Article
Multidisciplinary Sciences
Austin H. Patton, Luke J. Harmon, Maria del Rosario Castaneda, Hannah K. Frank, Colin M. Donihue, Anthony Herrel, Jonathan B. Losos
Summary: Research shows that neotropical Anolis lizards, originating in South America, colonized and radiated on Caribbean islands before returning to the mainland for further diversification. When mainland and island evolutionary radiations collide, extensive continental radiations can result from island ancestors, with incumbent and invading mainland clades achieving ecological and morphological disparity in different ways. In interactions between mainland radiation derived from island ancestors and incumbent mainland radiation, the island-derived clade tends to have an advantage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Christopher K. Boccia, Lindsey Swierk, Fernando P. Ayala-Varela, James Boccia, Isabela L. Borges, Camilo Andres Estupinan, Alexandra M. Martin, Ramon E. Martinez-Grimaldo, Sebastian Ovalle, Shreeram Senthivasan, Ken S. Toyama, Maria del Rosario Castaneda, Andres Garcia, Richard E. Glor, D. Luke Mahler
Summary: Diving arthropods and semi-aquatic anoles have evolved to respire underwater using air stored between their cuticle and surrounding water, allowing them to stay submerged for extended periods of time. This specialized adaptation, known as rebreathing, is facilitated by thin air layers supported by the animal's hydrophobic skin upon submergence, enhancing dive performance and enabling the clearance of carbon dioxide and uptake of oxygen from the surrounding water. The presence of this unique ability in semi-aquatic species suggests that specialized rebreathing is adaptive for habitat specialists in aquatic environments.
Review
Environmental Sciences
Jerome Delroisse, Laurent Duchatelet, Patrick Flammang, Jerome Mallefet
Summary: Bioluminescence, the emission of visible light by living organisms, is a complex biochemical reaction involving different luciferins and luciferases. Studies have shown that genes for luciferases and photoproteins may have emerged as new genes or have been co-opted from ancestral genes in phylogenetically distant organisms.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Genetics & Heredity
Renata M. Pirani, Carlos F. Arias, Kristin Charles, Albert K. Chung, John David Curlis, Daniel J. Nicholson, Marta Vargas, Christian L. Cox, W. Owen McMillan, Michael L. Logan
Summary: The slender anole is a small arboreal lizard found in the rainforests of central and eastern Panama. This study presents a high-quality genome for the slender anole, which is an important resource for studying this species. The genome was compared with other anole genomes and is one of the most complete genomes of any anole assembled to date.
G3-GENES GENOMES GENETICS
(2023)
Article
Evolutionary Biology
Marina Escalera-Zamudio, Sergei L. Kosakovsky Pond, Natalia Martinez de la Vina, Bernardo Gutierrez, Rhys P. D. Inward, Julien Theze, Lucy van Dorp, Hugo G. Castelan-Sanchez, Thomas A. Bowden, Oliver G. Pybus, Ruben J. G. Hulswit
Summary: Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties.
GENOME BIOLOGY AND EVOLUTION
(2023)
Review
Ecology
Martha M. Munoz, Luke O. Frishkoff, Jenna Pruett, D. Luke Mahler
Summary: After decades of research, Anolis lizards have become an important biological model system, providing insights into ecology and evolution. Recent studies have shown how changes in behavior can reshape ecological communities and drive evolution. Anolis lizards are also useful for studying the impact of human activities on species and environments. With ongoing advancements in genomics, phylogenetics, and ecology, Anolis lizards are poised to continue being a powerful model system for studying ecology and evolution.
ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS
(2023)
Review
Biology
Yibo Hu, Xiaoping Wang, Yongchao Xu, Hui Yang, Zeyu Tong, Ran Tian, Shaohua Xu, Li Yu, Yalong Guo, Peng Shi, Shuangquan Huang, Guang Yang, Suhua Shi, Fuwen Wei
Summary: Wild animals and plants have developed adaptive traits through adaptive evolution, which is crucial for their survival. Understanding the molecular mechanisms of adaptive evolution is important for studying species diversification and inter-species interaction. This study reviews the latest research on adaptive traits, convergent evolution, and coevolution in wild animals and plants, highlighting the advances in molecular mechanisms and the future prospects in evolutionary biology.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Biology
Michael L. Yuan, Erin P. Westeen, Guinevere O. U. Wogan, Ian J. Wang
Summary: This study investigates the evolution of female ornamentation in Anolis lizards. The results show that female dewlaps are evolutionarily labile and species with larger females and reduced sexual size dimorphism are more likely to possess female dewlaps. Furthermore, the presence of female dewlaps influences diversification rates in anoles, but only as a secondary effect to a hidden state.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Dipendra Nath Basu, Vaishali Bhaumik, Krushnamegh Kunte
Summary: Multitrait adaptive evolution is influenced by factors such as phylogenetic and functional constraints and the intensity and direction of selection. The tempo and mode of such evolution can impact the assembly of biological communities. Batesian mimicry involves adaptive evolution of multiple traits and we evaluated the tempo and mode of convergence in flight morphology and color patterns in mimetic butterfly communities. We found that models showed faster rates of aposematic trait evolution compared to mimics or nonmimetic sister species, and the degree of mimetic resemblance was correlated with character evolution rate, but not phylogenetic relatedness. Convergence was driven by the greater lability of color patterns, indicating differential selection pressures and constraints on trait evolution.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Damien Biot-Pelletier, Stefano Bettinazzi, Isabelle Gagnon-Arsenault, Alexandre K. Dube, Camille Bedard, Tuc H. M. Nguyen, Heather L. Fiumera, Sophie Breton, Christian R. Landry
Summary: Critical mitochondrial functions rely on interactions between mitochondrial and nuclear genomes. To test the prediction that different mitochondrial haplotypes affect the evolutionary paths of the same nuclear genome, populations of Saccharomyces cerevisiae were evolved under different conditions. The results showed gene-level evolutionary convergence among populations with the same mitonuclear background, indicating the influence of mitonuclear interactions on evolutionary trajectories.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Xiaoyue Ding, Li Cao, Yu Zheng, Xu Zhou, Xiaofang He, Shixia Xu, Wenhua Ren
Summary: During embryonic development in mammals, testicles generally descend into the scrotum to create a temperature environment more beneficial for spermatogenesis. Some mammals, however, have evolved abdominal testes through adaptive evolution to maintain reproductive health.
Article
Ecology
Timothy J. J. Thurman, Todd M. M. Palmer, Jason J. J. Kolbe, Arash M. M. Askary, Kiyoko M. M. Gotanda, Oriol Lapiedra, Tyler R. R. Kartzinel, Naomi Man In't Veld, Liam J. J. Revell, Johanna E. E. Wegener, Thomas W. W. Schoener, David A. A. Spiller, Jonathan B. B. Losos, Robert M. M. Pringle, Rowan D. H. Barrett
Summary: This experiment used a multigeneration field experiment with brown anole lizards to investigate the predictability of evolution. The study found that both phenotypic and genomic changes in the brown anole lizards were difficult to forecast and were not measurably correlated with experimental treatments or other environmental factors. This highlights the challenge of predicting evolutionary responses to multispecies interactions in natural conditions.
AMERICAN NATURALIST
(2023)
Article
Multidisciplinary Sciences
Rachel L. Moran, Emilie J. Richards, Claudia Patricia Ornelas-Garcia, Joshua B. Gross, Alexandra Donny, Jonathan Wiese, Alex C. Keene, Johanna E. Kowalko, Nicolas Rohner, Suzanne E. McGaugh
Summary: Laboratory studies have shown that a single phenotype can be produced by many different genotypes, but in natural systems, phenotypic convergence is often due to parallel genetic changes. This study used whole genome resequencing in Mexican tetra to investigate how selection has shaped the repeated evolution of trait loss and enhancement in cavefish. The results suggest that both standing genetic variation and de novo mutations contribute to repeated adaptation, and that genes with larger mutational targets are more likely to be involved in repeated evolution.
