Article
Ecology
Shujing Wang, Yanfei Li, Jiayue Zhou, Juhong Chen, Kun Jiang, Zhen Ye, Huaijun Xue, Wenjun Bu
Summary: This study reveals a novel disjunct distribution pattern at the population level between southwestern China and Taiwan Island, providing evidence of convergent evolution of local populations in high-elevation environments.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Biochemistry & Molecular Biology
Kelsey Jorgensen, Daisheng Song, Julien Weinstein, Obed A. Garcia, Laurel N. Pearson, Maria Inclan, Maria Rivera-Chira, Fabiola Leon-Velarde, Melisa Kiyamu, Tom D. Brutsaert, Abigail W. Bigham, Frank S. Lee
Summary: For over 10,000 years, Andeans have been living at high altitudes where the limited oxygen poses a challenge to human survival. Recent studies have discovered evidence of positive selection acting on the HIF2A locus in Andeans, which is associated with the hypoxia-inducible factor pathway. However, the specific mechanism by which this allele leads to altitude adaptation remains unknown. By analyzing the genomes of 46 Peruvian Andeans, researchers confirmed the presence of positive selection on HIF2A and identified a unique variation pattern surrounding the Andean-specific single nucleotide variant (SNV) rs570553380. This variant is associated with increased nitric oxide biosynthesis, as shown in a Peruvian Andean population living at high altitude.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Fanny E. Hartmann, Tiziana Vonlanthen, Nikhil Kumar Singh, Megan C. McDonald, Andrew Milgate, Daniel Croll
Summary: Convergent evolution was observed in pesticide resistance adaptation of the fungal pathogen Zymoseptoria tritici, with some loci showing convergent changes across populations while others displaying more population-specific allele frequency changes. Genome-wide association studies revealed unknown factors in azole resistance and showed that half of the known resistance loci overlapped with selective sweep regions, indicating the major selective pressure of fungicide application on the pathogen. Genomic analyses highlighted the contribution of both de novo mutations and gene flow to convergent pesticide adaptation.
Article
Microbiology
Yair E. Gatt, Dana Savion, Tal Bamberger, Hanah Margalit
Summary: Bacteria adapt to their host by mutating specific genes and by reprogramming their gene expression. Different strains of a bacterial species often mutate the same genes during infection, demonstrating convergent genetic adaptation. However, there is limited evidence for convergent adaptation at the transcriptional level.
Article
Multidisciplinary Sciences
Yalin Cheng, Matthew J. Miller, Dezhi Zhang, Ying Xiong, Yan Hao, Chenxi Jia, Tianlong Cai, Shou-Hsien Li, Ulf S. Johansson, Yang Liu, Yongbin Chang, Gang Song, Yanhua Qu, Fumin Lei
Summary: Parallel evolution is expected among closely related taxa exposed to similar selective pressures, but genetic solutions to achieve phenotypic similarities may differ. In East Asian Paridae species, high-elevation adaptation shows parallel functional response to extreme elevation relying on different genes, with no influence of heterozygosity on genetic parallelism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(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
Biology
Jory Thiel, Muzaffar A. Khan, Roel M. Wouters, Richard J. Harris, Nicholas R. Casewell, Bryan G. Fry, R. Manjunatha Kini, Stephen P. Mackessy, Freek J. Vonk, Wolfgang Wuster, Michael K. Richardson
Summary: Convergence is the phenomenon where similar phenotypes evolve independently in different lineages. Resistance to toxins in animals is an example of convergence, where molecular adaptations have evolved to counteract the harmful effects of toxins. However, resistance adaptations may carry fitness costs if they disrupt the normal physiology of the resistant animal.
