Article
Biochemistry & Molecular Biology
Guilherme C. Baiao, Daniela I. Schneider, Wolfgang J. Miller, Lisa Klasson
Summary: Hybridization and introgression of genomic elements contribute to genetic diversity in biological lineages. The mitochondrial evolutionary history of Drosophila paulistorum and the willistoni subgoup was investigated using phylogenetic and comparative analyses. The results show that D. paulistorum has polyphyletic mitochondria, which form two non-sister clades named alpha and beta. It is suggested that both alpha and beta mitochondria were acquired through introgression from unknown fly lineages within the willistoni subgroup.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Agnes Germot, Muhammad Gamal Khodary, Othman El-Mahdy Othman, Daniel Petit
Summary: The genetic relationships between several domestic sheep populations in Egypt were analyzed using mtDNA control region sequences. Most breeds seemed to fit with the archeologists' hypothesis, with one breed possibly migrating directly from Turkey. Unexpectedly, one breed from South Egypt showed strong links to thin-tailed desert breeds of Sudan, raising questions about the events leading to this situation.
Article
Biochemistry & Molecular Biology
Jonas Lescroart, Alejandra Bonilla-Sanchez, Constanza Napolitano, Diana L. Buitrago-Torres, Hector E. Ramirez-Chaves, Paola Pulido-Santacruz, William J. Murphy, Hannes Svardal, Eduardo Eizirik
Summary: Using whole-genome resequencing data, this study constructed a time-calibrated consensus phylogeny of Neotropical small felids in the genus Leopardus. The findings challenge previous notions about the relatedness of certain species and provide insights into the speciation history and diversity patterns of this felid radiation.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Daniel Wong, Hannah Norman, Thomas J. Creedy, Kurt Jordaens, Kevin M. Moran, Andrew Young, Ximo Mengual, Jeffrey H. Skevington, Alfried P. Vogler
Summary: Using genome skimming, researchers generated mitochondrial genomes for 91 species of hoverflies, revealing their phylogenetic relationships and the evolution of their larval life history traits. The study identified a basal split and several deep clades within the family, shedding light on the diversity and evolution of hoverflies.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Vaclav Gvozdik, Tadeas Necas, Daniel Jablonski, Emily Moriarty Lemmon, Alan R. Lemmon, David Jandzik, Jiri Moravec
Summary: A study revises the dated phylogenetic hypothesis on the evolutionary history of Western Palaeartic lizards using nuclear DNA and mitogenomes, finding overall concordance between the two methods except for A. veronensis. Mitochondrial DNA suggests a common clade between A. veronensis and A. cephallonica, while nuclear DNA clusters A. veronensis with A. fragilis. The discordance is explained by ancient mitochondrial capture in a geographically restricted population during the Messinian event. The study also provides dating estimates for the divergence of different lizard species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Iwona Giska, Joao Pimenta, Liliana Farelo, Pierre Boursot, Klaus Hacklaender, Hannes Jenny, Neil Reid, W. Ian Montgomery, Paulo A. Prodohl, Paulo C. Alves, Jose Melo-Ferreira
Summary: Understanding local adaptations in mountain hares is crucial for evolutionary biology and conservation, and combining RAD sequencing with whole-genome sequencing revealed genetic signatures of local adaptation in different geographical areas. Candidate genes associated with environment-related traits were identified, showing the importance of adaptive variation in shaping the post-glacial dynamics of species.
Article
Biology
Jiaming Hu, Michael V. Westbury, Junxia Yuan, Zhen Zhang, Shungang Chen, Bo Xiao, Xindong Hou, Hailong Ji, Xulong Lai, Michael Hofreiter, Guilian Sheng
Summary: Cave hyenas, extinct bone-cracking carnivores from the family Hyaenidae, were widespread across Eurasia during the Pleistocene and became extinct at the end of the Late Pleistocene. A study of two cave hyena fossils from northeastern China suggests a split of the Asian cave hyena mitochondrial lineage from their European and African relatives around 1.85 million years ago, in line with the earliest Crocuta fossil dating to approximately 2 million years ago. Comparisons of genetic diversity indicate cave hyenas had higher diversity than extant species, likely due to non-monophyletic lineages. The joint female effective population size of Crocuta experienced declines during the Late Pleistocene.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
John C. Santiago, Joan M. Boylan, Faye A. Lemieux, Philip A. Gruppuso, Jennifer A. Sanders, David M. Rand
Summary: The mitochondria not only play a crucial role in cellular energy production but also participate in regulating various signaling pathways that impact cellular functions. Mitochondrial dysfunction is associated with disorders like cancer and neurodegenerative diseases, underscoring the importance of understanding the interactions between mitochondrial and nuclear genomes. In a Drosophila model, it was found that different mitochondrial DNA genotypes influence the temporal transcriptional response to nutrients, especially in a rapamycin-dependent manner, affecting pathways related to oxidative phosphorylation, protein metabolism, and fatty acid metabolism. The study also identified specific genes in the testis that were differentially regulated based on mitochondrial genotype, highlighting the impact of mitochondrial retrograde signaling on nuclear gene expression. Additionally, the interaction between mitochondrial genotype and rapamycin treatment revealed new connections between mitochondria and the nutrient-sensing mTORC1 signaling pathway.