NATURE COMMUNICATIONS
(2023)
Article
Anatomy & Morphology
Camilo Cortes-Parra, Martha L. Calderon-Espinosa, Adriana Jerez
Summary: The study demonstrates that Anolis lizards have evolved different morphologies in response to selective factors related to microhabitat use. The mainland and island Anolis show convergent and unique regional evolution, with claws and toepads functional traits possibly influenced by microhabitat differences.
JOURNAL OF ANATOMY
(2022)
Article
Chemistry, Medicinal
Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C. Larson, Peng Tao
Summary: Conventional molecular dynamics simulation suffers from low efficiency in sampling protein conformations and dynamics. This paper proposes a new adaptive sampling method, LAST, which utilizes deep learning variational autoencoders to accelerate the exploration of protein conformational space. The method is validated through sampling four structures of two protein systems, demonstrating its effectiveness in achieving large conformational changes in a shorter simulation time.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Lenore Pipes, Hongru Wang, John P. Huelsenbeck, Rasmus Nielsen
Summary: Research on the rooting of the SARS-CoV-2 phylogeny shows that methods based on molecular clock tend to place the root in the B clade, while outgroup rooting methods tend to place it in the A clade. However, these results are statistically incompatible, and none of the methods provide strong statistical support for the placement of the root in any specific edge of the tree. This suggests that phylogenetic evidence alone is unlikely to identify the origin of the SARS-CoV-2 virus, cautioning against strong inferences about the early spread of the virus based solely on this evidence.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jesper Svedberg, Vladimir Shchur, Solomon Reinman, Rasmus Nielsen, Russell Corbett-Detig
Summary: Adaptive introgression, the flow of adaptive genetic variation between species or populations, has attracted significant interest and has been implicated in cases of adaptation, but methods for identifying it from population genomic data are lacking. Ancestry_HMM-S is a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying selection strength, showing good performance on moderately sized data sets. It was applied to an admixed Drosophila melanogaster population from South Africa, identifying loci with signatures of adaptive introgression and providing powerful insights into genetic consequences of admixture across diverse populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Lenore Pipes, Rasmus Nielsen
Summary: The study developed a phylogenetic clustering method called AncestralClust for clustering divergent sequences. Comparison with other state-of-the-art clustering methods showed that AncestralClust has higher accuracy and more even cluster sizes in divergent datasets.
Article
Biochemical Research Methods
Sandra Hui, Rasmus Nielsen
Summary: This study introduces a theoretical framework to accurately call CNAs using tumor evolutionary history, developing a method called SCONCE to analyze read depth data from tumor cells which accurately decodes copy number profiles and provides a useful tool for understanding tumor evolution.
Article
Biochemistry & Molecular Biology
Jade Yu Cheng, Aaron J. Stern, Fernando Racimo, Rasmus Nielsen
Summary: This article presents a new maximum likelihood method for detecting positive selection in the genome, which is orders of magnitude faster than existing techniques. By analyzing simulated and human genomic data, genes related to hair pigmentation, morphology, skin, and eye pigmentation were identified, as well as new candidate regions involving diverse biological functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Lei Zhao, Rasmus Nielsen, Thorfinn Sand Korneliussen
Summary: Commonly used methods for inferring phylogenies are not well-suited for handling challenges associated with noisy, diploid sequencing data. To address this problem, we introduce two new probabilistic approaches, distAngsd-geno and distAngsd-nuc, that account for uncertainty in genotype calling and are specifically designed for next-generation sequencing data.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Geno Guerra, Rasmus Nielsen
Summary: The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. This study derived and implemented exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size. It also derived approximations for the expectation and bias of a sequence-based estimator of F-ST and showed that the estimator is generally biased downward.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Corinna Breusing, Maximilian Genetti, Shelbi L. Russell, Russell B. Corbett-Detig, Roxanne A. Beinart
Summary: Symbiont specificity plays a crucial role in nutritional symbiosis between invertebrate animals and chemosynthetic bacteria at deep-sea hydrothermal vents. It affects habitat distribution, genetic structuring, and ecological adaptation of host populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Debora Y. C. Brandt, Xinzhu Wei, Yun Deng, Andrew H. Vaughn, Rasmus Nielsen
Summary: This study compared the estimates of coalescence times from three ancestral recombination graph inference programs using standard neutral coalescent simulations. The results showed that ARGweaver had the most accurate estimates at each locus, while Relate was often more accurate than tsinfer+tsdate. However, all three methods tended to overestimate small coalescence times and underestimate large ones. The posterior distribution of ARGweaver was closer to the expected distribution compared to Relate, but it sacrificed scalability.
