scholarly journals The information signature of diverging lineages

2021 ◽  
Author(s):  
Douglas G. Moore ◽  
Matheo Morales ◽  
Sara I. Walker ◽  
Greer A. Dolby
Keyword(s):  
Partial Information ◽  
Basic Question ◽  
Effective Population ◽  
Evolutionary Patterns ◽  
Specific Effects ◽  
Taxonomic Groups ◽  
Life On Earth ◽  
Lineage Divergence ◽  
Diversity Of Life ◽  
Partial Redundancy

The process of forming new species is the driving force behind the diversity of life on Earth. Yet, we have not answered the basic question: why are species unevenly distributed across taxonomic groups and geographic settings? This is because we lack the means to directly compare aspects of population (lineage) divergence across unrelated species because taxon-specific effects make comparisons difficult or impossible. Here, we present a new solution to this challenge by identifying the information signature of diverging lineages, calculated using partial information decomposition (PID), under different evolutionary scenarios. We show in silico how the informational decomposition of genetic metrics varies over time since divergence. Calculating PID over 97,200 lattices reveals that the decomposed nodes of Tajima’s D, θW, and π have strong information signatures, while FST was least useful for discriminating among divergence scenarios. The presence or absence of gene flow during divergence was the most detectable signature; mutation rate and effective population size (Ne) were also detectable whereas differences in recombination rate were not. This work demonstrates that PID can reveal evolutionary patterns that are minimally detectable using the raw metrics themselves; it does so by leveraging the architecture of the genome and the partial redundancy of information contained in genetic metrics. Our results demonstrate for the first time how to directly compare characteristics of diverging populations even among distantly related species, providing a foundational tool for understanding the diversity of life across Earth.

scholarly journals Spatial analyses of Ediacaran communities at Mistaken Point

Paleobiology ◽  
2018 ◽  
Vol 44 (1) ◽  
pp. 40-57 ◽  
Author(s):  
Emily G. Mitchell ◽  
Nicholas J. Butterfield
Keyword(s):  
Network Inference ◽  
Process Analysis ◽  
Interspecific Interactions ◽  
Bedding Plane ◽  
Habitat Associations ◽  
Spatial Correlations ◽  
Interspecific Facilitation ◽  
Taxonomic Groups ◽  
Life On Earth ◽  
Bayesian Network Inference

AbstractBedding-plane assemblages of Ediacaran fossils from Mistaken Point, Newfoundland, are among the oldest known records of complex multicellular life on Earth (dated to ~565 Ma). The in situ preservation of these sessile but otherwise deeply enigmatic organisms means that statistical analyses of specimen positions can be used to illuminate their underlying ecological dynamics, including the interactions between taxa.Fossil assemblages on Mistaken Point D and E surfaces were mapped to millimeter accuracy using differentiated GPS. Spatial correlations between 10 well-defined taxa (Bradgatia, Charniid,Charniodiscus,Fractofusus, Ivesheadiomorphs, Lobate Discs,Pectinifrons,Plumeropriscum,Hiemalora, andThectardis) were identified using Bayesian network inference (BNI), and then described and analyzed using spatial point-process analysis. BNI found that the E-surface community had a complex web of interactions and associations between taxa, with all but one taxon (Thectardis) interacting with at least one other. The unique spatial distribution ofThectardissupports previous, morphology-based arguments for its fundamentally distinct nature. BNI revealed that the D-surface community showed no interspecific interactions or associations, a pattern consistent with a homogeneous environment.On the E surface, all six of the abundant taxonomic groups (Fractofusus,Bradgatia, Charniid,Charniodiscus,Thectardis, andPlumeropriscum) were found to have a unique set of interactions with other taxa, reflecting a broad range of underlying ecological responses. Four instances of habitat associations were detected between taxa, of which two (Charniodiscus–PlumeropriscumandPlumeropriscum–Fractofusus) led to weak competition for resources. One case of preemptive competition between Charniid and Lobate Discs was detected. There were no instances of interspecific facilitation. Ivesheadiomorph interactions mirror those ofFractofususandCharniodiscus, identifying them as a form-taxonomic grouping of degradationally homogenized taphomorphs. The absence of increased fossil abundance in proximity to these taphomorphs argues against scavenging or saprophytic behaviors dominating the E-surface community.

scholarly journals The promise of next-generation taxonomy

Megataxa ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 35-38
Author(s):  
MIGUEL VENCES
Keyword(s):  
Machine Learning ◽  
Global Changes ◽  
Next Generation ◽  
Dna Taxonomy ◽  
Technological Developments ◽  
Baseline Information ◽  
Life On Earth ◽  
Diversity Of Life

Documenting, naming and classifying the diversity of life on Earth provides baseline information on the biosphere, which is crucially important to understand and mitigate the global changes of the Anthropocene. We should meet three main challenges, using new technological developments without throwing the well-tried and successful foundations of Linnaean nomenclature overboard. 1. Fully embrace cybertaxonomy, machine learning and DNA taxonomy to ease, not burden the workflow of taxonomists. 2. Emphasize diagnosis over description, images over words. 3. Understand promises and pitfalls of omics approaches to avoid taxonomic inflation.

