International Journal of Aquaculture, 2024, Vol.14, No.3, 126-138 http://www.aquapublisher.com/index.php/ija 135 relationships among species. It provides insights into the conservation value of different habitats by highlighting areas with unique evolutionary lineages. Freshwater habitats, despite their small area, exhibit exceptional phylogenetic diversity. This is largely due to the high diversification rates and the unique evolutionary histories of species that have adapted to these environments. The conservation importance of freshwater habitats is underscored by their high phylogenetic diversity, which is derived from both marine and terrestrial ancestors (Román‐Palacios et al., 2022). In marine environments, particularly tropical coral reefs, the integration of phylogenetic diversity with ancestral biogeographic data has revealed complex patterns of endemism and provinciality. These patterns are essential for understanding the origins and maintenance of biodiversity hotspots, such as the Indo-Australian Archipelago (IAA) (Cowman et al., 2017). 8.2 Conservation planning of historical biogeography Historical biogeography plays a pivotal role in conservation planning by providing a temporal and spatial framework to understand the distribution of biodiversity. The origins of biodiversity in different habitats, such as terrestrial, marine, and freshwater, are influenced by historical processes that have shaped current species distributions. For instance, the high species richness in freshwater habitats is linked to their historical connections with terrestrial environments, while marine species richness is often derived from marine ancestors (Román‐Palacios et al., 2022). In the context of tropical coral reefs, the biogeographic history of reef fishes has been elucidated through time-calibrated molecular phylogenies and ancestral biogeographic estimates. These studies have identified areas of species creation and demise, which are critical for developing effective conservation strategies (Cowman et al., 2017). By integrating phylogenetic and biogeographic data, conservation planning can prioritize regions with unique evolutionary histories and high biodiversity, ensuring the protection of both current and future biodiversity. 8.3 Case studies in conservation strategies Case studies in conservation strategies highlight the application of phylogenetic and biogeographic data in real-world scenarios. Freshwater habitats, for example, have been identified as critical conservation targets due to their high phylogenetic diversity and unique evolutionary lineages. Conservation efforts in these habitats can benefit from understanding the historical biogeography that has led to their current biodiversity patterns (Román‐Palacios et al., 2022). In marine environments, particularly tropical coral reefs, conservation strategies have been informed by the integration of phylogenetic diversity and ancestral biogeographic data. The IAA, as a major marine biodiversity hotspot, has been a focal point for such studies. The identification of paleo- and neo-endemic fishes in this region has provided insights into the historical processes that have shaped its biodiversity. These findings are essential for developing targeted conservation strategies that address both the protection of existing species and the preservation of evolutionary processes that generate biodiversity (Cowman et al., 2017). By examining these case studies, it becomes evident that a comprehensive understanding of phylogenetic diversity and historical biogeography is crucial for effective conservation planning and the long-term preservation of biodiversity. 9 Challenges and Future Directions 9.1 Methodological challenges The study of aquatic biodiversity origins and patterns is fraught with several methodological challenges. One significant issue is the under-sampling of certain taxa, particularly endemic species, which can obscure our understanding of biodiversity genesis and maintenance. For instance, the biogeography of tropical reef fishes has been complicated by the under-sampling of endemic fishes in phylogenetic studies, leading to incomplete data on species creation and demise in biodiversity hotspots like the Indo-Australian Archipelago (IAA) (Cowman et al., 2017). Additionally, the integration of phylogenetic relatedness and ancestral biogeography into metrics for defining discrete realms, regions, and provinces is still in its nascent stages, further complicating the analysis (Cowman et al., 2017). Another challenge is the accurate reconstruction of historical biogeography and diversification patterns. For example, the study of the Sciaenidae family revealed repeated habitat transitions between marine and euryhaline
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