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 genome, mitochondrial genome, nuclear genome and transcriptome has greatly enriched the information that can be used for phylogenetic analysis. Through these technical means, researchers began to reconstruct phylogenetic trees including prokaryotic algae (cyanobacteria) and various eukaryotic algae, and explore the origin and evolution of algae.

At present, algae research has accumulated a large amount of molecular and genomic data, but there are still many unsolved mysteries. For example, algae are not single-line groups, and there are complex factors such as endosynthetic events and horizontal gene transfer among different groups, which pose challenges to phylogenetic analysis. Different researchers also have certain disputes about the classification system and evolutionary history of algae, and need to systematically integrate multiple aspects of evidence to explain it. In this context, this study aims to review the phylogenetic relationship and evolutionary history of major algae lineages, and comprehensively review relevant research progress from multiple angles such as classification, molecular evidence, chloroplast origin, time scale and environmental drivers, providing a reference for understanding algae diversity and evolutionary mechanisms.

2 Overview of Classification of Major Algae Lineages

2.1 Prokaryotic algae: characteristics and systemic status of cyanobacteria (cyanobacteria)

Cyanobacteria is one of the oldest photosynthetic organisms on Earth, with Gram-negative prokaryotic cell structure, without nuclear membrane enclosure, photosynthesis releases oxygen. Traditionally, cyanobacteria have been classified as a primitive algae (blue-green algae) in the plant world, but it has been clearly stated that it belongs to the bacterial domain, unlike eukaryotic algae. The photosynthetic pigments of cyanobacteria are mainly chlorophyll a and phycobilidin. They are extremely extensive in freshwater and marine environments, forming various colorful and changeable biological symbiotic or coherence groups, such as snow algae, solidified algae, etc. Due to its diverse and ancient morphology, cyanobacteria are extremely complex in classification, and their classification system has undergone many revisions. Komárek et al. proposed a modern multiphase classification system for cyanobacteria, which divided cyanobacteria into many families, each containing fewer species, based on model species (Komárek et al., 2014). In terms of molecular systems, 16S rDNA, ITS sequence and functional genes (such as nitrogen fixation gene nifH, etc.) are widely used in the study of the evolutionary relationship of cyanobacteria. The current consensus is that cyanobacteria constitute an independent lineage of bacterial domains, and their chloroplasts originate from a cyanobacteria ancestor and become an important part of eukaryotic photosynthetic organisms. However, under the concept of algae, cyanobacteria and eukaryotic algae are not monophyletic, and should be regarded as independent branches of prokaryotic photosynthetic organisms.

2.2 The main groups of eukaryotic algae: green algae, brown algae, red algae, etc.

There are many species of eukaryotic algae and can be divided into multiple lineages. Green algae (Chlorophyta and Charophyta) together with terrestrial plants (Embryophyta) form the phylum of green plants (Viridiplantae). Most green algae contain chlorophyll a and b, the cell wall is mostly cellulose, the habitat covers freshwater and oceans, and most of them are single-cell, filamentous or large-scale groups; among them, Charophyta are close relatives of terrestrial plants. Brown algae (Phaeophyceae) belongs to the varicosome group of pigments originating from red algae (Ochromophyta). It is mainly dellate, nude algae, green algae, and other micro-groups, while the latter mainly refers to large seaweeds suchistributed on the cold temperate coast. It is known for its multicellular giant kelp and sea fog. It contains chlorophyll a, c and the co-pigmented fucoxanthin, and has complex morphology (Friedl and Rybalka, 2012). Red algae (Rhodophyta) mainly consists of marine red tide algae, lilac, etc., containing chlorophyll a and red algae (phycoerythrin, phycocyanin), and belongs to the primary membrane chloroplast group. In addition, there are a series of eukaryotic microalgae groups that obtain chloroplasts by secondary or tertiary endosymbiosis: such as diatoms (Bacillariophyceae), Chrysophyceae/Xanthophyceae), Cryptophyta, Dinophyta, nude algae (Euglenophyta), etc. Some experts have divided algae into "microalgae" and "macroalgae": the former includes cyanobacteria, diatoms, golden algae, zooxanthaceae, cryptoalgae, dinoflag as red algae, brown algae and streptaceae.

