Preface

The word phylogenetics comes from the combination of the Greek words "phylé" or "phy‐ lon" meaning tribe or family, and "geneticos" meaning the origin of relatedness; therefore, *Phylogenetics* aims to study the evolutionary relatedness of living organisms on our planet. While addressing and targeting the study of relatedness of living matter on Earth, phyloge‐ netics attempts to evolutionarily connect the origin and spread of living organisms or their populations by applying various mathematical models as well as bioinformatics tools and novel computing techniques. These models reconstruct historical relationships that we can‐ not see at present and infer evolutionary events and missing chains that help to explain the current 'Tree of Life.' At the same time, phylogenetics allows us to predict the future changes that may happen in the 'Tree of Life,' estimating its rate and future consequences. Therefore, the application of *Phylogenetics* is extended but not limited to evolution, classifica‐ tion and taxonomy of living organisms; ecology, diversity, and conservation biology of agrobiocenosis; forensic analyses; and monitoring of pathogen spread, outbreaks and source of transmissions, useful for novel public health or agricultural biosecurity policies.

Historically, phylogenetics studies were prevalently based on morphological features (phe‐ netics) of species that helped to classify the 'Tree of Life' on Earth. Although still useful for detecting approximate phylogenetic relationships, due to the fact that the same morphologi‐ cal traits could arise independently and be analogous by occurrence, in some specific cases morphology-based phylogenetic conclusions may be misleading and not reliable. Hence, modern phylogenetics studies rely more heavily on molecular sequence data including DNAs, RNAs, proteins, etc. The result of phylogenetics analyses based on both morphology and molecular data is a diagrammatic depiction of relatedness, which is known as a phylo‐ genetic tree. This is the most attractive side of *Phylogenetics* and helps to explain complex knowledge of relatedness, evolution and divergence of life in a simple pictorial level, where topology, rooting, nodding and branching patterns of a tree carry very important informa‐ tion on relatedness estimates that require specific skills to extract needed information with application of appropriate validation tools.

*Phylogenetics* studies have significantly increased over the past 50 years. The number of sci‐ entific publications on phylogenetics have drastically increased and as of June 2017, reached 3,415 scientific publications, indexed in *PubMed* database (https://www.ncbi.nlm.nih.gov/ pubmed/?term=phylogenetics), with its first raise in 1995-2000, following a significant in‐ crease after 2010. Phylogenetics studies have been more impacted by the recent develop‐ ment genomics and bioinformatics sciences in the genomics and post-genomics era. The emergence and availability of inexpensive, high-throughput next generation sequencing technologies together with the development of computing tools of large-scale biomedical data have shifted phylogenetics studies to new levels that are helping to solve many uncer‐ tainty cases in the 'Tree of Life.'

In this *Phylogenetics* book, therefore, we aimed to present readers the latest advances in phy‐ logenetics studies. Toward this goal, we succeeded to compile six chapters with a broad cov‐ erage of phylogenetics topics that include multi-kingdom system-based megasystimatics, new phylogenetic approaches for conservation biology, cytogenetics-based comparative phylogeny, phylogenetics of complex polyploidy genomes with reticulated evolution, meta‐ genomics-based phylogenetics of faecal microbiomes of pack animals, and whole genomebased phylogeny tools for prokaryotic organisms.

Although not all classical and modern phylogenetics topics, existing analyses tools and per‐ spective directions are covered by this edited volume, chapters do represent and re-visit some past and current highlights of phylogenetics research, which I believe will be interesting and an additional reading resource for scientists, students and readers of life science direction.

I thank all authors of the book chapters for their valuable contributions. I also thank the In‐ TechOpen book department for giving me the opportunity to work on this book project, and Ms. Diana Olloni, InTechOpen's Publishing Process Manager, for her coordination of this book project.

**Ibrokhim Y. Abdurakhmonov**

Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan

#### **Dedication**

"*In a memory of the First President of Uzbekistan, Islam Karimov, and my former advisor at Texas A&M University, Emeritus ProfessorKaml El-Zik - two great men with my untellable affection and gratitude for supporting my education and inspiring me to believe that I was capable of becoming a scientist* ."