BIOLOGICAL REVIEWS
(2022)
Article
Biology
Stefano G. Giulieri, Romain Guerillot, Sebastian Duchene, Abderrahman Hachani, Diane Daniel, Torsten Seemann, Joshua S. Davis, Steven Y. C. Tong, Bernadette C. Young, Daniel J. Wilson, Timothy P. Stinear, Benjamin P. Howden
Summary: This study provides a comprehensive analysis of the genetic variations and evolutionary patterns of Staphylococcus aureus during severe infections. The findings reveal distinct evolutionary signatures and convergent mutations in genes related to antibiotic response and pathogenesis, highlighting the clinical significance of these adaptations. Non-canonical loci associated with adaptation were also identified. These results contribute to a better understanding of the molecular changes when S. aureus transitions from colonization to severe infection and may have implications for predicting clinical outcomes and developing new treatment and prevention strategies.
Article
Ecology
Ryan Hill
Summary: This study examined convergent evolution in flight-related morphology among eight mimicry complexes of 51 butterfly species from Ecuador. Results showed significant morphological differences between mimicry complexes, divided into three clusters. Flight-related morphology adds complexity to predator-prey signals and limits the evolution of color patterns.
Article
Biology
Manman Li, Xinmei Li, Zhipei Wu, Guanghui Zhang, Nini Wang, Mingle Dou, Shanlin Liu, Chentao Yang, Guanliang Meng, Hailu Sun, Christina Hvilsom, Guoxiang Xie, Yang Li, Zhuo hui Li, Wei Wang, Yu Jiang, Rasmus Heller, Yu Wang
Summary: This study compared the genomes of muskox and reindeer, and identified common genetic variations related to thermogenesis and circadian rhythm in the Arctic adaptation. It was also found that muskox and reindeer may enhance brown adipose tissue thermogenesis by modulating mitochondrion, lipid metabolism, and angiogenesis pathways. Additionally, an amino acid substitution in the angiogenesis-related gene HIF2A was found to increase angiogenesis of brown adipose tissue. In conclusion, this work provides new insights into the molecular mechanisms involved in Arctic adaptation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Environmental Sciences
Giovanny M. Mosquera, Franklin Marin, Margaret Stern, Vivien Bonnesoeur, Boris F. Ochoa-Tocachi, Francisco Roman-Danobeytia, Patricio Crespo
Summary: High-elevation grasslands play a crucial role in providing hydrological services, but research on the hydrological function of grasslands in montane regions is still limited. Most hydrological studies have focused on paramos in the Andean region, especially in Ecuador, while research on punas and jalcas is scarce.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Review
Biology
Tami D. Lieberman
Summary: The human microbiome has the ability to adapt to within-person mutations. Adaptive mutations that occur during health can impact the immune system, nutrient and drug metabolism, and the stability of the microbiome. However, research on adaptive evolution within human-associated microbiomes is relatively limited.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Lian Deng, Yuwen Pan, Yinan Wang, Hao Chen, Kai Yuan, Sihan Chen, Dongsheng Lu, Yan Lu, Siti Shuhada Mokhtar, Thuhairah Abdul Rahman, Boon-Peng Hoh, Shuhua Xu
Summary: This study conducted a comprehensive analysis of the genetic distinction and connection of tropical indigenous peoples in Asia (TIA). The researchers identified a basal Asian ancestry (bASN) shared by these populations, which was relatively enriched in ancient Asian human genomes. The study also found shared adaptations inherited from the ancient Asian ancestry among the TIA groups and suggested that the bASN ancestry could have formed the genetic basis for the dark pigmentation observed in TIA peoples.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Amelia-Juliette Demery, Kevin J. Burns
Summary: This study investigates the extent of phenotypic convergence in the tanager family on a continental scale. Using a large dataset and computational methods, the study shows that around 45.3% of species and clades have evolved convergently in morphological space more than expected by chance alone. This reflects ecological opportunity and structural constraints in the group.
