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

Abstract The colonization of Sahul—the Pleistocene continent combining Australia, New Guinea, and Tasmania—remains one of the most profound chapters in the history of Homo sapiens . It marks the first time our species ventured beyond the biogeographical limits of Africa and Eurasia, crossing the formidable deep-water barriers of the Wallacean Archipelago. For decades, the "Southern Route" via the Lesser Sunda Islands (including Timor) was considered a primary conduit for this

1. Introduction: The Urban Crucible and the Anthropocene Phenotype The burgeoning field of urban evolutionary ecology posits that cities are not merely localized disruptions to natural ecosystems, but rather distinct, globally replicated biomes that exert potent, novel selective pressures on resident biota. This "urban crucible" accelerates evolutionary change, compressing into decades processes that might otherwise unfold over millennia. Within this context, the North Americ

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