scholarly journals Darwin and the Tree of Life: the roots of the evolutionary tree

2012 ◽  
Vol 39 (2) ◽  
pp. 234-252 ◽  
Author(s):  
Nils Petter Hellström
Keyword(s):  
Evolutionary History ◽  
Tree Of Life ◽  
Evolutionary Tree ◽  
Natural Order ◽  
Evolutionary Trees ◽  
The Past

To speak of evolutionary trees and of the Tree of Life has become routine in evolution studies, despite recurrent objections. Because it is not immediately obvious why a tree is suited to represent evolutionary history – woodland trees do not have their buds in the present and their trunks in the past, for a start – the reason why trees make sense to us is historically and culturally, not scientifically, predicated. To account for the Tree of Life, simultaneously genealogical and cosmological, we must explore the particular context in which Darwin declared the natural order to be analogous to a pedigree, and in which he communicated this vision by recourse to a tree. The name he gave his tree reveals part of the story, as before Darwin's appropriation of it, the Tree of Life grew in Paradise at the heart of God's creation.

Boltzmann’s Theory

2018 ◽  
Author(s):  
Olivier Darrigol
Keyword(s):  
Statistical Mechanics ◽  
Natural Order ◽  
The Past

In this last chapter, the reader will find synthetic reflections on Boltzmann’s sources, on the basic components of his theory, and on the ways it was received. The basic components are arranged according to the natural order in which they occurred in Boltzmann’s theory making: constructive tools, chief constructions, crucial predictions, underlying concepts, bridges between different approaches. To fully understand his enterprise, one must embrace his theory as an entire whole organism. This is a difficult and time-consuming task, which this book is meant to ease. In the past, Boltzmann’s readers fortunately did not need a historian’s thoroughness in order to benefit from his multiple constructs and insights. These elements, even taken out of context, had enough power to propel diverging theoretical projects from Boltzmann’s times to ours. In many ways, Boltzmann’s theory anticipated the richness, diversity, and residual opacity of modern statistical mechanics.

scholarly journals Extensive introgression and mosaic genomes of Mediterranean endemic lizards

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Weizhao Yang ◽  
Nathalie Feiner ◽  
Catarina Pinho ◽  
Geoffrey M. While ◽  
Antigoni Kaliontzopoulou ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Mediterranean Islands ◽  
The Past ◽  
Island Endemics ◽  
Extant Species ◽  
Mediterranean Island ◽  
History Of ◽  
Entire History ◽  
The Mediterranean ◽  
The Mediterranean Basin

AbstractThe Mediterranean basin is a hotspot of biodiversity, fuelled by climatic oscillation and geological change over the past 20 million years. Wall lizards of the genus Podarcis are among the most abundant, diverse, and conspicuous Mediterranean fauna. Here, we unravel the remarkably entangled evolutionary history of wall lizards by sequencing genomes of 34 major lineages covering 26 species. We demonstrate an early (>11 MYA) separation into two clades centred on the Iberian and Balkan Peninsulas, and two clades of Mediterranean island endemics. Diversification within these clades was pronounced between 6.5–4.0 MYA, a period spanning the Messinian Salinity Crisis, during which the Mediterranean Sea nearly dried up before rapidly refilling. However, genetic exchange between lineages has been a pervasive feature throughout the entire history of wall lizards. This has resulted in a highly reticulated pattern of evolution across the group, characterised by mosaic genomes with major contributions from two or more parental taxa. These hybrid lineages gave rise to several of the extant species that are endemic to Mediterranean islands. The mosaic genomes of island endemics may have promoted their extraordinary adaptability and striking diversity in body size, shape and colouration, which have puzzled biologists for centuries.

The first potential fossil record of a dibamid reptile (Squamata: Dibamidae): a new taxon from the early Oligocene of Central Mongolia

2019 ◽  
Vol 187 (3) ◽  
pp. 782-799 ◽  
Author(s):  
Andrej Čerňanský
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
New Taxon ◽  
Unique Combination ◽  
Central Mongolia ◽  
Squamate Reptiles ◽  
The Past ◽  
Early Oligocene ◽  
Fossil Material

Abstract Dibamid reptiles have a known current distribution on two continents (Asia and North America). Although this clade represents an early-diverging group in the Squamata and thus should have a long evolutionary history, no fossil record of these peculiar burrowing squamate reptiles has been documented so far. The fossil material described here comes from the early Oligocene of the Valley of Lakes in Central Mongolia. This material consists of jaws and is placed in the clade Dibamidae on the basis of its morphology, which is further confirmed by phylogenetic analyses. In spite of the fragmentary nature of this material, it thus forms the first, but putative, fossil evidence of this clade. If correctly interpreted, this material demonstrates the occurrence of Dibamidae in East Asia in the Palaeogene, indicating its distribution in higher latitudes than today. The preserved elements possess a unique combination of character states, and a new taxon name is therefore erected: Hoeckosaurus mongoliensis sp. nov. The dentary of Hoeckosaurus exhibits some characters of the two extant dibamid taxa. However, the open Meckel’s groove, together with other characters, show that this group was morphologically much more diverse in the past.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Y Miles Zhang ◽  
Jason L Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Abstract Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and biogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCEs in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