Article
Evolutionary Biology
Yuanting Jin, Diana Aguilar-Gomez, Debora Y. C. Brandt, Tyler A. Square, Jiasheng Li, Zhengxia Liu, Tao Wang, Peter H. Sudmant, Craig T. Miller, Rasmus Nielsen
Summary: This study analyzed the genome of the variegated toad-headed agama and found that substrate color plays an important role in the melanism adaptation of the lizard.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Mason Liang, Mikhail Shishkin, Anastasia Mikhailova, Vladimir Shchur, Rasmus Nielsen
Summary: Estimating admixture histories is crucial for understanding genetic diversity. A new statistical method based on analytical expressions for expected ALD in a three-locus system has been developed to resolve more complicated admixture histories.
Article
Biochemistry & Molecular Biology
Alexander Zee, Dori Z. Q. Deng, Matthew Adams, Kayla D. Schimke, Russell Corbett-Detig, Shelbi L. Russell, Xuan Zhang, Robert J. Schmitz, Christopher Vollmers
Summary: This research introduces a technique that makes Illumina short-read libraries compatible with the ONT MinION sequencer by using the rolling circle amplification method. By amplifying short DNA molecules into longer ones, the resulting DNA is better suited for ONT MinION sequencing, and high-accuracy consensus reads similar to Illumina MiSeq can be obtained.
Article
Ecology
Joana L. Rocha, Pedro Silva, Nuno Santos, Monia Nakamura, Sandra Afonso, Abdeljebbar Qninba, Zbyszek Boratynski, Peter H. Sudmant, Jose C. Brito, Rasmus Nielsen, Raquel Godinho
Summary: Analysis of whole genomes of four fox species shows that introgression facilitated adaptation to the hot arid environment of the Sahara Desert and suggests renal water homeostasis as a mechanism of adaptation in the extreme desert specialist species.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Shelbi L. Russell, Jennie Ruelas Castillo, William T. Sullivan
Summary: This study reveals that Wolbachia infection beneficially reinforces host fertility through regulating gene expression at multiple levels, and suggests that these mechanisms may promote the emergence of mutualism and the breakdown of host reproductive manipulations.
Article
Engineering, Biomedical
Hanqin Li, Rebecca Bartke, Lei Zhao, Yogendra Verma, Anna Horacek, Alma Rechav Ben-Natan, Gabriella R. R. Pangilinan, Netravathi Krishnappa, Rasmus Nielsen, Dirk Hockemeyer
Summary: By deleting one copy of the BRCA2 gene, human pluripotent stem cells can be used to annotate gene variants and test their sensitivity to poly(ADP-ribose) polymerase inhibition. Mutations in the BRCA2 gene are associated with sporadic and familial cancer, causing genomic instability and sensitizing cancer cells to poly(ADP-ribose) polymerase inhibition. The deletion of one copy of BRCA2 in human pluripotent stem cells allows for detailed characterization of essential regions in the gene and evaluation of clinical BRCA2 variants' sensitivity to poly(ADP-ribose) polymerase inhibitors.
NATURE BIOMEDICAL ENGINEERING
(2023)