyspora hainanensis were downloaded from the NCBI website (https://www.ncbi.nlm.nih.gov/). In total, 120 plastid genome sequences were aligned using MAFFT, which performs well in reducing CPU time and increasing the accuracy of alignments for sequences with large insertions or extensions  and n . Then, the Perl script denovo-map.pl was applied to process all the samples, and the procedure populations was used to filter the results by setting “--min-maf 0.05 --max-obs-het 0.8 -R 0.6 –write-random-snp,” in which one random SNP was extracted for each locus.The raw reads produced from the Illumina platform were processed using Stacks 2.55 software . InitialK) was set in the range of 2–6, and the optimal K was determined with the lowest cross-validation (CV) error. The produced VCF file was transformed to a PHY file using the Python script vcf2phylip.py  was performed using PLINK v1.90 , and a Phylip.py , and a pFST was calculated based on the Kimura 2P method, and NM was estimated based on the formula NM = 1/(4*FST + 1). The Mantel test was performed using GenAlEx 6.5 (FST/(1-FST) and geographic distance (ln) by setting 999 permutations . The values were projected downward to maximize the number of segregating sites for both species. Stairway Plot v. 2.1.1 was used to infer recent historical dynamics of the effective population size of C. granthamiana and C. albogigas based on unfolded SFS  were generated using easySFS . After filtering with the program “populations,” a total of 9,036 loci containing 7,152 variant sites were retained for further analysis. The observed heterozygosity (HO) ranged from 0.102 to 0.110, the expected heterozygosity (HE) ranged from 0.120 to 0.162, and the inbreeding coefficient (FIS) ranged from 0.065 to 0.174 , while the lowest FST was detected between P2 and P3 (FST = 0.365). The Mantel test showed that the genetic distance estimated using FST/(1-FST) between geographical distance (ln) was highly correlated .Pairwise timation  showed tNE) of C. granthamiana was estimated to have expanded quickly since ca. 60,000 years ago (YA), reached a maximum level 40,000 YA, then remained stable till 4,000 YA, and kept declining to date  clustered together with C. albogigas (population P4) with high support values  clustered with P1-1, whose geographic location  is just near Hong Kong, China, revealing that this individual should be introduced from the type locality of C. granthamiana . It is interesting that D-2 is located at the root of clade P4 with a weak support value in the nuclear tree  clustered together with the population P1 of C. granthamiana  could be caused by the limited number of populations (FIS of the species is estimated to be 0.065–0.174 (PCA and ADMIXTURE analysis , 3 showeion pair . These dulations . The demulations  showed tulations . The inb65–0.174 , suggest65–0.174 .C. granthamiana maintained a medium level of genetic diversity (HE: 0.120–0.162, Firmiana danxiaensis (average HE: 0.115, RAD-seq, Primulina danxiaensis (average HE: 0.064, RAD-seq, Thuja sutchuenensis (average HE: 0.082, RAD-seq, Hemiculter leucisculus in the Xinjiang Tarim River (average HE: 0.198, RAD-seq, It is inspiring that the four populations of


Gonatodescaudiscutatus is a gecko native to western Ecuador and introduced to the Galapagos Islands. Despite being a successful species in human-modified habitats along its native and non-native ranges, neither the colonisation process nor the genetic diversity of this gecko is known. In this study, we analysed 55 individuals from 14 localities in western Ecuador and six localities in San Cristobal Island, Galapagos — the only island with a large, self-sustaining population. We amplified and analysed the genetic variability of two nuclear genes (Cmos and Rag2) and one mitochondrial gene (16S). Cmos and Rag2 sequences presented little to none genetic variability, while 16S allowed us to build a haplotype network. We identified nine haplotypes across mainland Ecuador, two of which are also present in Galapagos. Low genetic diversity between insular and continental populations suggests that the introduction of G.caudiscutatus on the Islands is relatively recent. Due to the widespread geographical distribution of mainland haplotypes, it was not possible to determine the source population of the introduction. This study represents the first exploration of the genetic diversity of Gonatodescaudiscutatus, utilising genetic tools to gain insights into its invasion history in the Galapagos.Studies on genetic variability amongst native and introduced species contribute to a better understanding of the genetic diversity of species along their autochthonous distribution and identify possible routes of introduction.  