International Journal of Aquaculture, 2024, Vol.14, No.3, 126-138 http://www.aquapublisher.com/index.php/ija 127 The purpose of this study is to synthesize current knowledge on the origins of aquatic biodiversity, focusing on phylogenetic patterns and historical biogeography. By integrating findings from multiple studies, this study provides a comprehensive understanding of the evolutionary and biogeographic processes that have shaped aquatic biodiversity, and highlights the importance of both historical events and contemporary ecological factors in driving the diversity and distribution of aquatic species. This study will also identify gaps in current knowledge and suggest directions for future research to further elucidate the complex dynamics of aquatic biodiversity. 2 Phylogenetic Patterns in Aquatic Biodiversity 2.1 Methods of phylogenetic analysis Phylogenetic analysis in aquatic biodiversity research often employs a combination of molecular and computational techniques to infer evolutionary relationships among species (Figure 1). Common methods include the use of multilocus datasets, which incorporate sequences from both nuclear and mitochondrial genes. For instance, in the study of coastal rove beetles, a multilocus dataset comprising DNA sequences from five nuclear genes (ArgK, CAD, EF1-α, wg, and 28S) and three mitochondrial genes (COI, COII, and 16S) was utilized to infer gene trees and species trees using both model-based (maximum likelihood and Bayesian) and parsimony-based methods (Song et al., 2018). Additionally, coalescent-based approaches, such as *BEAST analysis, are employed to resolve phylogenetic relationships and reconstruct time-calibrated phylogenies (Song et al., 2018). The phylogenetic analysis by García-Girón et al. (2024) presents a comprehensive view of evolutionary relationships among key aquatic insect groups, using a vast dataset of 3125 gene sequences and 6038 nucleotide sites. The study achieves near-complete family-level coverage for stoneflies and caddisflies, and significant proportions for dragonflies, damselflies, and mayflies. The phylogenetic tree, detailed with colored lines indicating family extents and classification hypotheses, provides insight into monotypic families and polyphyletic assemblages. The inclusion of a time scale and palaeogeographical maps offers context for major evolutionary events. This work enhances the understanding of the diversification and biogeographical history of these aquatic insects, highlighting significant evolutionary patterns and divergence times within these aquatic lineages. 2.2 Major phylogenetic groups in aquatic environments Aquatic environments host a diverse array of phylogenetic groups, each with unique evolutionary histories. Marine habitats, which cover approximately 70% of Earth's surface, are home to a variety of species descended from marine ancestors. In contrast, freshwater habitats, despite covering only 2% of Earth's surface, exhibit high species richness and exceptional phylogenetic diversity. Interestingly, most extant animal richness in freshwater is derived from terrestrial ancestors, highlighting the complex evolutionary transitions between habitats (Román‐Palacios et al., 2022). The study of coastal rove beetles further illustrates the diversity within specific clades, with species distributed along the eastern and western Palearctic and the western Nearctic coasts (Song et al., 2018). 2.3 Evolutionary relationships and divergence The evolutionary relationships and divergence patterns among aquatic species are shaped by various historical and biogeographical factors. For example, the phylogenetic analysis of coastal rove beetles revealed that most divergence events occurred in the late Miocene and early Pliocene along the Pacific coasts. The East Asian seacoasts, in particular, harbored the most species-rich fauna within the ET clade (Song et al., 2018). Ancestral reconstructions of habitat indicate that marine species are predominantly descended from marine ancestors, while freshwater species often have terrestrial origins. This divergence is influenced by variation in diversification rates across different habitats (Román‐Palacios et al., 2022). The historical biogeography of these species is marked by dispersal and vicariance events, which have played significant roles in shaping their current distribution patterns (Song et al., 2018). 3 Historical Biogeography of Aquatic Species 3.1 Concepts and methods in historical biogeography Historical biogeography aims to understand the distribution of species over time and space, integrating
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