2.3 Disputes on non-single-system sources and system classification

It should be pointed out that "algae" is not a single-line group, and its members come from different phylogenetic origins. Based on the theory of endosymbiosis, experts propose that algae are divided into prokaryotic algae (i.e., cyanobacteria) and eukaryotic algae, and are further grouped according to the pigment membrane structure (Keeling, 2010). Among eukaryotic algae, primary chloroplasts (surrounded by two membranes) are only found in red algae, green algae and gray algae; while chloroplasts surrounded by more membranes appear in a series of variopoid groups (such as Cryptophyta, Mixoplankton, Prhinophyla, etc.) as well as some phyla and dinoflagellate phyla. Different scholars have different interpretations of these relationships, such as the theory of stained biosynthesis once assumed a single-original endosymbiotic event of red algae (Stiller et al., 2014 ), while others advocated multiple independent secondary or tertiary endosymbiotic events. In summary, algae taxonomy is controversial in terms of endosynthetic events and genealogical definition, suggesting the need for a re-evaluation of traditional classification in a comprehensive molecular, morphological and ecological evidence.

3 Molecular Evidence of Algae Phylogenetic Development

3.1 Comparative analysis of nuclear genes and chloroplast genes

In algae phylogenetic research, nuclear genes and chloroplast genes are widely used. Classic nuclear genes include the small subunit rRNA gene (18S rDNA) and the ITS region, while commonly used chloroplast genes such as rbcL, rbcS, psaA/psbA, etc. Both have their own characteristics: nuclear genes usually evolve slowly and are suitable for higher-order groups; chloroplast genes have moderate relative evolution speed and are commonly inherited by single parents, which is suitable for studying close relationships. In practical applications, people often compare the topological differences between nuclear gene trees and chloroplast gene trees to test system relationships (Fang et al., 2017). In recent years, the application of omics data has become mainstream, such as the entire chloroplast genome contains a large number of genomic loci, which can significantly improve resolution; some studies have pointed out that compared with traditional small number of gene markers, chloroplast genome and nuclear genome data provide more genetic information, especially suitable for the problems of related taxa or classification disorder (Fučíková et al., 2016). For example, joint analysis of the intact chloroplast genome reveals a more stable kinship hint than single gene analysis in certain green algae and cryptoalgae studies.

3.2 Multigenome joint analysis and molecular phylogenetic tree construction

Single-gene markers often find it difficult to fully reflect complex evolutionary history, so multigene joint analysis (supermatrix analysis) has become a necessary means. Studies have shown that short-sequence markers such as single rDNA or conservative protein-encoded genes are difficult to meet the needs of algae identification and phylogenetic analysis, and the use of multi-marker combination is an inevitable choice. Usually, researchers will select multiple nuclear genes to be selected with chloroplast genes or intranuclear insertion subregions, etc., to align and jointly build a phylogenetic tree (Lemieux et al., 2015). In the modern era of high-throughput sequencing, we will further use strategies such as chloroplast or mitochondrial genome sequences, multigenome splicing data (genome skimming) and haplotype networks to conduct comprehensive analysis of complex lineages. These multigenome joint analyses can sometimes unravel the problems of instability or insufficient branching support in single gene trees, providing more credible evidence for kinship among algae taxa. For example, by combining Bayesian and maximum likelihood analysis of nuclear and chloroplast genes, a relatively stable phylogenetic tree can be constructed among multiple algae phyla to provide a basis for discussing the origins of different groups.

3.3 Application of genomics and transcriptomics in algae lineage research

With the development of omics technology, genome-wide and transcriptome data have played an important role in the study of algae lineage evolution. Large-scale data sets such as chloroplast whole genome, mitochondrial whole genome, nuclear genome, and RNA-Seq transcriptome are used to build high-resolution phylogenetic trees (Figure 1) (Mekvipad and Satjarak, 2019). The chloroplast genome is particularly important, which contains hundreds to thousands of genes, providing more loci for phylogenetic analysis than a single or a few molecular markers. In addition, comparative genomics methods can identify conserved evolutionary genomic features, such as genomic structural rearrangement, gene family expansion or contraction, and assist in clarifying lineage branches. Transcriptome data (phylogenetic transcriptomics) can also be used to infer kinship, and in dinoflagellate studies, transcriptome studies of the genus Cyclone revealed the main phylogenetic turning points in the evolution of this group (Jia, 2014). At the same time, metagenomic and environmental genome analysis has been gradually used in the diversity and phylogenetic research of algae communities.