Human-mediated introductions of non-native species are a common and well-documented phenomenon, exponentially increasing in our globalised world . Human-iGekkota) are some of the most successful colonisers of novel areas amongst terrestrial vertebrate taxa. Many species in this group have established thriving non-native populations on oceanic islands , G.antillensis (G.caudiscutatus (G.vittatus (Kraus 2009b). Gonatodescaudiscutatus is native to the Pacific lowlands and western foothills of the Andes in Ecuador and northern Peru, between 0 and 1800 m elevation (Sturaro and Avila-Pires 2013). Non-native populations of G.caudiscutatus have established in the Galapagos Archipelago and on the eastern Andean slopes and Amazonian foothills of Ecuador due to human-mediated transoceanic and transmountain extra-range dispersions (Cisneros-Heredia 2018). Gonatodescaudiscutatus probably reached Galapagos as cargo stowaway on ships departing from ports along coastal Ecuador over the last two centuries and was first reported in San Cristóbal Island in 1891  and genetic data for such species in the Galapagos are limited . To deveG.caudiscutatus in mainland Ecuador and 12 localities in San Cristóbal Island, Galapagos Archipelago  and previous fieldwork conducted by the Laboratory of Terrestrial Zoology of Universidad San Francisco de Quito USFQ between 2008 and 2018. Localities in western mainland Ecuador covered all known ecosystems where G.caudiscutatus has been reported in six Provinces , including urban/periurban green areas in dry and humid lowlands and forested areas in dry, mesic and humid highlands. Localities in San Cristóbal Island covered ecosystems preferred by non-native populations of G.caudiscutatus, including urban/periurban green areas in the dry lowlands and agricultural and forested areas in the humid highlands.We surveyed 34 localities across the native range of G.caudiscutatus across all surveyed localities  under collection codes specified in Suppl. material Cell lysis was performed following the protocol described by G.caudiscutatus populations from San Cristóbal Island and mainland Ecuador, we built two trees using the three concatenated genes. The first tree was built using the Bayesian Inference  and haplotype diversity (Hd) in DNASP v.6 settings using default parameters , but there were few differences in Cmos  and no variation in Rag2 . The results of the overall mean genetic distance for each gene and the genetic pairwise distances between all individuals for each gene can be found in Suppl. material 16S sequences showed 21 variable sites in the 403 base-pair region Fig.  and the Fig. 1, Suppl. material 5). These most diverging haplotypes are found in individuals from two populations in western Ecuador (Cerro Blanco and Agua Blanca), the only surveyed localities covered by old-growth seasonal deciduous lowland dry forests.Haplotypes 1 and 4 were found widely throughout mainland Ecuador and are the only haplotypes found in the samples of San Cristóbal Fig. , Table 1caudiscutatusG  in mainland and insular Ecuador. A total of nine haplotypes were found along the native range of G.caudiscutatus in western Ecuador. We found low nucleotide diversity values in mainland sites, with minor differences amongst populations. However, haplotype diversity was high; six haplotypes were unique to specific sampling locations, but their distribution did not correspond to any discernible biogeographic pattern. High haplotype diversity values have been reported for other Gonatodes that inhabit complex geographic ranges   ; howeveralapagos . DespiteG.caudiscutatus are recurrently reported in mainland Ecuador and Galapagos, suggesting that the species may eventually hold a larger potential for colonisation of different lowland ecosystems  used for this work.File: oo_495688.xlsxhttps://binary.pensoft.net/file/495688Lía Altamirano-Ponce9A275F4E-7F69-5D97-9225-F20A304C973010.3897/BDJ.11.e113396.suppl4Supplementary material 4Genetic Pairwise and Overall DistancesData typeDistance matricesBrief descriptionEstimates of overall genetic diversity for each gene sequence  and estimates of pairwise genetic diversity between all individuals for each gene .File: oo_921131.xlshttps://binary.pensoft.net/file/921131Gabriela Pozo, María José Pozo, Martín Terán-Velástegui, Maria de Lourdes Torres7BDCA2F4-A73B-5DD7-A3DF-B413763DFD7B10.3897/BDJ.11.e113396.suppl5Supplementary material 5Haplotypes informationData typeOccurrencesBrief descriptionA detail of the sequences obtained for the 16S that conform to each of the nine haplotypes we found.File: oo_564990.xlsxhttps://binary.pensoft.net/file/564990Lía Altamirano-PonceB7CE1D0C-1B38-5734-93EF-3761412E412310.3897/BDJ.11.e113396.suppl6Supplementary material 6Field and Collection codesData typeList of codesBrief descriptionThis is a list of the collection codes of the specimens used for this research project.File: oo_922246.xlsxhttps://binary.pensoft.net/file/922246Mateo Dávila


Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study. Puccinia triticina Eriksson, is a major disease of wheat (Triticum aestivum L. and T. durum Desf.) globally . Pu. PuP. trf origin ,56. Addif origin . Converst parent . The vire events . In contectively ,59. Barlriticina ,61. Interiticina ,55. Basee) level ,63,64, aAs differences in the size of each set of isolates, grouped on the basis of host, sampling year, geographical area of origin or virulence phenotype, may affect the analysis of the genetic structure of populations, for the analysis of SSRs and ISSRs data we used LOCUS software, which assumes different models of evolution for these markers . NotablyP. triticina and provided different information on the genetic structure of populations. The genetic structure of the leaf rust pathogen populations in Iran, as determined by the analysis of ISRRs, correlated quite well with the grouping of isolates based on both the year of sampling and host of origin and was also consistent with their grouping based on virulence phenotype, as characterized in a recent