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.

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.

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.

Gang Research in the Twenty-First Century

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Caylin Louis Moore ◽  
Forrest Stuart
Keyword(s):  
Large Scale ◽  
Criminological Theory ◽  
First Century ◽  
Annual Review ◽  
Publication Date ◽  
Theoretical Frameworks ◽  
Twenty First Century ◽  
State Interventions ◽  
And Behavior ◽  
Analytical Approaches

For nearly a century, gang scholarship has remained foundational to criminological theory and method. Twenty-first-century scholarship continues to refine and, in some cases, supplant long-held axioms about gang formation, organization, and behavior. Recent advances can be traced to shifts in the empirical social reality and conditions within which gangs exist and act. We draw out this relationship—between the ontological and epistemological—by identifying key macrostructural shifts that have transformed gang composition and behavior and, in turn, forced scholars to revise dominant theoretical frameworks and analytical approaches. These shifts include large-scale economic transformations, the expansion of punitive state interventions, the proliferation of the Internet and social media, intensified globalization, and the increasing presence of women and LGBTQ individuals in gangs and gang research. By introducing historically unprecedented conditions and actors, these developments provide novel opportunities to reconsider previous analyses of gang structure, violence, and other related objects of inquiry. Expected final online publication date for the Annual Review of Criminology, Volume 5 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Linguistics Then and Now: Some Personal Reflections

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Noam Chomsky
Keyword(s):  
Twentieth Century ◽  
History Of Science ◽  
Online Publication ◽  
Annual Review ◽  
Publication Date ◽  
Theory Of Computation ◽  
Community Based ◽  
Explanatory Depth ◽  
History Of ◽  
Personal Reflections

By mid-twentieth century, a working consensus had been reached in the linguistics community, based on the great achievements of preceding years. Synchronic linguistics had been established as a science, a “taxonomic” science, with sophisticated procedures of analysis of data. Taxonomic science has limits. It does not ask “why?” The time was ripe to seek explanatory theories, using insights provided by the theory of computation and studies of explanatory depth. That effort became the generative enterprise within the biolinguistics framework. Tensions quickly arose: The elements of explanatory theories (generative grammars) were far beyond the reach of taxonomic procedures. The structuralist principle that language is a matter of training and habit, extended by analogy, was unsustainable. More generally, the mood of “virtually everything is known” became “almost nothing is understood,” a familiar phenomenon in the history of science, opening a new and exciting era for a flourishing discipline. Expected final online publication date for the Annual Review of Linguistics, Volume 7 is January 14, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Hereditary Diffuse Gastric Cancer: Approaches to Screening, Surveillance, and Treatment

2020 ◽  
Vol 72 (1) ◽  
Author(s):  
Nastazja Dagny Pilonis ◽  
Marc Tischkowitz ◽  
Rebecca C. Fitzgerald ◽  
Massimiliano di Pietro
Keyword(s):  
Gastric Cancer ◽  
Hereditary Diffuse Gastric Cancer ◽  
Prophylactic Surgery ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
Diffuse Gastric Cancer ◽  
Cancer Syndrome ◽  
Pathogenic Variants ◽  
History Of

Hereditary diffuse gastric cancer (HDGC) is a cancer syndrome associated with a significant lifetime risk of diffuse gastric cancer (DGC), a malignancy characterized by late clinical presentation and poor prognosis, as well as lobular breast cancer. HDGC is linked to germline pathogenic variants in the E-cadherin gene ( CDH1) that are inherited in an autosomal dominant pattern; however, in many families with DGC clustering, no genetic cause has been identified. This review discusses key elements that allow risk assessment of potential inherited DGC susceptibility. We provide a practical overview of the recommendations for surveillance and treatment of individuals at risk and patients with early disease. The review also outlines future research avenues to improve our understanding of the genetic background and natural history of the disease, the endoscopic detection of early lesions, and the outcome of prophylactic surgery in young individuals. Expected final online publication date for the Annual Review of Medicine, Volume 72 is January 27, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Phylogenomics Reveals Clear Cases of Misclassification and Genus-Wide Phylogenetic Markers for Acinetobacter

2019 ◽  
Vol 11 (9) ◽  
pp. 2531-2541 ◽  
Author(s):  
Valeria Mateo-Estrada ◽  
Lucía Graña-Miraglia ◽  
Gamaliel López-Leal ◽  
Santiago Castillo-Ramírez
Keyword(s):  
Evolutionary History ◽  
Ad Hoc ◽  
Acinetobacter Calcoaceticus ◽  
Recent Attempt ◽  
Evolutionary Relationships ◽  
Closely Related Species ◽  
Acinetobacter Baumannii Complex ◽  
History Of ◽  
To Come ◽  
Clear Cases

Abstract The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

scholarly journals Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 3511-3517
Author(s):  
Yanjun Shen ◽  
Na Yang ◽  
Zhihao Liu ◽  
Qiliang Chen ◽  
Yingwen Li
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Phylogenetic Perspective

VERIFICATION OF PHYLOGENETIC INFERENCE PROGRAMS USING METAMORPHIC TESTING

2011 ◽  
Vol 09 (06) ◽  
pp. 729-747 ◽  
Author(s):  
MD. SHAIK SADI ◽  
FEI-CHING KUO ◽  
JOSHUA W. K. HO ◽  
MICHAEL A. CHARLESTON ◽  
T. Y. CHEN
Keyword(s):  
Amino Acids ◽  
Software Testing ◽  
Evolutionary History ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Testing Technique ◽  
Metamorphic Testing ◽  
History Of ◽  
Scoring Algorithms

Many phylogenetic inference programs are available to infer evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids. These programs are often used to infer the evolutionary history of species. However, in most cases it is impossible to systematically verify the correctness of the tree returned by these programs, as the correct evolutionary history is generally unknown and unknowable. In addition, it is nearly impossible to verify whether any non-trivial tree is correct in accordance to the specification of the often complicated search and scoring algorithms. This difficulty is known as the oracle problem of software testing: there is no oracle that we can use to verify the correctness of the returned tree. This makes it very challenging to test the correctness of any phylogenetic inference programs. Here, we demonstrate how to apply a simple software testing technique, called Metamorphic Testing, to alleviate the oracle problem in testing phylogenetic inference programs. We have used both real and randomly generated test inputs to evaluate the effectiveness of metamorphic testing, and found that metamorphic testing can detect failures effectively in faulty phylogenetic inference programs with both types of test inputs.

scholarly journals Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Guillaume Morel ◽  
Lieven Sterck ◽  
Dominique Swennen ◽  
Marina Marcet-Houben ◽  
Djamila Onesime ◽  
...  
Keyword(s):  
Plant Material ◽  
Evolutionary History ◽  
Geotrichum Candidum ◽  
Evolutionary Relationships ◽  
Specific Gene ◽  
Gene Retention ◽  
History Of ◽  
Differential Gene ◽  
Phenotypic Specificity ◽  
Similar Gene

Abstract The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.

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