4 The Origin of Chloroplasts and The Evolution of Algae Photosynthetic Pigments

4.1 Primary endosymbiotic events and the formation of primitive photosynthetic eukaryotes

The origin of chloroplasts can be traced to primary endosymbiosis between eukaryotes and cyanobacteria ancestors. The study pointed out that after primary endosymbiosis occurs, three independent primary photosynthetic eukaryotic branches emerge: gray algae, red algae and green algae (including terrestrial plants), which are collectively called primitive photosynthetic organisms (Archaepastida). In this event, a heterotrophic eukaryotic host cell engulfs a cyanobacteria containing photosynthetic capacity, which eventually evolved into the first chloroplasts (Chan and Bhattacharya, 2011). Gray algae contains three outer membranes, a small amount of chlorophyll and chromophyll; red algae and green algae have evolved different combinations of pigment systems (red algae contains phycobiliproteins, and green algae contains chlorophyll a/b). After that, red algae, green algae and gray algae each evolve independently, and one branch of the green algae family eventually landed to form terrestrial plants. This primary symbiotic event laid the foundation for all photosynthetic eukaryotes, allowing eukaryotes to have the ability to perform photosynthesis.

4.2 Secondary and tertiary endosymbiosis and their impact on algae diversity

After primary endosymbiosis, chloroplasts further spread to other algae groups through eukaryotic-eukaryotic endosymbiosis, forming so-called complex chloroplasts (with additional membrane numbers). In secondary endosymbiosis, some native eukaryotic algae are again engulfed by other eukaryotic cells. For example, members of Cryptophyta and Cyclophyta obtained complex chloroplasts from red algae, while Ochromophyta (including brown algae, diatoms, etc.) came from the homologous pigment of red algae (Grisdale ad Archibald, 2016). Tertiary endosymbiosis occurs when algae containing complex chloroplasts are engulfed by higher eukaryotic cells, such as some Dinophyta that have obtained chloroplasts transferred from Dinoflagellates or Cryptoalgae. The chloroplasts of these multilayer membranes often retain the nucleus (nuclear matrix) of the endosymbol, forming the legacy markers of the chromosome. Multiple second- and third-level endosymbiosis greatly expands the diversity of algae, especially those groups containing red algae-derived chloroplasts (such as diatoms, nigra, dinoflagellate, etc.) that have acquired new metabolic abilities through endosymbiosis (Keeling, 2013). Therefore, secondary and tertiary endosymbiosis is a key driver of algae diversity, allowing photosynthesis to span multiple eukaryotic groups.

4.3 Evolutionary paths of photosynthetic pigment combinations in different algae

Algae of different lineages differ significantly in photosynthetic pigment composition, which reflects their different endosymbiotic history and ecological adaptation. Green algae and terrestrial plants mainly contain chlorophyll a and b, which perform photosynthesis by capturing blue and red light; red algae contains chlorophyll a and phycoerythrin, making them often red and absorbing blue-green light (Figure 2) (Stadnichuk and Kusnetsov, 2023); brown algae and Nagyl algae contain chlorophyll a, c and the orange-brown pigment fucoxanthin, which often makes them appear brown or golden yellow; dinoflagellates have chloroplasts of various types, some retain red algae-type chloroplasts, containing chlorophyll and chlorophyll, and some contain other algae chloroplasts through tertiary endosymbiosis. Cryptocyanates contain chlorophyll a and c and co-acetic bile protein (drawing from red algae pigments); nude algae (Euglenophyta) contain chlorophyll a and b, similar to higher plants (Ponce-Toledo et al., 2018). The photosynthetic pigment combination of algae is the result of their internal symbiotic origin and environmental adaptation, and different groups optimize the light quality of their respective niches through their respective pigment combinations.

5 Phylogenetic Relationships of Major Algae Lineages

5.1 Red and green algae: two key branches of primary photosynthetic eukaryotes

The Red Algae and the Green Algae are the two main branches of primary photosynthetic eukaryotes (Archaepastida) (the third branch has very few gray algae). On the phylogeny, red and green algae (and Charophyta) occupy independent lineages respectively. Studies have shown that red algae are mostly marine large algae, and the cells contain unique phylobilin, and their phylogenetic history is relatively closed; the green algae lineage is divided into multiple branches, including flagellar green algae, filamentous green algae and chain green algae (the latter is closely related to terrestrial plants). When Strassert et al. (2020) analyzed major algae phyla in the world, they regarded red algae, green algae and gray algae as the earliest photosynthetic branches. Red and green algae show clear separations on both the chloroplast genome and nuclear genome lineage trees (Strassert et al., 2020), and are not among the most recent common ancestors, but both originate from early primitive photosynthetic events (primary endosymbiosis). Therefore, red algae and green algae constitute two basic lineages of eukaryotic photosynthetic organisms, and their comparative analysis helps to understand the evolutionary differences after primary chloroplast acquisition.