study [The overall results of this analysis provide circumstantial evidence that mutation, migration, and gene flow are major evolutionary events shaping the populations of the leaf rust pathogen in Iran. In particular, the high proportion of heterozygous alleles revealed by SSRs is consistent with the assumption that clonal reproduction prevails in these populations. In fact, it is assumed that even if sexual reproduction contributes to increasing heterozygosity, clonal reproduction is essential to maintain it in a population. The SSR and ISSR markers differed in their ability to detect genetic polymorphisms in nt study . ConversP. triticina populations in Central Asia and Caucasus [The two clustering methods used for analyzing the data obtained with SSRs (neighbor-joining and STRUCTUREv 2.3) produced almost consistent results. This is in agreement with a previous study that compared the two methods for characterizing the genetic diversity of Caucasus . STRUCTUCaucasus .P. triticina in Iran.A recent study of the diversity of virulence phenotypes in populations of the leaf rust fungus in Iran demonstrated that new genotypes are mainly introduced from neighboring and even distant countries through wind-dispersed urediniospores . Based oTriticum species) and alternate  hosts of P. triticina overlap [P. triticina populations in this country. To this end, research should focus on less disturbed areas, such as parks or nature reserves, where wheat and related ancestral species coexist with potential alternate hosts.Iran is within the Fertile Crescent macroregion, where the natural range of the primary ( overlap ,66,67. D


Glossina brevipalpis. In this study, we screened the genome of G. brevipalpis to search for suitable microsatellite markers and nine were found to be efficient enough to distinguish between different tsetse populations. The availability of these novel microsatellite loci will help to better understand the population biology of G. brevipalpis and to assess the level of gene flow between different populations. Such information will help with the development of appropriate strategies to implement the sterile insect technique (SIT) in the framework of an area-wide integrated pest management (AW-IPM) approach to manage tsetse populations and ultimately address the trypanosomoses problem in these targeted areas.Tsetse flies, the vectors of African trypanosomes are of key medical and economic importance and one of the constraints for the development of Africa. Tsetse fly control is one of the most effective and sustainable strategies used for controlling the disease. Knowledge about population structure and level of gene flow between neighbouring populations of the target vector is of high importance to develop appropriate strategies for implementing effective management programmes. Microsatellites are commonly used to identify population structure and assess dispersal of the target populations and have been developed for several tsetse species but were lacking for  Tsetse flies (Diptera: Glossinidae) are the only cyclical vectors of two parasitic diseases, human African trypanosomiasis (HAT), or sleeping sickness, and African animal trypanosomosis (AAT), or nagana in livestock , 33, 58.Glossina Wiedeman, 1830 >output file name” in Linux Ubuntu 20.04.4 LTS. The fastq sequence data, consisting of 26209954 reads of 200 bp length were assembled with ABYSS assembler /[(nHT − HS)(1 − HS)]  , where Hersities  and n th to Wang , when thNe) – roughly the number of reproducing adults in a population – were estimated for wild tsetse fly samples. We utilised five different methods: linkage disequilibrium  , as indicated in FST = 0.115 in 95% CI   .Out of the 12 microsatellites, Gb50 was excluded due to the low success of fragment analysis reads. Gb70 was considered X-linked as it displayed different amplicon patterns with DNA from females comparing to males in preliminary tests  with a trend to be negative (ρ = −0.115), indicating that null alleles do not affect FST enough to result in a significant positive correlation with FIS . The Spearman correlation between the FIS and the observed missing genotypes (blanks) for some loci  was significantly positive  and at least 95% of the variance of FIS is explained by the number of blank genotypes found across these loci . Other loci displayed an excess of missing genotypes. No significant stuttering signature was observed for all tested microsatellites. However, an indication of SAD was detected for the locus Gb48 with a p-value of 0.09867 and negative ρ (−0.367033) with Spearman’s rank correlation test. The weighted regression correlation test was significant , therefore Gb48 was excluded from further analysis. In conclusion, nine microsatellites  were retained for further analysis after excluding Gb50 for low success of fragment analyser reads, Gb70 for X-linkage and Gb48 for SAD.The correlation between Ht) of 0.816. The overall FIS decreased to 0.082 . Genetic differentiation remained significant , with a marginal increase of FST to 0.116. Four locus pairs were in significant LD ; again none of these pairs remained significant after BY-correction. The correlation test between FIS and FST remained non-significant  .Analysing the data from all samples with the nine selected loci resulted in a total heterozygosity  and NJ-tree analysis based on Cavalli-Sforza and