International Journal of Aquaculture, 2024, Vol.14, No.3, 126-138 http://www.aquapublisher.com/index.php/ija 128 phylogenetic data with geological and climatic history. Key methods include time-calibrated molecular phylogenies and ancestral range reconstruction. These approaches allow researchers to infer the historical distributions and diversification patterns of species. For instance, time-calibrated molecular phylogenies have been instrumental in examining the origins of coral reef fish biodiversity across the tropics, providing insights into the temporal patterns of marine endemism and tropical provinciality (Cowman et al., 2017). Similarly, the use of multi-gene datasets in phylogenetic studies has enabled the reconstruction of the historical biogeography of widely distributed groups like the Sciaenidae, revealing their origins and diversification patterns (Lo et al., 2015). 3.2 Historical distribution patterns The distribution patterns of aquatic species are shaped by a combination of historical processes, including vicariance, dispersal, and extinction. In the case of tropical reef fishes, the Indo-Australian Archipelago (IAA) serves as a major biodiversity hotspot, characterized by a steep gradient in species richness from the center to the periphery of the Indo-Pacific region. This pattern is maintained by a mixture of paleo- and neo-endemic species, indicating multiple historical processes at play (Cowman et al., 2017). For the Sciaenidae family, ancestral range reconstruction suggests an origin in tropical America during the Oligocene to Early Miocene, followed by range expansions to the Eastern Atlantic and Indo-West Pacific, where the highest species richness is observed (Lo et al., 2015). 3.3 Major biogeographic events Several major biogeographic events have significantly influenced the distribution and diversity of aquatic species (Figure 2). The formation of the IAA, for example, has been a critical factor in the genesis and maintenance of coral reef fish biodiversity. This region's complex geological history, including tectonic movements and sea-level changes, has created a dynamic environment for species diversification (Cowman et al., 2017). For the Sciaenidae, the transition between marine and euryhaline environments, as well as the occasional shift to freshwater habitats, highlights the role of habitat transitions in their biogeographic history. These transitions, coupled with fossil evidence, suggest that sciaenids first diversified in tropical America before expanding their range to other regions (Lo et al., 2015). Cardoso et al. (2021) examines the phylogeny and biogeographic history of the Hypostomus catfish genus in the La Plata Basin. The time-calibrated phylogeny highlights significant evolutionary and dispersal events. Key geomorphological changes, including the Michicola Arc uplift (~30 Mya), river capture events, and Miocene marine transgressions, influenced species distribution and diversification. Using ancestral area reconstructions, the study traces Amazonian species' colonization routes into the La Plata Basin and their diversification. This integrated approach, combining phylogenetic and hydrogeological data, elucidates how orogenic and environmental changes shaped species evolution in the region. By integrating phylogenetic diversity with ancestral biogeographic estimation, researchers can better understand how assemblage structures and biogeographic patterns have evolved over time, shedding light on the origins and maintenance of aquatic biodiversity hotspots. 4 Integration of Phylogenetics and Biogeography 4.1 Combined phylogenetic and biogeographic studies Recent studies have demonstrated the power of integrating phylogenetic and biogeographic data to uncover the origins and maintenance of biodiversity in various aquatic habitats. For instance, a study on global biodiversity across land, sea, and freshwater habitats revealed that the relative richness of these habitats is closely related to variations in diversification rates. Ancestral reconstructions indicated that most marine species are descended from marine ancestors, while most terrestrial species originated from freshwater ancestors. Interestingly, the majority of extant animal richness in freshwater is derived from terrestrial ancestors, underscoring the complex evolutionary transitions between habitats (Román‐Palacios et al., 2022).
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