scholarly journals New Remains of Scandiavis mikkelseni Inform Avian Phylogenetic Relationships and Brain Evolution

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 651
Author(s):  
Miriam Heingård ◽  
Grace Musser ◽  
Stephen A. Hall ◽  
Julia A. Clarke
Keyword(s):  
Brain Evolution ◽  
Three Dimensions ◽  
Brain Anatomy ◽  
Character State ◽  
Additional Material ◽  
Biogeographic Pattern ◽  
Divergence Dating ◽  
History Of ◽  
X Ray Computed ◽  
State Changes

Although an increasing number of studies are combining skeletal and neural morphology data in a phylogenetic context, most studies do not include extinct taxa due to the rarity of preserved endocasts. The early Eocene avifauna of the Fur Formation of Denmark presents an excellent opportunity for further study of extinct osteological and endocranial morphology as fossils are often exceptionally preserved in three dimensions. Here, we use X-ray computed tomography to present additional material of the previously described taxon Scandiavis mikkelseni and reassess its phylogenetic placement using a previously published dataset. The new specimen provides novel insights into the osteological morphology and brain anatomy of Scandiavis. The virtual endocast exhibits a morphology comparable to that of modern avian species. Endocranial evaluation shows that it was remarkably similar to that of certain extant Charadriiformes, yet also possessed a novel combination of traits. This may mean that traits previously proposed to be the result of shifts in ecology later in the evolutionary history of Charadriiformes may instead show a more complex distribution in stem Charadriiformes and/or Gruiformes depending on the interrelationships of these important clades. Evaluation of skeletal and endocranial character state changes within a previously published phylogeny confirms both S. mikkelseni and a putative extinct charadriiform, Nahmavis grandei, as charadriiform. Results bolster the likelihood that both taxa are critical fossils for divergence dating and highlight a biogeographic pattern similar to that of Gruiformes.

scholarly journals Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Thomas Schmitt ◽  
Uwe Fritz ◽  
Massimo Delfino ◽  
Werner Ulrich ◽  
Jan Christian Habel
Keyword(s):  
Meta Analysis ◽  
Balkan Peninsula ◽  
Po Plain ◽  
Genetic Lineages ◽  
Biogeographic Patterns ◽  
Italian Peninsula ◽  
Biogeographic Pattern ◽  
History Of ◽  
Multiple Species ◽  
Micro Plates

AbstractWarm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.

Indigenous Written Sources for the History of Bonny

1989 ◽  
Vol 16 ◽  
pp. 185-196
Author(s):  
Susan M. Hargreaves
Keyword(s):  
Nineteenth Century ◽  
Niger Delta ◽  
Colonial History ◽  
Additional Material ◽  
Court Records ◽  
General Terms ◽  
Early Colonial ◽  
History Of ◽  
Similar Character ◽  
Written Sources

It is well known that indigenous contemporary written documentation exists for the precolonial and early colonial history of some of the coastal societies of South-Eastern Nigeria. The best known example is Old Calabar, for which there exists most notably the diary of Antera Duke, covering the years 1785-88, a document brought from Old Calabar to Britain already during the nineteenth century. More recently John Latham has discovered additional material of a similar character still preserved locally in Old Calabar, principally the Black Davis House Book (containing material dating from the 1830s onwards), the papers of Coco Bassey (including diaries covering the years 1878-89), and the papers of E. O. Offiong (comprising trade ledgers, court records, and letter books relating to the period 1885-1907). In the Niger Delta S. J. S. Cookey, for his biography of King Jaja of Opobo, was able to use contemporary documents in Jaja's own papers, including correspondence from the late 1860s onwards. In the case of the neighboring community of Bonny (from which Jaja seceded to found Opobo after a civil war in 1869), while earlier historians have alluded to the existence of indigenous written documentation, they have done so only in very general terms and without any indication of the quantity or nature of this material.

scholarly journals Exploring and Reconstructing Ancestral Anatomies using Ontology-Informed Approaches

2019 ◽  
Vol 3 ◽  
Author(s):  
Sergei Tarasov ◽  
Istvan Miko ◽  
Matthew Yoder ◽  
Josef Uyeda
Keyword(s):  
Phylogenetic Trees ◽  
Character State ◽  
Ancestral Reconstruction ◽  
Anatomy Ontology ◽  
Insect Order ◽  
Ancestral Character State ◽  
Body Regions ◽  
Individual Traits ◽  
History Of ◽  
Complex Characters