Edwards chord distances between subsamples, with INA correction for null alleles.To determine the genetic relationship between the The OVI laboratory colony appeared distant from the other two wild subpopulations . RegardiFST = 0.067 in 95% CI =  . There was still a significant heterozygote deficit: FIS = 0.068 in 95% CI =   .In the field samples only, genetic differentiation remained significant, with FIS variations. We always observed enough numbers of blanks as compared to the expected ones as provided by FreeNA with the EM algorithm to estimate null allele frequencies . The regression of FIS as a function of expected null homozygotes (Nblanks – expected) provided a R2 = 0.7251 and an intercept of FIS_no-null = −0.0247  and geographic (>150 km) distances.As explained above, null alleles explained most of  −0.0247 , as expeFIS based Ne = 10, in minmax =  is very close to the one obtained with the intercept of the regression FIS ~ Nblanks-expected (Ne = 10.51). This brings confidence on the interpretation regarding the effect of null alleles. The weighted grand average gave effective population sizes: Ne = 76 in minmax = .Results of the estimation of effective population sizes are presented in FST_FreeNA′ = 0.0983 in 95% CI =   in South Africa and FST_FreeNA′ = −0.0206 in 95% CI =   on average between traps in Mozambique.Within each country, the average genetic differentiation was small and not significant with G. brevipalpis and to evaluate the suitability and efficiency of these markers to investigate population structure and the level of gene flow between populations in the field. The search for microsatellites across the genome sequence of G. brevipalpis indicated that dinucleotide repeats were more common than trinucleotide repeats confirming the theory that the microsatellite abundance decreases with the increase of motif repeat number and repeat length [G. brevipalpis, allowing a broader analysis of the population genetics of this species in southeast Africa.This study aimed to develop novel microsatellite markers for t length . To our Ht = 0.816, which is a satisfying rate for population genetics studies. Among these nine loci, four  displayed null alleles at different levels of frequency. As for the FST between the two countries, given the importance of the geographic distances between the two countries, relative to the modest number of generations separating those, it is probable that most of the genetic differentiation observed between the two countries, as measured by FST_FreeNA′, was due to geography, though we cannot quantify by what proportion exactly. The same consideration applies to the FCA and NJ-tree analyses. Nevertheless, we can forecast that contemporaneous subsamples from the two zones would lead to a considerable genetic differentiation and thus that these two zones exchange very few immigrants per generation. Regarding effective population sizes, variations of Ne estimates are often important, with the LD-based estimate giving the highest values and the coancestry-based estimate providing the smallest values [The selected microsatellite markers used in this study were inspected for their efficiency to explore genetic heterogeneity within and between tested populations using several quality control tests. As a result of the quality control tests, nine markers were retained, with an average genetic diversity t values , 22, 66.et al. [et al. [Results of the NJ-tree and FCA indicated that the OVI colony was distant from the wild populations of South Africa and Mozambique. The results agree with the results of de Beer et al.  who’s mo [et al.  can be eG. brevipalpis collected from different locations in Mozambique and South Africa demonstrates that microsatellite markers will provide an enhanced resolution of the genetic structure of this species and therefore allow accurate investigations of the population genetics, the immigration rate and the dispersal distances in this species. Although these results demonstrate the suitability of the selected loci to explore the genetic diversity of G. brevipalpis in the tested locations, the low number of tested samples, and the fact that Mozambique and South Africa populations were investigated at different times did not allow us to calculate dispersal or the immigration rates between these populations. Therefore, the genetic structure of these populations should not be considered finally established. For future studies, it is recommended to analyse more samples collected at the same time from more locations to obtain a complete and conclusive analysis of the population genetics of the flies.The distinction between G. brevipalpis. The selected microsatellite markers showed the possibility to differentiate between wild flies from different locations in Mozambique and South Africa as well as the flies from a laboratory population. Analysing more field samples collected from more locations of the same tsetse generation with these microsatellite markers will provide a better understanding of the population genetics and dynamics of G. brevipalpis. It will allow for precise assessment of the level of gene flow between adjacent populations that could be targeted with an area-wide integrated pest management strategy.In this study, nine selected microsatellite markers were characterised and found to be suitable for analysing the population genetics of