Huang, Jun Thawornwattana, Yuttapong Flouri, Tomáš Mallet, James Yang, Ziheng
Published in
Molecular biology and evolution
Genomic sequence data provide a rich source of information about the history of species divergence and interspecific hybridization or introgression. Despite recent advances in genomics and statistical methods, it remains challenging to infer gene flow, and as a result, one may have to estimate introgression rates and times under misspecified models...
Guo, Zhonglong Kuang, Zheng Tao, Yihan Wang, Haotian Wan, Miaomiao Hao, Chen Shen, Fei Yang, Xiaozeng Li, Lei
Published in
Molecular biology and evolution
MicroRNAs (miRNAs) are fast evolving endogenous small RNAs that regulate organism function and behavior in both animals and plants. Although models for de novo miRNA biogenesis have been proposed, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 21 phylogeneti...
Carruthers, Madeleine Edgley, Duncan E Saxon, Andrew D Gabagambi, Nestory P Shechonge, Asilatu Miska, Eric A Durbin, Richard Bridle, Jon R Turner, George F Genner, Martin J
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Published in
Molecular biology and evolution
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw ...
Li, Duojia Gandhi, Dhyey Kumon, Tomohiro Yamashita, Yukiko M
Published in
Molecular biology and evolution
Karyotype refers to the configuration of the genome into a set of chromosomes. The karyotype difference between species is expected to impede various biological processes, such as chromosome segregation and meiotic chromosome pairing, potentially contributing to incompatibility. Karyotypes can rapidly change between closely related species and even...
Brinkmeier, Julia Coelho, Susana de Massy, Bernard Bourbon, Henri-Marc
Published in
Molecular biology and evolution
Type II DNA topoisomerases regulate topology by double-stranded DNA cleavage and ligation. The TopoVI family of DNA topoisomerase, first identified and biochemically characterized in Archaea, represents, with TopoVIII and mini-A, the type IIB family. TopoVI has several intriguing features in terms of function and evolution. TopoVI has been identifi...
Goutte, Sandra Hariyani, Imtiyaz Utzinger, Kole Deroy Bourgeois, Yann Boissinot, Stéphane
Published in
Molecular biology and evolution
Traits shared among distantly related lineages are indicators of common evolutionary constraints, at the ecological, physiological, or molecular level. Here, we show that the vertebral stripe, a cryptic color pattern, has evolved hundreds of times in the evolutionary history of anurans (frogs and toads) and is favored in terrestrial habitats. Using...
Fusca, Daniel D Sharma, Eesha Weiss, Jörg G Claycomb, Julie M Cutter, Asher D
Published in
Molecular biology and evolution
Geographically distinct populations can adapt to the temperature conditions of their local environment, leading to temperature-dependent fitness differences between populations. Consistent with local adaptation, phylogeographically distinct Caenorhabditis briggsae nematodes show distinct fitness responses to temperature. The genetic mechanisms unde...
Hirata, Mayu Ichiyanagi, Tomoko Katoh, Hirokazu Hashimoto, Takuma Suzuki, Hikaru Nitta, Hirohisa Kawase, Masaki Nakai, Risako Imamura, Masanori Ichiyanagi, Kenji
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Published in
Molecular biology and evolution
Changes in the epigenome can affect the phenotype without the presence of changes in the genomic sequence. Given the high identity of the human and chimpanzee genome sequences, a substantial portion of their phenotypic divergence likely arises from epigenomic differences between the two species. In this study, the transcriptome and epigenome were d...
Zhang, Jia Richards, Zoe T Adam, Arne A S Chan, Cheong Xin Shinzato, Chuya Gilmour, James Thomas, Luke Strugnell, Jan M Miller, David J Cooke, Ira
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Published in
Molecular biology and evolution
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to...
Krause, David J Hittinger, Chris Todd
Published in
Molecular biology and evolution
The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression o...