Data from: Early photosynthetic eukaryotes inhabited low-salinity habitats

The early evolutionary history of the chloroplast lineage remains an open
question. It is widely accepted that the endosymbiosis that established
the chloroplast lineage in eukaryotes can be traced back to a single
event, in which a cyanobacterium was incorporated into a protistan host.
It is still unclear, however, which Cyanobacteria are most closely related
to the chloroplast, when the plastid lineage first evolved, and in what
habitats this endosymbiotic event occurred. We present phylogenomic and
molecular clock analyses, including data from cyanobacterial and
chloroplast genomes using a Bayesian approach, with the aim of estimating
the age for the primary endosymbiotic event, the ages of crown groups for
photosynthetic eukaryotes, and the independent incorporation of a
cyanobacterial endosymbiont by Paulinella. Our analyses include both broad
taxon sampling (119 taxa) and 18 fossil calibrations across all
Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support
the hypothesis that the chloroplast lineage diverged from its closet
relative Gloeomargarita, a basal cyanobacterial lineage, ∼2.1 billion y
ago (Bya). Our analyses suggest that the Archaeplastida, consisting of
glaucophytes, red algae, green algae, and land plants, share a common
ancestor that lived ∼1.9 Bya. Whereas crown group Rhodophyta evolved in
the Mesoproterozoic Era (1,600–1,000 Mya), crown groups Chlorophyta and
Streptophyta began to radiate early in the Neoproterozoic (1,000–542 Mya).
Stochastic mapping analyses indicate that the first endosymbiotic event
occurred in low-salinity environments. Both red and green algae colonized
marine environments early in their histories, with prasinophyte green
phytoplankton diversifying 850–650 Mya.

叶绿体谱系的早期演化历史仍是一个悬而未决的学术问题。学界普遍认为，在真核生物中确立叶绿体谱系的内共生作用可追溯至单一事件：即一株蓝细菌被整合进入原生生物宿主。然而，目前仍不清楚哪些蓝细菌与叶绿体亲缘关系最近、质体谱系最初演化于何时，以及该内共生事件发生在何种生境之中。
本研究开展了系统基因组学与分子钟分析，采用贝叶斯（Bayesian）方法整合蓝细菌与叶绿体基因组数据，旨在估算初级内共生事件的发生时间、光合真核生物冠群的分化时间，以及保罗虫属（Paulinella）独立获取蓝细菌内共生体的时间。
本次分析涵盖了蓝细菌与光合真核生物的宽泛类群采样（119个分类单元）与18个化石校准点。系统基因组学分析支持以下假说：叶绿体谱系与其最近缘类群——基底蓝细菌谱系格洛玛尔加藻属（Gloeomargarita）——的分化时间约为21亿年前（Bya）。
分析结果显示，由灰胞藻、红藻、绿藻与陆生植物构成的原始色素体生物（Archaeplastida）拥有约19亿年前的共同祖先。冠群红藻门（Rhodophyta）演化于中元古代（16亿至10亿年前），而冠群绿藻门（Chlorophyta）和链形植物门（Streptophyta）则在新元古代早期（10亿至5.42亿年前）开始辐射演化。
随机映射分析表明，首次内共生事件发生于低盐生境中。红藻与绿藻均在演化早期就已定植海洋环境，其中青绿藻（Prasinophyte）绿藻浮游植物的分化时间为8.5亿至6.5亿年前。