Article
Biochemistry & Molecular Biology
Michael Westbury, Diana Le Duc, David A. Duchene, Arunkumar Krishnan, Stefan Prost, Sereina Rutschmann, Jose H. Grau, Love Dalen, Alexandra Weyrich, Karin Noren, Lars Werdelin, Fredrik Dalerum, Torsten Schoeneberg, Michael Hofreiter
Summary: During the Miocene, the highly diverse family of Carnivora, Hyaenidae, has been reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage was found, with high levels of genetic diversity and stable population sizes seen in the spotted hyena and aardwolf.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Kara Ryan, Ryan Greenway, Jake Landers, Lenin Arias-Rodriguez, Michael Tobler, Joanna L. Kelley
Summary: Hydrogen sulfide is a toxic gas that disrupts biological processes, yet fish in the Poecilia mexicana species complex have evolved sulfide tolerance multiple times. This study investigates whether the repeated evolution of tolerance is due to similar genomic changes, finding evidence of both convergence and divergence in gene variation associated with sulfide processes and toxicity.
Article
Biochemistry & Molecular Biology
Catalina Palacios, Pengcheng Wang, Nan Wang, Megan A. Brown, Lukas Capatosto, Juan Du, Jiahu Jiang, Qingze Zhang, Nishma Dahal, Sangeet Lamichhaney
Summary: Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study the genomic variation, gene expression, and long-term adaptation in Tibetan Partridge populations residing across the elevational gradient of the Tibetan Plateau. We found evidence of gene flow between different elevations and identified genetic divergence and fixed alleles in high-altitude populations. Additionally, we identified differentially expressed genes that correlate with altitude differences and are enriched in pathways known to respond to hypoxia.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Liyuan Ma, Weiyi Yang, Shanshan Huang, Rui Liu, Huiying Li, Xinping Huang, Junming Xiong, Xueduan Liu
Summary: This study isolated a new acidophile from acid mine drainage (AMD) and analyzed its complete genome sequence to explore its taxonomic and adaptive features. The results highlighted the unique genetic constitution of the acidophile and identified diverse mobile genetic elements that may contribute to its advantageous genome. This study improves our understanding of evolutionary adaptation mechanisms and expands the potential utilization of this acidophile in industrial bioleaching.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Claire Merot, Emma L. Berdan, Hugo Cayuela, Haig Djambazian, Anne-Laure Ferchaud, Martin Laporte, Eric Normandeau, Jiannis Ragoussis, Maren Wellenreuther, Louis Bernatchez
Summary: This study examines how chromosomal inversions shape genetic variation in a species across different environmental gradients, finding that these structural variants influence population differentiation and adaptation to environmental factors. The results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at both local and large scales.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Plant Sciences
Sariel Huebner
Summary: Graph-based pangenomes can provide a comprehensive platform to study diversity in populations or species, but still face challenges in species with large complex genomes. However, with advancing technology, the graph-pangenome is expected to become a central platform in genomics studies and applications.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Ecology
Prabodh Kumar Bajpai, Arye Harel, Sharoni Shafir, Oz Barazani
Summary: This study explored ecotypic differentiation in populations of Eruca sativa from arid and Mediterranean habitats at the genomic level. The results showed that climatic conditions significantly influenced genetic diversity, and genes related to transcription factors and phytohormone signaling played a crucial role in adaptation to both abiotic and biotic conditions.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Virology
Vanessa E. Schulz, Jeffrey F. Tuff, Riley H. Tough, Lara Lewis, Benjamin Chimukangara, Nigel Garrett, Quarraisha Abdool Karim, Salim S. Abdool Karim, Lyle R. Mckinnon, Ayesha B. M. Kharsany, Paul J. Mclaren
Summary: This study identifies the association between genetic variations near CHD1L and HIV viral replication control in a South African population, and further uncovers the impact of other genes on HIV viral genes.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mohammed Errbii, Jens Keilwagen, Katharina J. Hoff, Raphael Steffen, Janine Altmueller, Jan Oettler, Lukas Schrader
Summary: The study reveals strong genetic differentiation between the New World and Old World lineages of the heart node ant Cardiocondyla obscurior, with transposable elements (TEs) activity playing a significant role in their divergence. Additionally, introgression from the Old World lineage is identified as the dominant source of genetic diversity in the New World lineage, despite their strong genetic differentiation.