Article
Biochemistry & Molecular Biology
Claudine Bleykasten-Grosshans, Romeo Fabrizio, Anne Friedrich, Joseph Schacherer
Summary: Transposable elements (TE) play an important role in genetic variation and show significant differences in content among different species. Surveying the Ty LTR-retrotransposons in a wide collection of Saccharomyces cerevisiae natural isolates revealed unique and specific TE repertoires in each subpopulation, reflecting the species' evolutionary history. Ancient interspecific hybridization events were found to have a major impact on the birth of new sequence variants and shaping of TE repertoires. The transpositional activity of these elements varied widely among natural isolates, influenced by ploidy level and genetic background.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Genis Garcia-Erill, Christian H. F. Jorgensen, Vincent B. Muwanika, Xi Wang, Malthe S. Rasmussen, Yvonne A. de Jong, Philippe Gaubert, Ayodeji Olayemi, Jordi Salmona, Thomas M. Butynski, Laura D. Bertola, Hans R. Siegismund, Anders Albrechtsen, Rasmus Heller
Summary: African wild pigs, desert warthog and common warthog, have a contentious evolutionary history. Through whole-genome sequencing, it was found that the divergence between these two species occurred later than previously estimated, and the origin and range expansion of the common warthog were revealed. The study also identified the adaptively introgressed immune system-related genes in the common warthog, indicating the role of disease resistance in their evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Mechanics
Zhicheng Wang, Dixia Fan, Michael S. Triantafyllou
Summary: The role of the added mass coefficient in vortex induced vibration is complex and elusive, but understanding the relationship between added mass and vibration patterns can help predict and prevent VIV. Studies on VIV of a long flexible cylinder and forced vibration of a rigid cylinder show that there is a correlation between the phase angle and negative added mass coefficients in the cross-flow direction, as well as the vortex shedding mode.
Review
Plant Sciences
Edgar L. Y. Wong, Dmitry A. Filatov
Summary: It is well known that closely related species can hybridize and exchange genetic material, which can either promote or hinder adaptation and speciation. The heterogeneity of genomes in most eukaryotic species, such as variations in gene density, repetitive DNA, and chromatin compactness, can determine susceptibility to gene exchange from other species. Recombination rates also greatly influence the permeability of genomic regions to interspecific introgression, with regions lacking recombination impeding genetic exchange. The presence of large rarely recombining regions in plant genomes plays a significant role in preserving species identity in hybridizing plant species.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yuting Qian, Minghui Meng, Chaowei Zhou, Haiping Liu, Haifeng Jiang, Youwei Xu, Wenjun Chen, Zufa Ding, Yang Liu, Xiong Gong, Cheng Wang, Yi Lei, Tai Wang, Ying Wang, Xiaoni Gan, Axel Meyer, Shunping He, Liandong Yang
Summary: Recent genomic analyses reveal that ancient gene flow could promote rapid diversification and adaptive radiation. Triplophysa, a loach genus mainly distributed in the Tibetan Plateau, demonstrates ecological diversity, rapid evolution, and potential adaptive radiation associated with the plateau's uplift. Through genome sequence analysis, phylogenetic reconstruction, introgression quantification, and simulation of speciation and migration processes, we find extensive gene flow events among different Triplophysa species. Our results indicate that introgression plays a more significant role than incomplete lineage sorting in supporting phylogenetic discordance in Triplophysa. Genomic regions affected by ancient gene flow exhibit lower recombination rates and nucleotide diversity, potentially linked to selection. Simulation analysis suggests that Triplophysa tibetana may have been affected by the Gonghe Movement during the third uplift of the Tibetan Plateau, leading to founder effects and a reduction in population size.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Weiwei Fu, Rui Wang, Jiantao Yu, Dexiang Hu, Yudong Cai, Junjie Shao, Yu Jiang
Summary: GGVD is a comprehensive goat genome variation database that hosts a large number of SNPs and indels, allowing researchers to visualize genomic variations in geographical maps and interactive tables, and track the status of genetic variants. The database also integrates various tools for accessing sequence features conveniently.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Andrew W. Wood, Thomas F. Duda Jr
Summary: This study evaluated whether hybridization and introgression have impacted the evolutionary history of a subgenus of Conidae (Virroconus). The findings indicate that these mechanisms may have contributed to the adaptive radiation of Conidae by generating novel gene combinations and facilitating exploitation of distinct niches. Introgression of mitochondrial and nuclear gene regions was identified among Virroconus species, suggesting a complex interplay of genetic exchange in their evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)