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Everson I Fish biology. In: Laws RM ed Antarctic ecology, vol 2. Fransz HG Vernal abundance, structure and development of epipelagic copepod populations of the eastern Weddell Sea Antarctica.
Himantothallus grandifolius and Desmarestia anceps evolved high photosynthetic efficiency, low light requirements for photosynthesis and notable UV tolerance [ 20 ]. Interestingly, the Antarctic ice diatom Amphiprora kufferathii utilizes epiphytic bacteria to consume the reactive oxygen species ROS produced during photosynthesis [ 21 ]. The increasing molecular data of Antarctic plants will help to investigate the adaptation of photosynthesis to the extreme environment of Antarctica from an evolutionary perspective.
It has been reported that positively selected and rapidly evolving genes in animals contributed to extreme environment adaptations [ 22 , 23 , 24 ]. In plants, the evidence of positive selection in the Rubisco gene involved in carbon fixation from mosses has been associated with its adaptation to the declining levels of atmospheric CO 2 since their origination in the Ordovician [ 25 ].
The genes related to the photosynthetic machinery in an endolithic green alga Ostreobium quekettii show strong purifying selection due to its low light lifestyle [ 26 ]. The genomic analyses of salt-tolerant Populus euphratica demonstrate rapid evolution in genes encoding photosynthetic electron transport chain [ 27 ]. The green alga Chlamydomonas sp.
As the primary productivity of the Antarctic sea ice, Chlamydomonas sp. ICE-L evolved specific morphological characteristics as adaptation to the extreme environment, such as the changes in pigments, lipids and fatty acids content for maintaining the stability of the thylakoid membranes and the normal physiological function of the chloroplast [ 7 ].
The particularly harsh environment in Antarctica may leave footprints in the photosynthetic genes of Chlamydomonas sp. ICE-L by changing rates of molecular evolution. However, there is little genetic evidence on the adaptation to the extreme environment regarding photosynthesis of this alga. There are other green algae that potentially adapt to similar environmental stress. Chlorella sp. ArMB is isolated from drift ice in the Arctic region [ 29 ], and low temperature is regarded as the main environmental stress. Dunaliella salina is a halotolerant alga thriving in extreme saline environments [ 30 ], and high salinity is the abiotic stress for Dunaliella salina.
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These green algae as well as Chlamydomonas sp. ICE-L living in extreme environments are ideal organisms to comparatively investigate adaptive strategies in different abiotic stresses. In this study, we sequenced 60 chloroplast protein-coding genes of Chlamydomonas sp. ICE-L, and used other available chloroplast genomes of aforementioned green algae living in similar extreme environments low light, low temperature and high salinity to investigate the potential genetic basis of adaptation to abiotic stress in the photosynthetic machinery of Chlamydomonas sp.
Adaptive evolution appears to target the protein-coding components of the chloroplast in a function photosynthetic components and lineage specific manner, and the adaptive modifications in these positively selected genes were in functionally important regions. Our analyses revealed signatures of positive selection and convergent evolution among the chloroplast protein-coding genes of Antarctic ice algae, supporting the notion that the adaptation to extreme environments in algae are associated with the altered patterns of selection on chloroplast proteins. The strain of Chlamydomonas sp.
The Chlamydomonas sp. ICE-L was isolated from Antarctic sea ice and monoclonal cultured in the lab. All downstream analyses were based on the clean reads. We further used Geneious version 9. Stop codons were removed from the sequences prior to alignment. Each aligned nucleotide sequence was trimmed to exclude poorly aligned positions using Gblocks0. Two alignments were almost identical except for a few sites. The rpoB1 , rpoB2 and rpoC genes were excluded due to alignment ambiguities according to visual assessment.
The 3rd codon positions are problematic to phylogenetic inference because of high saturation [ 40 ], then only 1st and 2nd codon positions of nucleotide data are used for phylogenetic analyses to minimize negative effects of saturation [ 41 ]. Alignment gaps and uncertainties were deleted to avoid false positives [ 43 ]. The remaining 46 genes were divided into two functional classifications photosynthesis and genetic system , and were separately concatenated. Three different codon-based likelihood models branch-specific, site-specific and branch-site models were used to explore the selection patterns and identify positive selection on each of the 46 protein-coding genes and two concatenated data.
The branch and branch-site model tests need to assign foreground branch based on a priori knowledge, and incorrect assignments may compromise the power of the test. The goal of our study is to explore the role of positive selection in the adaptive patterns of Antarctic sea ice algae, thus four selected algae adapted to extreme environments are used to perform the selection analyses.
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To detect adaptive evolving genes in Chlamydomonas sp. ICE-L and background lineages. Furthermore, the other three green algae Coccomyxa subellipsoidea C, Chlorella sp. ArMB and Dunaliella salina with extreme living conditions were specified as foreground and repeated branch-model test. We applied the FDR correction to the P values for the multiple tests performed with a significance level of 0. The site-specific model assumes that selection pattern varies among sites in the alignment but not among branches in the phylogeny.
We used a pair of site model comparisons to test for positive selection. The alternative models allow for site-specific positive selection, but the null models do not M8 vs. Because branch-site models do not allow for multiple foreground branches, the branch leading to Chlamydomonas sp.
ArMB and Dunaliella salina was separately chosen as foreground branch in each analysis. We applied the FDR correction to the P values calculated above to account for the multiple tests performed with a significance level of 0. To determine whether similar patterns of adaptive evolution occurred in distant lineages habitually exposed to similar environmental factors, we performed convergent evolution analyses.