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., 2021). Studies have found that during the Post-Glacial Age to the Cambrian period, rapid radiation occurred in multiple algae phyla, which significantly improved the primary productivity of the ocean. At the same time, supercontinental division, sea level changes and transformations in paleomarine chemistry (such as increased oxygen content) have also created opportunities for the expansion of algae's ecological niche. Another critical period was the Cretaceous period (about 100 million years ago), when the earth's carbon dioxide concentration was high, and groups such as diatoms and dinoflages flourished rapidly, having a profound impact on the global carbon cycle (Strassert et al., 2021). After the mass extinction event about 65 million years ago, algae (especially diatoms) seized ecological spaces and continued to diversify, showing strong adaptability. These associations suggest that the evolution of algae lineages is not an isolated process, but a history of interweaving with changes in geophysical and chemical conditions.

6.3 Spatial and time background of evolutionary explosion and ecological adaptation

Algae have undergone multiple evolutionary bursts and ecological adaptation stages at different temporal and spatial scales. For example, the warm period of the Cambrian climate promoted the increase of soluble nutrients and the prosperity of photosynthetic microorganisms. Changes in paleomarine transparency and nutrient configuration also promote differentiation of different groups: the advantages of large algae under low temperature and high nutritional conditions, while clean and transparent seas are conducive to the expansion of phytoplankton algae (Ho and Duchêne, 2014). Geographic isolation (such as continental drift to form ocean current partitions) promotes the speciesization of algae species. In addition, biological interactions within the biological world often accelerate the evolutionary innovation of algae under environmental pressure. Overall, the time frame and geological historical background of algae lineage evolution reflect the combined effect of multiple factors of climate, geological and ecological, and each major turning point lays the foundation for the current status of algae diversity.

7 The Driving Effect of Environmental Factors on Algae Evolution

7.1 The influence of marine chemistry and climate change on lineage evolution

Global marine chemistry (such as nutrients, pH, dissolved oxygen) and climate change have far-reaching effects on algae evolution. In ancient marine history, warming or cooling climates and the arrival of glaciers will change light and nutritional conditions, thereby screening and driving changes in algae community structure. During the period of increasing atmospheric carbon dioxide, the photosynthesis of algae increases, which promotes the expansion of photosynthetic groups; while the increase in oxygen content brings new ecological niches to aerobic algae (Zhou et al., 2022). In addition, ocean acidification can affect the calcium carbonate structure of algae (such as some dinoflagellates and seaweed), changing the basis of the food web. Modern marine environmental studies have shown that algae can exhibit variable adaptive responses to nutrient enrichment (eutrophication) and rising seawater temperatures, but these environmental pressures may also accelerate the emergence of certain harmful algae bloom taxa (Cabrera et al., 2019). Therefore, marine environmental chemistry and climate change continue to shape the evolutionary paths of algae lineages on different time scales.

7.2 Adaptive response to water transparency, temperature and nutrient changes

The differences in light conditions, temperature gradients and nutrient content in freshwater and marine ecosystems play an important driving role in the diversification of algae. In shallow water transparent environments, blue-green light-rich light-rich is conducive to the growth of cyanobacteria and red algae containing phycobilin (Gordillo, 2012); in turbid and nutritious water bodies, green algae and some diatoms show stronger competitiveness. Under high temperature environment, some tropical seaweeds (such as brown algae) can adapt to heat stress by accumulating heat shock proteins and changing cell membrane composition; while under low temperature conditions, Antarctic algae (such as ice green algae) maintain photosynthetic ability by accumulating antifreeze proteins and adjusting lipid ratios (Il’ichev and Il’icheva, 2021). These environmental gradients prompted the algae to evolve specific physiological strategies, such as changing pigment ratios to adapt to light, enhancing competitiveness for nutrients, etc., to fill the ecological niches in different habitats. In addition, the interoperability and breakage of freshwater and seawater environment also causes some algae groups to evolve independently, forming different lineages of freshwater algae and seawater algae.

