Comparative Genome and Transcriptome Analysis Reveals Gene Selection Patterns Along with the Paleo-Climate Change in the Populus Phylogeny

Poplars are widely distributed in the northern hemisphere and have good adaptability to different living environments. The accumulation of genome and transcriptome data provides a chance to conduct comparative genomics and transcriptomics analyses to elucidate the evolutionary patterns of Populus phylogeny. Transcript sequences of eight Salicaceae species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of divergence. The divergence times of the phylogenetic clades were mainly estimated during the Middle Miocene Climate Transition (MMCT) to Quaternary Ice Age. We also identified all of the fast-evolving sequences of positive selection and found some resistance genes that were related to environmental factors. Our results suggest that drought-, H2O2- and cold-stress genes are involved in positive selection along with the paleoclimate change. These data are useful in elucidating the evolutionary patterns and causes of speciation in the Populus lineage.

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Boundary conditions for the Middle Miocene Climate Transition (MMCT v1.0)

10.5194/gmd-2017-171 ◽

2017 ◽

Author(s):

Amanda Frigola ◽

Matthias Prange ◽

Michael Schulz

Keyword(s):

Boundary Conditions ◽

General Circulation ◽

Middle Miocene ◽

Climate Models ◽

Global Climate ◽

Co2 Concentration ◽

General Circulation Models ◽

Global Climate Models ◽

Ice Volume ◽

Climate Transition

Abstract. The Middle Miocene Climate Transition was characterized by major Antarctic ice-sheet expansion and global cooling during the interval ~ 15–13 Ma. Here we present two sets of boundary conditions for global general circulation models characterizing the periods before (Middle Miocene Climatic Optimum; MMCO) and after (Middle Miocene Glaciation; MMG) the transition. These boundary conditions include Middle Miocene global topography, bathymetry and vegetation. Additionally, Antarctic ice volume and geometry, sea-level and atmospheric CO2 concentration estimates for the MMCO and the MMG are reviewed. The boundary-condition files are available for use as input in a wide variety of global climate models and constitute a valuable tool for modeling studies with a focus on the Middle Miocene.

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Transcriptome analysis reveals positive selection on the divergent between topmouth culter and zebrafish

Gene ◽

10.1016/j.gene.2014.09.053 ◽

2014 ◽

Vol 552 (2) ◽

pp. 265-271 ◽

Cited By ~ 12

Author(s):

Li Ren ◽

Xing-Jun Tan ◽

Ya-Feng Xiong ◽

Kang Xu ◽

Yi Zhou ◽

...

Keyword(s):

Positive Selection ◽

Transcriptome Analysis

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Astronomical tuning of the La Vedova High Cliff section (Ancona, Italy)—Implications of the Middle Miocene Climate Transition for Mediterranean sapropel formation

Earth and Planetary Science Letters ◽

10.1016/j.epsl.2010.06.026 ◽

2010 ◽

Vol 297 (1-2) ◽

pp. 249-261 ◽

Cited By ~ 28

Author(s):

A.A. Mourik ◽

J.F. Bijkerk ◽

A. Cascella ◽

S.K. Hüsing ◽

F.J. Hilgen ◽

...

Keyword(s):

Middle Miocene ◽

Astronomical Tuning ◽

Climate Transition

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Hydrological change and human activity during Yuan–Ming Dynasties in the Loulan area, northwestern China

The Holocene ◽

10.1177/0959683618771495 ◽

2018 ◽

Vol 28 (8) ◽

pp. 1266-1275 ◽

Cited By ~ 3

Author(s):

Kangkang Li ◽

Xiaoguang Qin ◽

Lei Zhang ◽

Zhaoyan Gu ◽

Bing Xu ◽

...

Keyword(s):

Human Activity ◽

Little Ice Age ◽

Environmental Changes ◽

Ice Age ◽

Flood Events ◽

Lop Nur ◽

Plant Remains ◽

Ancient Silk Road ◽

Climate Transition ◽

Changes Over Time

Human activity on arid lands has been related to oases evolution. The ancient Loulan, an important transportation hub of the ancient Silk Road, developed on an ancient oasis on the west bank of the lake Lop Nur in Xinjiang, China. Previous studies and historical documents suggest that the region has experienced dramatic natural environmental and human activity–related changes over time, transitioning from a particularly prosperous oasis to a depopulated zone with harsh environment after about 1500 a BP (before present, where present = AD 1950). Based on systematic radiocarbon (14C) dating for natural plant remains and archeological sites in the Loulan area, it was revealed that the region re-experienced oasis environment from 1260 to 1450 cal. AD, corresponding to the Yuan–Ming Dynasties, which is the climate transition stage from the ‘Medieval Warm Period’ to the ‘Little Ice Age’, encompassing a series of pulse-like flood events which cannot be identified from lacustrine deposition due to the limits of sampling resolution and dating. It was found that humans re-occupied the Loulan area and built canals to irrigate farmlands during the period. The more habitable hydrological conditions that resulted from these environmental changes present one major reason for the re-emergence of human activities in the Loulan area.

