International Journal of Marine Science, 2025, Vol.15, No.2, 107-117 http://www.aquapublisher.com/index.php/ijms 107 Review Article Open Access Phylogenetic Relationships and Evolutionary History of Major Algal Lineages: A Comprehensive Review Zhen Liu, Yeping Han Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: yeping.han@jicat.org International Journal of Marine Science, 2025, Vol.15, No.2, doi: 10.5376/ijms.2025.15.0010 Received: 12 Mar., 2025 Accepted: 15 Apr., 2025 Published: 26 Apr., 2025 Copyright © 2025 Liu and Han, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Liu Z., and Han Y.P., 2025, Phylogenetic relationships and evolutionary history of major algal lineages: a comprehensive review, International Journal of Marine Science, 15(2): 107-117 (doi: 10.5376/ijms.2025.15.0010) Abstract Algae, as important photosynthetic organisms on the earth, occupy a fundamental position in the global carbon cycle, oxygen supply and marine food networks. Algae lineage research is a key means to reveal the origin and evolution mechanism of their diversity. In recent years, large-scale genomic and transcriptome data have provided rich information for analyzing algae lineages, and joint multigene analysis has revealed the complex relationships between different groups such as red algae, green algae, brown algae, and dinoflagea. This study outlines the importance of algae in ecosystems and the current research status; systematically introduces the main group characteristics of prokaryotic algae (cyanobacteria) and eukaryotic algae (green algae, brown algae, red algae, etc.) by classification; then discusses the contribution of molecular phylogenetic evidence to algae evolution research, including comparison of nuclear genes and chloroplast genes, multigene joint analysis and the application of "omics" methods in phylogenetic construction; reviews the approaches to the evolution of chloroplasts (primary, secondary and tertiary endosymbiosis) and photosynthetic pigment evolution; further analyzes the phylogenetic relationships of major algae lineages (red algae, green algae, brown algae, cryptoalgae, diatoms, dinoflagellate, etc.); discusses the molecular clock estimation of algae origin and its connection with geological events (such as snowball earth); and finally explains the implications and application prospects of algae phylogenetic research on global carbon cycle, biodiversity conservation and biotechnology development. This study seeks to integrate the latest research progress and analyze the controversial analysis, providing a systematic perspective for understanding the origin and evolution of major algae lineages. Keywords Algae phylogenetic; Endosymbiosis; Chloroplast origin; Photosynthetic pigment; Molecular clock 1 Introduction Algae, as photosynthetic organisms, play a crucial role in global ecology. On the one hand, marine algae (including phytoplankton and large seaweed) undertake a large amount of photosynthesis, and net fixed organic carbon accounts for a very high proportion of the total amount of the earth. For example, studies have pointed out that marine organisms have completed more than half of the biocarbon fixation on Earth, and large-scale cultivation of macroalgae can significantly increase marine carbon sink capacity (Larkum, 2016). Algae release oxygen through photosynthesis, providing oxygen to aquatic and terrestrial ecosystems, and jointly maintaining an atmospheric oxygen atmosphere with terrestrial plants. On the other hand, algae are also the basis of aquatic food networks. They are rich in species and have strong environmental sensitivity, which are indicative of nutrient circulation, water quality status, etc. (Koushalya et al., 2021). Due to these ecological and economic values, the diversity and origin of algae have always been a hot topic in biological research. The development of molecular systems provides a powerful tool for understanding algae evolution. In the past, the classification of algae mainly relied on morphological characteristics, but due to morphological convergence and plasticity, traditional classifications were difficult to accurately reflect evolutionary relationships. In recent years, with the popularization of DNA sequencing technology, phylogenetic research based on nuclear genes and chloroplast genes has been deepened. For example, by comparing gene sequences such as 18S rDNA and rbcL, the kinship relationship between different algae lineages can be initially inferred. These studies show that single molecular markers of different groups often struggle to provide sufficient resolution, and multigene joint analysis has become a trend (Sun et al., 2016). In addition, the emergence of "omics" data such as the entire chloroplast
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