7.3 The role of biological interactions (such as predation and symbiosis) in algae evolution

Interactions between organisms are also important factors driving algae evolution. Predation pressure (such as feeding algae by fishing and protozoa) can reshape algae communities by selecting smaller sizes or toxin-producing algae; the emergence of harmful algae blooms (HABs) are the result of mutual competition between algae and predators and competitive species. Symbiotic relationships also affect algae evolution: corals and algae symbiosis, moss and green algae symbiosis, etc., suggest that algae can form mutually beneficial symbiosis with multiple hosts and broaden their habitats (Brodie et al., 2017). Endosymbiosis directly shapes the diversity of algae chloroplasts; symbiotic networks among groups promote the exchange of metabolic capacity and the formation of new ecological niches. In addition, algae relationships (algae and symbiotic bacteria) have also been found to play a role in vegetative cycles and ecological stability, possibly promoting the evolution of algae metabolic characteristics (Figure 3) (Kudela et al., 2023). Therefore, biological interaction mechanisms such as predation-defense evolution and symbiotic reciprocity provide an external driving force for algae to drive innovation, accelerating the differentiation and adaptation of the lineage.

8 The significance of Algae Phylogenetic Research in Ecological and Applied Science

8.1 Understanding the implications of algae evolution on global carbon cycle and climate regulation

Algae phylogenetic studies help us reveal the functional differentiation of different algae in the carbon cycle. For example, understanding the evolutionary timing and environmental adaptability of taxa such as diatoms and dinoflages can help quantify their contribution to global carbon sinks in different eras (such as the primary productivity of diatoms contributed to the sum of world forests). At the same time, studying the origin and distribution history of algae chloroplasts provides a basis for evaluating the changes in the marine carbon pump mechanism in geological history. The phylogenetic background of algae community structure also provides clues to predict the impact of future climate change on marine ecosystems: algae of different kinship may respond differently to environmental perturbations, and community succession trends and carbon flux changes can be better predicted through lineage information (Li, 2024). Therefore, the study of the evolutionary history of algae is not only a basic science topic, but also has reference value for quantitative prediction of global climate regulation.

8.2 Application of phylogenetic information in biodiversity conservation and ecological restoration

Understanding algae diversity from a phylogenetic perspective can help guide biodiversity conservation. On the one hand, identifying key evolutionary branches (such as members of the genus phylum related to terrestrial plants) can focus on the protection of species with unique evolutionary status (Xue, 2022); on the other hand, the origin and distribution of specific ecological functions (such as nitrogen fixation, drug production) can be evaluated through phylogenetic trees, providing a basis for the diversity of conservation functions. In ecological restoration, algae lineage information can also play a role: when restoring damaged oceans and freshwater ecosystems, selecting algae species that are close to the phylogenetic development of the original ecological community can improve the recovery success rate. In addition, phylogenetic analysis can help prevent alien algae invasion: by assessing the potential risks of invasive algae by comparing with locally related species, developing targeted management strategies (Raimundo et al., 2018).

8.3 Provide an evolutionary basis for the development of algae biotechnology (such as biofuels, medicinal resources)

Algae phylogenetic research has also pointed out the direction for biotechnology development. Understanding the evolutionary relationships between different groups can help screen algae species with specific traits. For example, the high-yield oil green algae or carbon-capturing dominant algae commonly used in the biofuel industry often originates from specific green algae lineages; the development of biologically active substances such as alginate and red algae polysaccharides in the medical and healthcare fields also relies on phylogenetic information to find new varieties (Landi and Esposito, 2020). Through comparative genomics, metabolic pathways and enzyme systems unique to certain groups can be discovered, and genetic engineering targeted transformation can be carried out. In addition, the mechanisms for algae to adapt to extreme environments (such as thermophilic or salty algae) are also of application value in the study of industrial enzymes and reversible environmental microorganisms. In short, algae phylogenetics provides a theoretical basis for the discovery and utilization of resource algae species, and promotes the application and development of algae in the fields of biofuels, drugs, environmental restoration, etc.

Acknowledgments

The authors thank Professor Li and the research team for their guidance and support during the writing of this paper, and also appreciates the reviewers' constructive comments.

Conflict of Interest Disclosure

The authors confirm that the study was conducted without any commercial or financial relationships and could be interpreted as a potential conflict of interest.

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