1. Introduction 1.1 The Five-Year Milestone In November 2025, the scientific community arrived at a pivotal vantage point: the fifth anniversary of the unveiling of AlphaFold 2. As reported by Ewen Callaway in Nature , this milestone offers a unique opportunity to survey a revolution that has fundamentally altered the landscape of structural biology, pharmacology, and evolutionary science. 1  What began as an entry in a computational competition has metastasized into the oper

Abstract The evolutionary trajectory of the domestic dog ( Canis lupus familiaris ) has long been a subject of intense scientific scrutiny, often framed within a simplified cladistic model of a singular, ancient divergence from a gray wolf ancestor. However, the advent of high-throughput whole-genome sequencing (WGS) and advanced computational analyses of Identity-by-Descent (IBD) haplotypes has precipitated a paradigm shift. Emerging research, including seminal studies highl

1. Introduction: The Dynamic Architecture of Genomic Vulnerability The human genome is frequently conceptualized in the popular imagination as a static archive—a crystalline library of three billion base pairs, faithfully preserved within the nucleus, its integrity guarded by molecular sentinels. In this classical view, the genetic code is a passive repository of information, retrieved only when needed, and mutations are viewed as stochastic errors—random typos introduced pri

Abstract The biodiversity crisis has traditionally been cataloged through the binary lens of species extinction—the complete cessation of a lineage. However, a far more insidious and widespread phenomenon precedes species loss: the erosion of genetic diversity within surviving populations. This "cryptic extinction" removes the evolutionary fuel required for adaptation to a rapidly changing biosphere, leaving species demographically present but genetically impoverished—the "li

Abstract The architectural reconstruction of the eukaryotic tree of life (eToL) has long been hindered by the existence of "orphan" lineages—microbial eukaryotes that defy classification within the established supergroups of Amorphea, TSAR (Telonemia, Stramenopiles, Alveolata, Rhizaria), Archaeplastida, and Excavata. These lineages, often termed Protists with Uncertain Phylogenetic Affiliations (PUPAs), represent deep evolutionary branches that hold the keys to understanding

1. Introduction and Definition Environmental DNA (eDNA) is defined as genetic material obtained directly from environmental samples (such as soil, water, or air) without any obvious signs of biological source material. This method bypasses the need to isolate a specific target organism. Instead, it relies on the cellular material shed by organisms into their surroundings. eDNA is categorized into two primary types: * Microbial eDNA: DNA from unicellular organisms (bacteria,

The Theoretical Framework: From Morphology to Molecules Historically, taxonomy relied on morphological species concepts—defining species based on physical characteristics. This method, while foundational, suffers from phenotypic plasticity, cryptic speciation (where species look identical but are genetically distinct), and the inability to identify juvenile stages or fragmentary remains. DNA barcoding, proposed formally by Paul Hebert et al. in 2003, introduced a standardized