Article
Multidisciplinary Sciences
Monica H. Keith, Mark Flinn, Harly J. Durbin, Troy N. Rowan, Gregory E. Blomquist, Kristen H. Taylor, Jeremy F. Taylor, Jared E. Decker
Summary: The Caribbean region is genetically diverse, with Dominica showing unique patterns of migration, mixture, and isolation. African ancestry is the predominant component, followed by European and indigenous components. The genetic results support local narratives about the community's history and founding.
Article
Biochemistry & Molecular Biology
Marvin Choquet, Felix Lenner, Arianna Cocco, Gaelle Toullec, Erwan Corre, Jean-Yves Toullec, Andreas Wallberg
Summary: This study used comparative genomics to investigate the genetic variation and adaptation potential of 20 krill species collected from different oceans. The results showed that Antarctic krill species had lower levels of genetic variation and evolutionary rates, indicating a potentially lower adaptive potential to rapid climate change. Additionally, the study identified several candidate genes associated with adaptive evolution in Antarctic krill.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Haruna Nakamura, Mitsuto Aibara, Rei Kajitani, Hillary D. J. Mrosso, Semvua Mzighani, Atsushi Toyoda, Takehiko Itoh, Norihiro Okada, Masato Nikaido
Summary: The cichlids of Lake Victoria exhibit rapid adaptive radiation, with low genetic differentiation among species and highly differentiated genes related to vision playing a crucial role in speciation. Comparative genomic analyses of three Lake Victoria cichlid species in different habitats revealed distinct patterns of population history and identified novel adaptive candidate genes, some with long divergent haplotypes between species, indicating selective sweep events. Phylogenetic analyses showed that much of the allelic diversity among Lake Victoria cichlids originated from standing genetic variation before the adaptive radiation. The study uncovered the species-specific adaptation processes and complex genomic substrate that facilitated this adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Nathan W. Byer, Emily D. Fountain, Brendan N. Reid, Kristen Miller, Paige J. Kulzer, M. Zachariah Peery
Summary: Our study found divergent patterns of spatial clustering between neutral and putatively adaptive genetic variation in both turtle species, with stronger environmental associations detected for stress response genes and for the more specialized Blanding's turtle. Land cover appeared to play a more important role than climate in shaping spatial variation in functional genes, suggesting that human landscape alterations may impact adaptive capacity crucial for climate change responses.
Article
Biotechnology & Applied Microbiology
Derek E. Kelly, Shweta Ramdas, Rong Ma, Renata A. Rawlings-Goss, Gregory R. Grant, Alessia Ranciaro, Jibril B. Hirbo, William Beggs, Meredith Yeager, Stephen Chanock, Thomas B. Nyambo, Sabah A. Omar, Dawit Woldemeskel, Gurja Belay, Hongzhe Li, Christopher D. Brown, Sarah A. Tishkoff
Summary: By mapping expression and splicing QTLs in a diverse cohort of 162 Africans, we found that the gene regulatory architecture is broadly shared between African and non-African populations, but individual loci show significant variation across populations. QTL mapping in Africans improves the detection and fine-mapping of expression QTLs compared to European Americans. Integrating QTL scans with signatures of natural selection revealed genes related to immunity, metabolism, and pigmentation that are highly differentiated between Africans and non-Africans.
Article
Multidisciplinary Sciences
Marty Kardos, Ellie E. Armstrong, Sarah W. Fitzpatrick, Samantha Hauser, Philip W. Hedrick, Joshua M. Miller, David A. Tallmon, W. Chris Funk
Summary: Conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential, while focusing on functional genetic variation is not always feasible and can often lead to misleading and counterproductive outcomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)