Article
Biochemistry & Molecular Biology
Laura Buggiotti, Andrey A. Yurchenko, Nikolay S. Yudin, Christy J. Vander Jagt, Nadezhda V. Vorobieva, Mariya A. Kusliy, Sergei K. Vasiliev, Andrey N. Rodionov, Oksana Boronetskaya, Natalia A. Zinovieva, Alexander S. Graphodatsky, Hans D. Daetwyler, Denis M. Larkin
Summary: Native cattle breeds, such as Yakut and Kholmogory, represent an important cultural heritage and reservoir of genetic variation for addressing agricultural needs in the face of climate change. The evolutionary history of these breeds reveals distinct genetic adaptations for surviving in harsh conditions, with common gene pathways related to adaptation to extreme climates but mostly different genes affected by selection. Additionally, a unique missense mutation in the NRAP gene of Yakut cattle suggests convergent evolution with hibernating/cold-adapted mammals and rapid fixation in response to harsh climate conditions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Christopher R. Cooney, Gavin H. Thomas
Summary: The rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but exhibit substantial heterogeneity in strength and direction at finer scales across vertebrate clades. Different vertebrate clades show varying degrees of lineage-specific relationships between rates of speciation and body size evolution.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Ecology
Giorgio Bianchini, Patricia Sanchez-Baracaldo
Summary: Trait evolution analyses allow comparison of characters across different species, useful for inferring ancestral phenotypes. sMap, a new program for stochastic mapping analyses, offers a wide variety of models and prior distributions, ability to use posterior distribution of trees for model selection, and implementation of three types of characters. sMap enables accurate analyses of discrete character evolution, including conditioned characters to study interaction of traits and can be used in various systems for academic research and teaching.
METHODS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
John A. Raven, Patricia Sanchez-Baracaldo
Summary: The earliest branching cyanobacterium, Gloeobacter, lacks thylakoids and exhibits ancestral traits. It grows epilithically in microbial mats in low-salinity environments. The absence of thylakoids may limit photosynthetic processes in the plasma membrane, impacting productivity in nature.
Article
Biochemistry & Molecular Biology
Thomas Oliver, Patricia Sanchez-Baracaldo, Anthony W. Larkum, A. William Rutherford, Tanai Cardona
Summary: This study compares the core antenna subunit duplication in photosystem II with early events in the history of life, providing additional evidence supporting the premise that water oxidation originated closer to the origin of life and bioenergetics than previously thought.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biology
B. D. A. Naafs, G. Bianchini, F. M. Monteiro, P. Sanchez-Baracaldo
Summary: The 2-methylhopanes are molecular fossils of 2-methylbacteriohopanepolyols and are among the oldest biomarkers on Earth. Studies show that the gene responsible for their synthesis is widespread in cyanobacteria and proteobacteria, suggesting their dominant presence in these bacterial cultures. Geological records indicate the occurrence of 2-methylhopanes from the Paleoproterozoic onwards, with high abundances associated with climatic and biogeochemical perturbations during the Phanerozoic.
Review
Biochemistry & Molecular Biology
Patricia Sanchez-Baracaldo, Giorgio Bianchini, Jamie D. Wilson, Andrew H. Knoll
Summary: Cyanobacteria, as the only prokaryotes with oxygenic photosynthesis, have had a significant impact on the biology and chemistry of our planet. Genomic and evolutionary studies have enriched our understanding of early phototrophs and their role in the global carbon cycle. Cyanobacteria diversified after the Great Oxidation Event and played a crucial role in shaping the Earth's environment.
