الفهرس 
Environmental Diversity and the Distribution Modelling of Funaria hygrometrica HedwigOnly 14 pages are availabe for public view
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Abstract
Ongoing climatic changes and warming trends have various effects on species and affect their selection. Organisms have become between two options either adapt and survive or be vulnerable and further extinct depending on their response to surrounding environmental conditions. Bioindicators have a significant role to reveal the changes in the environment. Therefore, they are considered as a potentially effective and economical performing manner to assess environmental health.
Here. The aim was to verify the applicability of mosses as bioindicators of spatial and temporal environmental changes. The cosmopolitan moss Funaria hygrometrica Hedwig had the characteristics that qualify it to be a model for this study e.g., the most abundant existing moss in Egypt, sporulates in different climatic conditions, easy to be recognized in the field, and so on. Therefore, 25 samples of F. hygrometrica were collected from seven out of 10 phytogeographic regions, in which the species have been reported in Egypt. Four samples from Spain were added to represent a wider range of climatic diversity. In addition, geographical occurrences recorded globally at the GBIF database and herbarium samples at CAIA herbarium represented a part of our materials.
To achieve this aim, the work was divided into three axes, which are presented here in four chapters (articles). The first axis (Chapter 1) was to investigate the environmental diversity of F. hygrometrica at the global and regional (Egypt) levels as well as modelling of species distribution at both levels. The second axis was to assess the molecular variations between 17 samples (13 samples from Egypt and 4 samples from Spain), at the level of nuclear ribosomal DNA repeats (Chapter 2), extranuclear genomes (Chapter 3), and nuclear genome (Chapter 4-in part). The third axis (Chapter 4- in part) was a study of the correlation between nuclear genetic differences and environmental variables, as well as determining the functional categories of the corresponding genes to these variables. The following paragraphs will summarize these four chapters.
Chapter 1: Environmental Diversity and the Distribution Modelling of Funaria hygrometrica Hedwig.
It included the statistical analysis of environmental variables of global geo-occurrences of F. hygrometrica (about 2900). In addition, the determination of the most important variables, which are affecting the species distribution globally and regionally, was done via using a species distribution modelling algorithm. Descriptive analyses of their environmental variables (bioclimatic data) showed a wide range of F. hygrometrica ecological conditions. The moderate temperature and low precipitation were the ecological preferences of the major part of the samples. The occurrences were statistically clustered at four global ecological groups. The global distribution modelling of F. hygrometrica showed a good fit model (AUC > 0.9) with a high probability of existing the species mainly in temperate climate zones and decreasing gradually around them. The most affecting variables were annual temperature as well as temperature and precipitation of the coldest months. The regional analysis of 25 samples, newly collected from Egypt, showed dividing the samples into 5 clusters. The regional distribution model of F. hygrometrica had an accurate probability of the species niches and predicted a new one for the species (mosses) in Egypt.
Chapter 2: ¬Molecular Variation of Nuclear Ribosomal DNA Repeats of the moss Funaria hygrometrica
It included the assessment of nuclear ribosomal DNA (nrDNA) repeats, as clear-cut phylogenetic biomarkers, and its variations between 17 samples (13 samples from Egypt and 4 samples from Spain). The investigation of phylogenetic relations and variations was done at the level of four spacers. These samples were subjected to wide genome resequencing using Illumina NovaSeq 6000 technique. The obtained data per each sample was used for de novo assembling of its nuclear ribosomal DNA repeats. The results produced the full sequence of the nrDNA (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) with a length ranging from 10,648 to 10,971 bp. Furthermore, the phylogenetic analyses of the nrDNA spacers, either separately or concatenated, showed close affinities of the Spanish samples and some of their relatives from Egypt.
Chapter 3: Extranuclear Inheritance of Chloroplast and Mitochondrial Genomes Reveal the Complexity of the Moss Funaria hygrometrica Hedwig
It included the molecular assessment of the intra-specific variations of maternal inheritance (chloroplast genome and Mitogenome), as the best molecular marker for studying the diversification of the species, between the samples under study (see chapter 2). Here, it is the first complete description of the cp-g of F. hygrometrica and new versions of mitogenome. The cp-g was highly represented in the NGS reads than mt-g by percentages of 1.22%-12.29%, and 0.13%-1.23%, respectively, from the total reads of each sample. Both the de Novo assembled cp-g and mt-g divided the samples into three length groups and two evolutionary lineages. It is concluded that F. hygrometrica has to be defined as F. hygrometrica sensu lato or a species complex.
Chapter 4: Wide Genome Sequencing of Funaria hygrometrica Hedwig, Uncovering Molecular Pathways of Ecological Adaptation
Nuclear diversity between the samples was investigated by using the Physcomitrium patens genome as a reference. In addition, it included the determination of genes related to genetic groups. The investigation of the correlation between genetic groups and ecological variables was carried out in the shadow of geographical distance using PCA and partial Mantel analysis. In addition, the functional categories of candidate genes, related to genetic groups and ecological adaption, were determined.
Herein, the measuring units for the nuclear diversity between the samples were single nucleotide polymorphism (SNP) and the corresponding genes, in which SNPs are located. The results showed that a percentage of 39.5% of single nucleotide polymorphism was at coding regions of 17,761 genes from about four million variants detected with a reliable significant probability. The assessment of genetic variation led to detect two genetic groups A (GGA) and B (GGB). The evolutionary process of selection between them showed that GGA had higher positive selection genes than GGB by 1535 to 1344 genes. Both genetic groups shared the same evolutionary process for 1844 genes i.e., 1093, 6, and 745 genes, which have undergone negative, neutral, and positive selection, respectively. The gene ontology of a specific set of genes at each group showed that functional categories of genes can be the same, but both genetic groups are activating different genes in the same physiological pathway. In addition, they have evolved mechanisms of adaptation to environmental conditions through various manners.
PCA analyses of the 17 samples of F. hygrometrica formed three sets of samples i.e., samples from the north of Egypt (set-EgN), samples from the south of Egypt (set-EgS) and samples from Spain (set-Sp). Mantel test with geographic distance indicated that genetic differentiation increases with geographic distances. The partial Mantel test was statistically significant with most of the climatic and bioclimatic variables. The genetic diversity of samples was highly significantly correlated to temperature variables of climatic and bioclimatic data, which is agreed with the results of MaxEnt. The adaption ability of the samples of Spain has been observed through a wide set of genes correlated to the environmental processes. While the samples of Egypt needed only regulatory genes for biological and cellular processes of the cell.
A hypothesis for the explanation of the diversification of F. hygrometrica was that it is a species complex, which changes gradually along a geographical gradient. It can diversify metabolic and physiological genes at the cellular level that leading to optimizing adaptations to different environments. Consequently, its life span is stretchable according to the surrounding environment via controlling fugitive growth, growth reduction or growth interruption of various stages of the life cycle. Its molecular variation increased and correlated with temperature more than precipitation.
Thus, it was concluded that F. hygrometrica can be a good indicator of adaptation to spatial-environmental changes as it can record adaptation responses to environmental changes over time and evolve itself. But it needs more indices to be clarified as a bioindicator.