Ancestral character state reconstruction has been long used to gain insight into the evolution of individual traits in organisms. However, organismal anatomies (= entire phenotypes) are not merely ensembles of individual traits, rather they are complex systems where traits interact with each other due to anatomical dependencies (when one trait depends on the presence of another trait) and developmental constraints. Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of entire organismal anatomies or organismal body regions. Herein, we present a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies, Tarasov and Uyeda 2019) that takes into account anatomical dependencies and uses stochastic maps (i.e., phylogenetic trees with an instance of mapped evolutionary history of characters, Huelsenbeck et al. 2003) along with anatomy ontologies to reconstruct organismal anatomies. Our approach treats the entire phenotype or its component body regions as single complex characters and allows exploring and comparing phenotypic evolution at different levels of anatomical hierarchy. These complex characters are constructed by ontology-informed amalgamation of elementary characters (i.e., those coded in character matrix) using stochastic maps. In our approach, characters are linked with the terms from an anatomy ontology, which allows viewing them not just as an ensemble of character state tokens but as entities that have their own biological meaning provided by the ontology. This ontology-informed framework provides new opportunities for tracking phenotypic radiations and anatomical evolution of organisms, which we explore using a large dataset for the insect order Hymenoptera (sawflies, wasps, ants and bees).

scholarly journals High biogeographic and latitudinal variability in gastropod drilling predation on molluscs along the eastern Indian coast: Implications on the history of fossil record of drillholes

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256685
Author(s):  
Subhronil Mondal ◽  
Hindolita Chakraborty ◽  
Sandip Saha ◽  
Sahana Dey ◽  
Deepjay Sarkar
Keyword(s):  
Spatial Variability ◽  
Large Scale ◽  
Abiotic Factors ◽  
Eastern Coast ◽  
Detailed Knowledge ◽  
Biogeographic Pattern ◽  
Drilling Predation ◽  
History Of ◽  
Latitudinal Patterns ◽  
Consecutive Time

Studies on the large-scale latitudinal patterns of gastropod drilling predation reveal that predation pressure may decrease or increase with increasing latitude, or even show no trend, questioning the generality of any large-scale latitudinal or biogeographic pattern. Here, we analyze the nature of spatio-environmental and latitudinal variation in gastropod drilling along the Indian eastern coast by using 76 samples collected from 39 locations, covering ~2500 km, incorporating several ecoregions, and ~15° latitudinal extents. We find no environmental or latitudinal gradient. In fact, drilling intensity varies highly within the same latitudinal bin, or oceanic sub-basins, or even the same ecoregions. Moreover, different ecoregions with their distinctive biotic and abiotic environmental variables show similar predation intensities. However, one pattern is prevalent: some small infaunal prey taxa, living in the sandy-muddy substrate—which are preferred by the naticid gastropods—are always attacked more frequently over others, indicating taxon and size selectivity by the predators. The result suggests that the biotic and abiotic factors, known to influence drilling predation, determine only the local predation pattern. In the present case, the nature of substrate and prey composition determines the local predation intensity: soft substrate habitats host dominantly small, infaunal prey. Since the degree of spatial variability in drilling intensity within any time bin can be extremely high, sometimes greater than the variability across consecutive time bins, temporal patterns in drilling predation can never be interpreted without having detailed knowledge of the nature of this spatial variability within a time bin.

How Do We Think the Present? From Ontology of Contemporary Reality to Ontology without Being1

2016 ◽  
Author(s):  
Gabriel Rockhill
Keyword(s):  
Michel Foucault ◽  
Social Practice ◽  
Three Dimensions ◽  
Apparent Contradiction ◽  
New Era ◽  
Late Work ◽  
Critical Attitude ◽  
Time Space ◽  
History Of ◽  
Contemporary Reality

The opening chapter explores a philosophic question that reflexively sheds light on the orientation of the book as a whole: how can we write the history of the present? Against the backdrop of the more specific question of how to understand the present state of philosophy, it turns to the late work of Michel Foucault and his unique account of the ontology of actuality or of contemporary reality (ontologie de l’actualité). It carefully reconstitutes his concern with providing a historico-philosophical justification of his own project, which he situates in a trajectory that begins with the emergence of the ontology of actuality in the later Kant. It assesses the contemporary relevancy of his critique of historical periodization and his redefinition of modernity in terms of a critical attitude. Given the apparent contradiction between his rejection of periodic history and his identification of a new era of historical thought, the chapter goes on to suggest that an alternative logic of history—founded on the three dimensions of time, space and social practice—would allow us to completely reformulate the way in which we think the present.

Graph Applications in Chemoinformatics and Structural Bioinformatics

2011 ◽  
pp. 386-420
Author(s):  
Eleanor Joyce Gardiner
Keyword(s):  
Graph Theory ◽  
Molecular Graph ◽  
Structural Bioinformatics ◽  
Three Dimensions ◽  
Chemical Graph ◽  
Labeled Graph ◽  
3D Space ◽  
Chemical Graph Theory ◽  
Computer Representation ◽  
History Of

The focus of this chapter will be the uses of graph theory in chemoinformatics and in structural bioinformatics. There is a long history of chemical graph theory dating back to the 1860’s and Kekule’s structural theory. It is natural to regard the atoms of a molecule as nodes and the bonds as edges (2D representations) of a labeled graph (a molecular graph). This chapter will concentrate on the algorithms developed to exploit the computer representation of such graphs and their extensions in both two and three dimensions (where an edge represents the distance in 3D space between a pair of atoms), together with the algorithms developed to exploit them. The algorithms will generally be summarized rather than detailed. The methods were later extended to larger macromolecules (such as proteins); these will be covered in less detail.