TRENDS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Joanne S. Boden, Kurt O. Konhauser, Leslie J. Robbins, Patricia Sanchez-Baracaldo
Summary: Research shows that ancestral cyanobacteria had the ability to deal with oxidative stress as early as the Archaean, gradually evolving more cofactors. The evolutionary history of metalloenzymes reveals how early cyanobacteria managed reactive oxygen species.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Louie M. K. Rombaut, Elliot J. R. Capp, Emma C. Hughes, Zoe K. Varley, Andrew P. Beckerman, Natalie Cooper, Gavin H. Thomas
Summary: The study found that the evolution of traplining in hummingbirds involves morphological specialization through the coevolution of longer bills with long-tubed flowers. It was previously believed that this specialization was irreversible and an evolutionary dead end, but the study discovered multiple independent transitions to traplining and suggested that it does not lead to lower rates of diversification.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Evolutionary Biology
Louie M. K. Rombaut, Elliot J. R. Capp, Christopher R. Cooney, Emma C. Hughes, Zoe K. Varley, Gavin H. Thomas
Summary: This study explores the allometric relationships in the evolution of bird beaks across millions to tens of millions of years, finding that the relationship between beak size and body size remains relatively conserved among species. However, occasional shifts occur in the slopes and intercepts of these relationships, contributing to the vast diversity of beak size relative to body size observed in birds today.
Article
Ecology
Alejandro Gonzalez-Voyer, Gavin H. Thomas, Andras Liker, Oliver Kruger, Jan Komdeur, Tamas Szekely
Summary: Sex roles describe sex differences in courtship, mate competition, social pair-bonds and parental care. A key challenge is to identify associations among the components and the drivers of sex roles. We found that proxies of sex roles showed extensive variation and lability, indicating independent evolution among sex role components. Climate and life history weakly associated with sex roles, while adult sex ratio was associated with sexual dimorphism, mating system and parental care.
Article
Ecology
Emma C. Hughes, David P. Edwards, Jen A. Bright, Elliot J. R. Capp, Christopher R. Cooney, Zoe K. Varley, Gavin H. Thomas
Summary: Understanding the origins and conservation of morphological diversity is crucial for determining biogeographical patterns, evolutionary processes, and environmental factors. A study on bird species found that avian morphological diversity is unevenly distributed globally, with dense species packing in tropical hotspots. These regions also exhibit high phenotypic diversity. Evolutionary history plays a key role in shaping these patterns, with old species contributing to niche expansion and young species contributing to niche packing.
Article
Ecology
Christopher R. Cooney, Yichen He, Zoe K. Varley, Lara O. Nouri, Christopher J. A. Moody, Michael D. Jardine, Andras Liker, Tamas Szekely, Gavin H. Thomas
Summary: This study confirms the long-held belief that tropical bird species are more colorful than temperate species by analyzing a dataset of over 4,500 bird species.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Yichen He, Zoe K. Varley, Lara O. Nouri, Christopher J. A. Moody, Michael D. Jardine, Steve Maddock, Gavin H. Thomas, Christopher R. Cooney
Summary: In this study, a deep learning-based image segmentation pipeline is developed to extract information on plumage UV reflectance from bird photographs. The results demonstrate that UV reflectance is widespread and phylogenetically conserved in passerine birds, and the light environment plays a significant role in promoting the evolution of UV plumage colouration.
NATURE COMMUNICATIONS
(2022)
Article
Behavioral Sciences
Frane Babarovic, Christopher R. Cooney, Zoe K. Varley, Lara O. Nouri, Nicola J. Nadeau, Gavin H. Thomas
Summary: The evolution of bird plumage color is influenced by both natural and sexual selection. Natural selection may favor evolution towards crypsis or camouflage, while sexual selection may favor evolution towards conspicuousness. The response to selection is related to the species' ecology, behavior, and life history. Our study on the Coraciiformes, a clade of colorful non-passerine birds, reveals that the correlates of color evolution vary across body regions and depend on the type of color property.
BEHAVIORAL ECOLOGY
(2023)
Article
Biochemical Research Methods
Yichen He, Christopher V. Cooney, Steve Maddock, Gavin V. Thomas
Summary: This paper introduces a pose estimation approach based on Deep Learning that accurately places point labels to identify key locations on specimen images. The approach is applied to avian plumage colouration and Littorina snail shell shape variation. The study demonstrates that Deep Learning can generate high-quality and high-throughput point-based measurements for digitised image-based biodiversity datasets, marking a potential step change in data mobilisation.
PLOS COMPUTATIONAL BIOLOGY
(2023)