scholarly journals Phylogeography of Puumala orthohantavirus in Europe

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 679 ◽  
Author(s):  
Guillaume Castel ◽  
François Chevenet ◽  
Maria Razzauti ◽  
Séverine Murri ◽  
Philippe Marianneau ◽  
...  
Keyword(s):  
Bank Vole ◽  
Evolutionary History ◽  
Rna Virus ◽  
European Countries ◽  
Myodes Glareolus ◽  
Puumala Virus ◽  
The Past ◽  
Baltic Countries ◽  
The Baltic ◽  
Bank Vole Myodes Glareolus

Puumala virus is an RNA virus hosted by the bank vole (Myodes glareolus) and is today present in most European countries. Whilst it is generally accepted that hantaviruses have been tightly co-evolving with their hosts, Puumala virus (PUUV) evolutionary history is still controversial and so far has not been studied at the whole European level. This study attempts to reconstruct the phylogeographical spread of modern PUUV throughout Europe during the last postglacial period in the light of an upgraded dataset of complete PUUV small (S) segment sequences and by using most recent computational approaches. Taking advantage of the knowledge on the past migrations of its host, we identified at least three potential independent dispersal routes of PUUV during postglacial recolonization of Europe by the bank vole. From the Alpe-Adrian region (Balkan, Austria, and Hungary) to Western European countries (Germany, France, Belgium, and Netherland), and South Scandinavia. From the vicinity of Carpathian Mountains to the Baltic countries and to Poland, Russia, and Finland. The dissemination towards Denmark and North Scandinavia is more hypothetical and probably involved several independent streams from south and north Fennoscandia.

Not all written in stone: interdisciplinary syntheses in echinoderm paleontology

2001 ◽  
Vol 79 (7) ◽  
pp. 1209-1231 ◽  
Author(s):  
Rich Mooi
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Body Wall ◽  
Developmental Trajectories ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Primary Target ◽  
The Past ◽  
Broad Scale

The fossil record of the Echinodermata is relatively complete, and is represented by specimens retaining an abundance of features comparable to that found in extant forms. This yields a half-billion-year record of evolutionary novelties unmatched in any other major group, making the Echinodermata a primary target for studies of biological change. Not all of this change can be understood by studying the rocks alone, leading to synthetic research programs. Study of literature from the past 20 years indicates that over 1400 papers on echinoderm paleontology appeared in that time, and that overall productivity has remained almost constant. Analysis of papers appearing since 1990 shows that research is driven by new finds including, but not restricted to, possible Precambrian echinoderms, bizarre new edrioasteroids, early crinoids, exquisitely preserved homalozoans, echinoids at the K-T boundary, and Antarctic echinoids, stelleroids, and crinoids. New interpretations of echinoderm body wall homologies, broad-scale syntheses of embryological information, the study of developmental trajectories through molecular markers, and the large-scale ecological and phenotypic shifts being explored through morphometry and analyses of large data sets are integrated with study of the fossils themselves. Therefore, recent advances reveal a remarkable and continuing synergistic expansion in our understanding of echinoderm evolutionary history.

Green Comedy

2018 ◽  
pp. 249-262
Author(s):  
Steve Mentz
Keyword(s):  
First Century ◽  
Literary Texts ◽  
Natural Order ◽  
Natural Structure ◽  
Twelfth Night ◽  
Midsummer Night's Dream ◽  
The Past ◽  
As You Like It ◽  
Order And Disorder ◽  
Ecological Thinking

The marriage-driven and reconciliatory structures of Shakespeare’s comic form resemble traditional ecological understandings of the interconnections in nature. Over the past forty years, literary ecocriticism has explored parallels between the way literary texts are formed and ecological structures. One seminal claim that helped launch the ecocritical movement in the 1970s was biologist Joseph Meeker’s assertion that comedy is the genre of ecological harmony. This chapter tests Meeker’s adaptive theory by looking at As You Like It, A Midsummer Night’s Dream, Twelfth Night, and Two Gentlemen of Verona. Putting Meeker’s sentimental notions of natural harmony in touch with post-equilibrium ecological thinking and twenty-first-century ecocritical work that recognizes catastrophe as a ‘natural’ structure produces a more dynamic notion of comedy. By juxtaposing green pastoral spaces with their blue oceanic opposites, Shakespeare’s comedies offer global and expansive notions of natural order and disorder, ones better suited to an age of ecological disaster.

scholarly journals The past, present and future of ancient bacterial DNA

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Nicolas Arning ◽  
Daniel J. Wilson
Keyword(s):  
Demographic Transition ◽  
Dental Plaque ◽  
Evolutionary History ◽  
High Throughput Sequencing ◽  
Industrial Revolution ◽  
Environmental Isolates ◽  
Bacterial Dna ◽  
Content Type ◽  
The Past ◽  
History Of

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

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