We investigate an individual-based model of adaptive radiation based on the biogeographical changes of the Great African Lakes where cichlid fishes radiated. In our model, the landscape consists of a mosaic of three habitat types which may or may not be separated by geographic barriers. We study the effect of the alternation between allopatry and sympatry called landscape dynamics. We show that landscape dynamics can generate a significantly higher diversity than allopatric or sympatric speciation alone. Diversification is mainly due to the joint action of allopatric, ecological divergence, and of disruptive selection increasing assortative mating and allowing for the coexistence in sympatry of species following reinforcement or character displacement. Landscape dynamics possibly increase diversity at each landscape change. The characteristics of the radiation depend on the speed of landscape dynamics and of the number of geographically isolated regions at steady state. Under fast dynamics of a landscape with many fragments, the model predicts a high diversity, possibly subject to the temporary collapse of all species into a hybrid swarm. When fast landscape dynamics induce the recurrent fusion of several sites, diversity is moderate but very stable over time. Under slow landscape dynamics, diversification proceeds similarly, although at a slower pace.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1111/evo.12008 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Exploring force-driven stochastic folding dynamics in mechano-responsive proteins and implications in phenotypic variation.
Nat Commun
January 2025
Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India.
Single-point mutations are pivotal in molecular zoology, shaping functions and influencing genetic diversity and evolution. Here we study three such genetic variants of a mechano-responsive protein, cadherin-23, that uphold the structural integrity of the protein, but showcase distinct genotypes and phenotypes. The variants exhibit subtle differences in transient intra-domain interactions, which in turn affect the anti-correlated motions among the constituent β-strands.
View Article and Find Full Text PDFLigand interaction landscape of transcription factors and essential enzymes in E. coli.
Cell
January 2025
Program in Bioinformatics, Boston University, Boston, MA 02215, USA; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Center for Network Systems Biology, Boston University, Boston, MA 02218, USA; Department of Chemistry, Boston University, Boston, MA 02215, USA; Department of Chemical Physiology and Biochemistry, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA. Electronic address:
Knowledge of protein-metabolite interactions can enhance mechanistic understanding and chemical probing of biochemical processes, but the discovery of endogenous ligands remains challenging. Here, we combined rapid affinity purification with precision mass spectrometry and high-resolution molecular docking to precisely map the physical associations of 296 chemically diverse small-molecule metabolite ligands with 69 distinct essential enzymes and 45 transcription factors in the gram-negative bacterium Escherichia coli. We then conducted systematic metabolic pathway integration, pan-microbial evolutionary projections, and independent in-depth biophysical characterization experiments to define the functional significance of ligand interfaces.
View Article and Find Full Text PDFMapping conformational landscape in protein folding: Benchmarking dimensionality reduction and clustering techniques on the Trp-Cage mini-protein.
Biophys Chem
January 2025
Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India. Electronic address:
Quantitative characterization of protein conformational landscapes is a computationally challenging task due to their high dimensionality and inherent complexity. In this study, we systematically benchmark several widely used dimensionality reduction and clustering methods to analyze the conformational states of the Trp-Cage mini-protein, a model system with well-documented folding dynamics. Dimensionality reduction techniques, including Principal Component Analysis (PCA), Time-lagged Independent Component Analysis (TICA), and Variational Autoencoders (VAE), were employed to project the high-dimensional free energy landscape onto 2D spaces for visualization.
View Article and Find Full Text PDFWas extinction of New Zealand's avian megafauna an unavoidable consequence of human arrival?
Sci Total Environ
January 2025
School of Biological Sciences, University of Adelaide, Adelaide, SA 5000, Australia; The Environment Institute, University of Adelaide, Adelaide, SA 5000, Australia; Center for Macroecology, Evolution, and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. Electronic address:
Human overexploitation contributed strongly to the loss of hundreds of bird species across Oceania, including nine giant, flightless birds called moa. The inevitability of anthropogenic moa extinctions in New Zealand has been fiercely debated. However, we can now rigorously evaluate their extinction drivers using spatially explicit demographic models capturing species-specific interactions between moa, natural climates and landscapes, and human colonists.
View Article and Find Full Text PDFDecoding the Biobased Blueprint: Key Players and Evolutionary Trends in Materials Innovation.
Polymers (Basel)
January 2025
Department of Mechanical Engineering, Debre Markos University, Debre Markos 251, Ethiopia.
In the rapidly evolving biobased materials innovation landscape, our research identifies key players and explores the evolutionary perspective of biobased innovation, offering insights into promising research areas to be further developed by biobased material scientists in search of exploiting their knowledge in novel applications. Despite the crucial role of these materials in promoting sustainable production and consumption models, systematic studies on the current innovation terrain are lacking, leaving gaps in understanding key players, emerging technologies, and market trends. To address this void, we focused on examining patents related to biobased monomers and polymers, aiming to describe the innovation strategies and business dynamics of leading assignees.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!