Introduction

Mind Shift ◽  
2021 ◽  
pp. 1-16
Author(s):  
John Parrington
Keyword(s):  
Human Brain ◽  
Past History ◽  
Good Reason ◽  
Brain Evolution ◽  
Human Mind ◽  
Basic Knowledge ◽  
Human Uniqueness ◽  
History Of ◽  
The Brain

This introductory chapter begins by providing an overview of the power of the human brain, which is displayed in the wonders of modern civilization. Despite the human brain’s capacity for such intellectual and technological feats, we still know astonishingly little about how it achieves them. This deficit in understanding is a problem not only because it means we lack basic knowledge of the biological factors that underlie our human uniqueness, but also because, for all its amazing capabilities, the human mind seems particularly prone to dysfunction. Still, some would argue there is good reason to be optimistic about the prospect of developing new and better treatments for mental disorders in the not-so-distant future. Such optimism is based on the increasing potential to study how the brain works in various important new ways thanks to recent technological innovations. The chapter then considers two overly polarised views of the human mind. Ultimately, this book argues that society radically restructures the human brain within an individual person’s lifetime, and that it has also played a central role in the past history of our species, by shaping brain evolution.

A Brief History of Life and Brain Evolution

2020 ◽  
pp. 1-26
Author(s):  
Frederick L. Coolidge
Keyword(s):  
Natural Selection ◽  
Homo Sapiens ◽  
Brain Evolution ◽  
Cognitive Differences ◽  
Behavioral Features ◽  
Survival And Reproduction ◽  
History Of ◽  
The Brain ◽  
Brain Shape ◽  
Evolutionary Fitness

This chapter reviews some of the fundamentals of evolution, particularly adaptations and exaptations. Adaptations are physical or behavioral features that through natural selection aided survival and reproduction. Exaptations are physical or behavioral features that have been co-opted from their initial adaptive functions and subsequently enhanced fitness. The reuse, recycling, or redeployment of brain neurons for purposes other than their original adaption may be considered a central organizing principle of the brain. The chapter reviews the beginnings of life and presents a timeline of life through the evolution of hominins. The term hominin refers to all current and extinct relatives and ancestors of Homo sapiens, including the australopithecines and habilines, within about the last 6 million years. The chapter introduces the hypothesis that Homo sapiens survived and flourished, instead of Neandertals, Denisovans, and other hominins, because of brain shape differences, which created cognitive differences that enhanced the evolutionary fitness of Homo sapiens.

scholarly journals A Darwinian Uncertainty Principle

2019 ◽  
Vol 69 (3) ◽  
pp. 521-529 ◽  
Author(s):  
Olivier Gascuel ◽  
Mike Steel
Keyword(s):  
Uncertainty Principle ◽  
Evolutionary Biology ◽  
Biochemical Properties ◽  
Simultaneous Estimation ◽  
Character State ◽  
Migration Routes ◽  
Region Of Origin ◽  
Large Classes ◽  
State Changes ◽  
Patterns And Processes

Abstract Reconstructing ancestral characters and traits along a phylogenetic tree is central to evolutionary biology. It is the key to understanding morphology changes among species, inferring ancestral biochemical properties of life, or recovering migration routes in phylogeography. The goal is 2-fold: to reconstruct the character state at the tree root (e.g., the region of origin of some species) and to understand the process of state changes along the tree (e.g., species flow between countries). We deal here with discrete characters, which are “unique,” as opposed to sequence characters (nucleotides or amino-acids), where we assume the same model for all the characters (or for large classes of characters with site-dependent models) and thus benefit from multiple information sources. In this framework, we use mathematics and simulations to demonstrate that although each goal can be achieved with high accuracy individually, it is generally impossible to accurately estimate both the root state and the rates of state changes along the tree branches, from the observed data at the tips of the tree. This is because the global rates of state changes along the branches that are optimal for the two estimation tasks have opposite trends, leading to a fundamental trade-off in accuracy. This inherent “Darwinian uncertainty principle” concerning the simultaneous estimation of “patterns” and “processes” governs ancestral reconstructions in biology. For certain tree shapes (typically speciation trees) the uncertainty of simultaneous estimation is reduced when more tips are present; however, for other tree shapes it does not (e.g., coalescent trees used in population genetics).

Sign in / Sign up

Export Citation Format

Share Document