Beyond Casual Resemblances: Rigorous Frameworks for Comparing Regeneration Across Species

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Mansi Srivastava
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Adult Stem Cells ◽  
Annual Review ◽  
Publication Date ◽  
Animal Phyla ◽  
History Of ◽  
Gene Regulatory ◽  
Unifying Principles

The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Time-Based Systems Biology Approaches to Capture and Model Dynamic Gene Regulatory Networks

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Jose M. Alvarez ◽  
Matthew D. Brooks ◽  
Joseph Swift ◽  
Gloria M. Coruzzi
Keyword(s):  
Systems Biology ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Environmental Changes ◽  
Annual Review ◽  
Publication Date ◽  
Learning Approaches ◽  
Dynamic Events ◽  
Genome Wide ◽  
Gene Regulatory

All aspects of transcription and its regulation involve dynamic events. However, capturing these dynamic events in gene regulatory networks (GRNs) offers both a promise and a challenge. The promise is that capturing and modeling the dynamic changes in GRNs will allow us to understand how organisms adapt to a changing environment. The ability to mount a rapid transcriptional response to environmental changes is especially important in nonmotile organisms such as plants. The challenge is to capture these dynamic, genome-wide events and model them in GRNs. In this review, we cover recent progress in capturing dynamic interactions of transcription factors with their targets—at both the local and genome-wide levels—and using them to learn how GRNs operate as a function of time. We also discuss recent advances that employ time-based machine learning approaches to forecast gene expression at future time points, a key goal of systems biology. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nikhil Mishra ◽  
Carl-Philipp Heisenberg
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Annual Review ◽  
Publication Date ◽  
Technological Advances ◽  
Complex Shapes ◽  
Gene Regulatory ◽  
And Mathematics ◽  
Multicellular Organisms ◽  
Shape Changes

Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Alex Dornburg ◽  
Thomas J. Near
Keyword(s):  
Paradigm Shift ◽  
Evolutionary History ◽  
First Century ◽  
Evolutionary Relationships ◽  
Annual Review ◽  
Publication Date ◽  
Living Fossils ◽  
Actinopterygian Fishes ◽  
History Of ◽  
Phylogenetic Perspective

The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Human Evolution in Asia: Taking Stock and Looking Forward

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Sang-Hee Lee ◽  
Autumn Hudock
Keyword(s):  
Gene Flow ◽  
Fossil Record ◽  
Evolutionary History ◽  
Annual Review ◽  
Publication Date ◽  
History Of ◽  
Different Populations ◽  
Critical Understanding ◽  
New Research ◽  
Complex Evolutionary History

We review the state of paleoanthropology research in Asia. We survey the fossil record, articulate the current understanding, and delineate the points of contention. Although Asia received less attention than Europe and Africa did in the second half of the twentieth century, an increase in reliably dated fossil materials and the advances in genetics have fueled new research. The long and complex evolutionary history of humans in Asia throughout the Pleistocene can be explained by a balance of mechanisms, between gene flow among different populations and continuity of regional ancestry. This pattern is reflected in fossil morphology and paleogenomics. Critical understanding of the sociocultural forces that shaped the history of hominin fossil research in Asia is important in charting the way forward. Expected final online publication date for the Annual Review of Anthropology, Volume 50 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Sign in / Sign up

Export Citation Format

Share Document