The Parallel Molecular Adaptations to the Antarctic Cold Environment in Two Psychrophilic Green Algae

Abstract Psychrophilic green algae from independent phylogenetic lines thrive in the polar extreme environments, but the hypothesis that their psychrophilic characteristics appeared through parallel routes of molecular evolution remains untested. The recent surge of transcriptome data enables large-scale evolutionary analyses to investigate the genetic basis for the adaptations to the Antarctic extreme environment, and the identification of the selective forces that drive molecular evolution is the foundation to understand the strategies of cold adaptation. Here, we conducted transcriptome sequencing of two Antarctic psychrophilic green algae (Chlamydomonas sp. ICE-L and Tetrabaena socialis) and performed positive selection and convergent substitution analyses to investigate their molecular convergence and adaptive strategies against extreme cold conditions. Our results revealed considerable shared positively selected genes and significant evidence of molecular convergence in two Antarctic psychrophilic algae. Significant evidence of positive selection and convergent substitution were detected in genes associated with photosynthetic machinery, multiple antioxidant systems, and several crucial translation elements in Antarctic psychrophilic algae. Our study reveals that the psychrophilic algae possess more stable photosynthetic apparatus and multiple protective mechanisms and provides new clues of parallel adaptive evolution in Antarctic psychrophilic green algae.

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Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion

Biology Letters ◽

10.1098/rsbl.2015.0349 ◽

2015 ◽

Vol 11 (7) ◽

pp. 20150349 ◽

Cited By ~ 18

Author(s):

Alexander Van Nynatten ◽

Devin Bloom ◽

Belinda S. W. Chang ◽

Nathan R. Lovejoy

Keyword(s):

Molecular Evolution ◽

Positive Selection ◽

Visual Pigment ◽

Large Scale ◽

Marine Species ◽

South American ◽

Sequence Analyses ◽

Freshwater Habitats ◽

Varying Environments ◽

Visual Pigment Evolution

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.

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The effects of increasing the number of taxa on inferences of molecular convergence

10.1101/081612 ◽

2016 ◽

Cited By ~ 1

Author(s):

Gregg W.C. Thomas ◽

Matthew W. Hahn ◽

Yoonsoo Hahn

Keyword(s):

Positive Selection ◽

Sample Size ◽

Comparative Studies ◽

Convergent Evolution ◽

Marine Mammals ◽

Large Scale ◽

Marine Species ◽

Original Analysis ◽

Insight Into ◽

Molecular Convergence

AbstractConvergent evolution provides insight into the link between phenotype and genotype. Recently, large-scale comparative studies of convergent evolution have become possible, but researchers are still trying to determine the best way to design these types of analyses. One aspect of molecular convergence studies that has not yet been investigated is how taxonomic sample size affects inferences of molecular convergence. Here we show that increased sample size decreases the amount of inferred molecular convergence associated with the three convergent transitions to a marine environment in mammals. The sampling of more taxa—both with and without the convergent phenotype—reveals that alleles associated only with marine mammals in small datasets are actually more widespread, or are not shared by all marine species. The sampling of more taxa also allows finer resolution of ancestral substitutions, revealing that they are not in fact on lineages leading to solely marine species. We revisit a previous study on marine mammals and find that only 7 of the reported 43 genes with convergent substitutions still show signs of convergence with a larger number of background species. However, 4 of those 7 genes also showed signs of positive selection in the original analysis and may still be good candidates for adaptive convergence. Though our study is framed around the convergence of marine mammals, we expect our conclusions on taxonomic sampling are generalizable to any study of molecular convergence.

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FUSTr: a tool to find gene families under selection in transcriptomes

PeerJ ◽

10.7717/peerj.4234 ◽

2018 ◽

Vol 6 ◽

pp. e4234 ◽

Cited By ~ 6

Author(s):

T. Jeffrey Cole ◽

Michael S. Brewer

Keyword(s):

Molecular Evolution ◽

Positive Selection ◽

High Performance ◽

Large Scale ◽

Simulated Data ◽

Gene Families ◽

Strong Positive Selection ◽

Transcriptomic Data ◽

Downstream Analysis ◽

User Friendly

Background The recent proliferation of large amounts of biodiversity transcriptomic data has resulted in an ever-expanding need for scalable and user-friendly tools capable of answering large scale molecular evolution questions. FUSTr identifies gene families involved in the process of adaptation. This is a tool that finds genes in transcriptomic datasets under strong positive selection that automatically detects isoform designation patterns in transcriptome assemblies to maximize phylogenetic independence in downstream analysis. Results When applied to previously studied spider transcriptomic data as well as simulated data, FUSTr successfully grouped coding sequences into proper gene families as well as correctly identified those under strong positive selection in relatively little time. Conclusions FUSTr provides a useful tool for novice bioinformaticians to characterize the molecular evolution of organisms throughout the tree of life using large transcriptomic biodiversity datasets and can utilize multi-processor high-performance computational facilities.

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Adaptation to extreme environments: The Antarctic volunteer.

PsycEXTRA Dataset ◽

10.1037/e401092004-001 ◽

1966 ◽

Cited By ~ 1

Author(s):

E. K. Gunderson

Keyword(s):

Extreme Environments ◽

The Antarctic

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Large-scale Rossby waves in the Antarctic stratosphere

Kosmìčna nauka ì tehnologìâ ◽

10.15407/knit2010.05.005 ◽

2010 ◽

Vol 16 (5) ◽

pp. 5-11

Author(s):

A.V. Agapitov ◽

◽

A.V. Grytsai ◽

D.A. Salyuk ◽

◽

...

Keyword(s):

Large Scale ◽

Rossby Waves ◽

The Antarctic

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A Turbulent Silk Road: China's Vulnerable Foreign Policy in the Middle East and North Africa

The China Quarterly ◽

10.1017/s0305741020001216 ◽

2021 ◽

pp. 1-21

Author(s):

Andrea Ghiselli ◽

Pippa Morgan

Keyword(s):

Middle East ◽

North Africa ◽

Security Policy ◽

Large Scale ◽

Chinese Government ◽

Horn Of Africa ◽

Host Countries ◽

Security Risks ◽

Significant Evidence ◽

Chinese Workers

Abstract The nexus between China's human and economic presence abroad and its security policy is increasingly important. Within this nexus, this study statistically explores whether and to what extent Chinese contractors reduce the number of Chinese nationals they send to work in North Africa, the Middle East and the Horn of Africa when the security situation in host states worsens. We find no significant evidence that either warnings from Chinese embassies and consulates to leave host countries or expert perceptions of host stability influence the number of Chinese workers. Worker numbers appear to decrease significantly only in the aftermath of large-scale violent events. These findings suggest that Chinese companies are relatively acceptant of security risks and uncertainties, despite the decade-long regulatory efforts of the Chinese government to make them more security-conscious overseas and, thus, to reduce pressure to use diplomatically and economically expensive military means for their protection.

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Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions

Genetics ◽

10.1093/genetics/157.2.667 ◽

2001 ◽

Vol 157 (2) ◽

pp. 667-677

Author(s):

Hitoshi Araki ◽

Nobuyuki Inomata ◽

Tsuneyuki Yamazaki

Keyword(s):

Drosophila Melanogaster ◽

Molecular Evolution ◽

Positive Selection ◽

Natural Populations ◽

Sliding Window ◽

Selective Constraint ◽

Proximal Region ◽

Coding Regions ◽

Asian Populations ◽

Flanking Region

Abstract In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.

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