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Evolutionary patterns of chimeric retrogenes in Oryza species

Scientific Reports ◽

10.1038/s41598-019-54085-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Yanli Zhou ◽

Chengjun Zhang

Keyword(s):

Positive Selection ◽

Genome Evolution ◽

Rice Genome ◽

Chimeric Gene ◽

Oryza Species ◽

Evolutionary Patterns ◽

Plant Genomes ◽

Parental Gene ◽

Flanking Sequences ◽

Substitution Ratio

AbstractChimeric retroposition is a process by which RNA is reverse transcribed and the resulting cDNA is integrated into the genome along with flanking sequences. This process plays essential roles and drives genome evolution. Although the origination rates of chimeric retrogenes are high in plant genomes, the evolutionary patterns of the retrogenes and their parental genes are relatively uncharacterised in the rice genome. In this study, we evaluated the substitution ratio of 24 retrogenes and their parental genes to clarify their evolutionary patterns. The results indicated that seven gene pairs were under positive selection. Additionally, soon after new chimeric retrogenes were formed, they rapidly evolved. However, an unexpected pattern was also revealed. Specifically, after an undefined period following the formation of new chimeric retrogenes, the parental genes, rather than the new chimeric retrogenes, rapidly evolved under positive selection. We also observed that one retro chimeric gene (RCG3) was highly expressed in infected calli, whereas its parental gene was not. Finally, a comparison of our Ka/Ks analysis with that of other species indicated that the proportion of genes under positive selection is greater for chimeric retrogenes than for non-chimeric retrogenes in the rice genome.

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The MHC Class Ia Genes in Chenfu’s Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Animals ◽

10.3390/ani10010034 ◽

2019 ◽

Vol 10 (1) ◽

pp. 34

Author(s):

Hu Chen ◽

Siqi Huang ◽

Ye Jiang ◽

Fuyao Han ◽

Qingyong Ni ◽

...

Keyword(s):

Gene Duplication ◽

Positive Selection ◽

Phylogenetic Relationships ◽

Molecular Mechanisms ◽

Coding Region ◽

Evolutionary Mechanisms ◽

Evolutionary Patterns ◽

Mhc Genes ◽

Mhc Class Ia ◽

Related Proteins

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

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Stromatolites in the Paratethys Sea during the Middle Miocene climate transition as witness of the Badenian salinity crisis

Facies ◽

10.1007/s10347-013-0391-z ◽

2013 ◽

Vol 60 (2) ◽

pp. 429-444 ◽

Cited By ~ 5

Author(s):

Mathias Harzhauser ◽

Jörn Peckmann ◽

Daniel Birgel ◽

Erich Draganits ◽

Oleg Mandic ◽

...

Keyword(s):

Middle Miocene ◽

Climate Transition

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Supplementary material to "Southern Ocean bottom water cooling and ice sheet expansion during the middle Miocene climate transition"

10.5194/cp-2020-157-supplement ◽

2020 ◽

Author(s):

Thomas J. Leutert ◽

Sevasti Modestou ◽

Stefano M. Bernasconi ◽

A. Nele Meckler

Keyword(s):

Southern Ocean ◽

Bottom Water ◽

Middle Miocene ◽

Ice Sheet ◽

Ocean Bottom ◽

Water Cooling ◽

Supplementary Material ◽

Climate Transition

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Discovery of the Badenian evaporites inside the Carpathian Arc: implications for global climate change and Paratethys salinity

Geologica Carpathica ◽

10.1515/geoca-2017-0015 ◽

2017 ◽

Vol 68 (3) ◽

pp. 193-206 ◽

Cited By ~ 12

Author(s):

Katalin Báldi ◽

Felicitász Velledits ◽

Stjepan Ćorić ◽

Viktor Lemberkovics ◽

Katalin Lőrincz ◽

...

Keyword(s):

Climate Change ◽

Global Climate Change ◽

Normal Saline ◽

Middle Miocene ◽

Global Climate ◽

Great Plain ◽

Geological Record ◽

Central Paratethys ◽

Growing Body ◽

Climate Transition

Abstract Massive evaporites were discovered in the Soltvadkert Trough (Great Plain, Hungary) correlating to the Badenian Salinity Crisis (13.8 Ma, Middle Miocene) on the basis of nannoplankton and foraminifera biostratigraphy. This new occurrence from Hungary previously thought to be devoid of evaporites is part of a growing body of evidence of evaporitic basins inside the Carpathian Arc. We suggest the presence of evaporites perhaps in the entire Central Paratethys during the salinity crisis. Different scenarios are suggested for what subsequently happened to these evaporites to explain their presence or absence in the geological record. Where they are present, scenario A suggests that they were preserved in subsiding, deep basins overlain by younger sediments that protected the evaporites from reworking, like in the studied area. Where they are absent, scenario B suggests recycling. Scenario B explains how the supposedly brackish Sarmatian could have been hyper/normal saline locally by providing a source of the excess salt from the reworking and dissolving of BSC halite into seawater. These scenarios suggest a much larger amount of evaporites locked up in the Central Paratethys during the salinity crisis then previously thought, probably contributing to the step-like nature of cooling of the Mid Miocene Climate Transition, the coeval Mi3b.

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