International Journal of Marine Science, 2025, Vol.15, No.2, 107-117 http://www.aquapublisher.com/index.php/ijms 112 5.2 Brown algae, golden algae and cryptoalgae: pigment source and lineage relationship Brown algae (Raphidophyceae) and golden algae (Xanthophytes) belong to varicosmic algae, and chloroplasts originate from secondary endosymbiotic events of red algae. Although they vary greatly in morphology and ecologically, they are often classified as the same group in genealogical trees - the Ochromophyta (Stramenopiles). Cryptophyta is a special case, and its pigment also comes from red algae, but unlike brown algae/gold algae, Cryptophyta retains the nuclear matrix. Phylogenetic studies have shown that brown and genus algae are related to other isophage algae (such as diatoms), while cryptoalgae are usually classified as independent branches. Because these groups have the same origin of pigmentos, their gene sequences are similar in the chloroplast genome, but each evolves independently in the nuclear genome (Dorrell et al., 2017; Pietluch et al., 2024). Overall, Stramenopiles and cryptoalgae are not sister groups on the molecular phylogenetic trees, suggesting that their ecological similarity stems mainly from a common endosymbiotic history rather than a recent kinship. Modern analysis generally believes that all eukaryotic algae containing chloroplasts from red algae (including the phylum Belly, cryptozoa, dinoflagea, etc.) may form a large evolutionary cascade system, which is also feasible in time through multiple endosymbiotic events being connected in series (i.e., serial endosymbiotic hypothesis). 5.3 Diatoms and dinoflagellates: molecular characteristics under complex phylogenetic pathways Diatoms (Bacillariophyta) and dinoflagea (Dinophyta) are two important aquatic microalgae, and the phylogenetic relationship is very complex. Diatoms belong to the heterophage algae group, and the cell walls are composed of silic cell wall panels. Genome studies have shown that diatoms and other Stramenopiles such as brown algae and genus algae have common red algae-derived chloroplast origin, and their lineage is closer to other heterophage algae. A genetic time estimate shows that the three major categories of diatoms (Chona and Cymbidium) began to differentiate about 100 million years ago. RuBisCO is extremely efficient in the diatom genome and contributes greatly to the global carbon cycle; they usually remain kinship with brown algae on molecular phylogen trees. Dinoflagellates are a highly evolved algae. Some species lose their photosynthetic function and become parasitic or heterotrophic. They have a variety of chloroplast types, including their own derived and tertiary symbiotic acquisition (Yamada et al., 2017). The dinoflagellate genome is very large and complex, often containing highly repetitive and exogenous sequences, posing challenges in building phylogenetic trees. Molecular analysis shows that dinoflagellates have different lineage relationships with other red algae-containing chloroplasts. Some studies attribute dinoflagellates to the Dingfumen Group, and some studies believe that they are independent of other major algae groups (Zhao et al., 2024). 6 Evolution Time and Geological History of Algae Lineages 6.1 Molecular clock method to estimate the age of origin of algae Molecular clock analysis provides time-scale estimates for algae lineage evolution. By calibrating the differences between fossil records and gene sequences, the origin and differentiation time of algae branches can be inferred. Taking diatoms as an example, dating analysis based on genome-wide data infers that their main groups appeared in the Mesozoic Era (about 100 million years ago) (Strassert et al., 2021). Similarly, studies of green and red algae have shown that differentiation of primitive eukaryotic photosynthetic organisms (Archaeplastida) is likely to occur hundreds of millions of years before the Pleistocene (Cavalier-Smith, 2018). The current analysis results show that the origin of mainstream algae lineages (red algae, green algae, gray algae, etc.) can be traced back to at least the Mesoproterozoic, and the heterophage algae co-generated within the secondary level also appeared during the Cambrian to Carboniferous. It should be noted that the calibration point and sequence data used in different studies are different, and the age estimates obtained vary, but the overall trend is consistent: algae diversification earlier than land plants, and many modern phylae were formed in the old period of geological history. 6.2 The association between algae diversity and key geological events (such as snowball earth) The main differentiation events of algae are closely related to changes in the earth's environment. For example, the greenhouse climate after the end of the "Snowball Earth" Ice Age (about 700 to 600 million years ago) may provide conditions for the explosive diversification of photosynthetic eukaryotes (including algae) (Strassert et al.,
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