Many: The Diversity of Life on Earth by Nicola Davies

2017 ◽  
Vol 71 (3) ◽  
pp. 113-113
Author(s):  
Deborah Stevenson
Keyword(s):  
Life On Earth ◽  
Diversity Of Life

Adaptive Radiation

Ecology ◽  
2019 ◽  
Author(s):  
Linyi Zhang ◽  
Scott P. Egan
Keyword(s):  
Adaptive Radiation ◽  
Evolutionary Process ◽  
Ecological Traits ◽  
Rapid Diversification ◽  
African Rift ◽  
Rift Lake ◽  
Multiple Species ◽  
Definition Of ◽  
Life On Earth ◽  
Diversity Of Life

The spectacular diversity of life on earth presents one of the most intriguing questions for biologists: why and how does the variation among organisms arise? One powerful concept that has its origins with Darwin (late 1800s) and was developed in detail during the Modern Synthesis (early to mid-1900s), is “adaptive radiation.” This evolutionary process refers to the rapid diversification of a single lineage into many different species during which different morphological/ecological traits evolve in association with different environments and niches. The central components of adaptive radiation are (1) rapid diversification of multiple species from a single common ancestor and (2) different species exhibit different ecological traits that are adaptive to different niches. While many great individual cases of adaptive radiation have been studied, such as Darwin’s finches, African rift lake cichlids, and Hawaiian silverswords, controversies remain on topics such as the definition of an adaptive radiation, the appropriate approach to test for it, and the ultimate causes of an adaptive radiation. This article provides a general overview of the literature addressing the study of adaptive radiation, including taxa-specific examples and major literature reviews. The article will highlight literature that helps to clarify the concept of adaptive radiation by distinguishing it from other related biological processes. Then the literature on specific approaches to test for adaptive radiation is featured. Next, connections to the literature aiming to understand the proximate and ultimate causes of adaptive radiation are provided, including explicit tests of the role of ecology, as well as an exploration of the source of genetic variation and geographic conditions promoting adaptive radiation. Lastly, we connect to the literature addressing the constraints on adaptive radiations. Overall, this article will address research on the origin of new species and the evolution of ecological differences between them.

Questioning Nature and Environmental Ethics in Schools

2020 ◽  
Author(s):  
Jorge Moreira ◽  
Fátima Alves ◽  
Ana Mendonça
Keyword(s):  
Environmental Ethics ◽  
Social Order ◽  
Learning System ◽  
Social Dimensions ◽  
Pedagogical Strategies ◽  
The World ◽  
Relevant Role ◽  
Educational Paradigm ◽  
Life On Earth ◽  
Diversity Of Life

Contemporary sciences and societies are facing several problems when analyzing the relationship between the natural and social dimensions of the world as reflected in the field of education. A serious effort must be urgently made to identify and tackle environmental problems in order to understand the world in which we live, in ways that are beneficial to present and future life on Earth. In this context, it is fundamental to create a new social order in a way that thinking “out of the box” can emerge with other orders closer to the diversity of life that coexist on the planet. Consequently, the awareness of the complexity and multidimensionality of our world requires the building of new forms of reflexivity and the development of critical thinking, reversing the still predominant characteristics of modern societies such as compartmentalization of knowledge, unhealthy competition, profit-seeking motivations, the exploitation of nature, and excessive individualist and anthropocentric approaches. In this regard, educational institutions play a relevant role in shaping future human actions to be more ethically harmonic (both environmentally and socially) as they are sites of knowledge production and sharing. Hence, it is crucial to rethink the entire educational paradigm and learning system (objectives, curricula, pedagogical strategies, instruments, competencies, school management framework, and even school buildings), because schools often function as “islands,” isolating students from nature, the community, and the “real world,” not preparing them to be well-informed and conscious citizens nor for the challenges that lie ahead. Some theoretical and practical alternatives are needed since schools actually embody the paradoxes and dilemmas of the current societal malaise but have not yet been able to deal with them or to provide adequate effective responses.

scholarly journals Preface

1996 ◽  
Vol 351 (1345) ◽  
pp. 1227-1231 ◽  
Keyword(s):  
Natural Selection ◽  
20Th Century ◽  
Comparative Morphology ◽  
Biological Science ◽  
Selective Pressures ◽  
Evolutionary Pathways ◽  
Life On Earth ◽  
Diversity Of Life ◽  
Violent Conflicts

The great Darwinian truth that underlies our attempts to discover rhyme and reason in the diversity of life on Earth is that natural selection has shaped the form and behaviour of organisms. The search for the evolutionary pathways that lead to the present diversity of life, the study of phylogeny, was among the most powerful forces in the development of biological science in the latter part of the 19th and first half of the 20th century. It provided a fascinating intellectual exercise to draw out putative evolutionary sequences and gave the excuse for quite violent conflicts of interpretation. Comparative morphology was the main (and often the only) source of data for such phylogenetic speculation. It acknowledged that some features, ‘conservative characters’, were more resistant than others to evolutionary pressures and so were more reliable for tracing lineages. To establish phylogenies it became vitally important to identify these ‘conservative’ characters and to distinguish them from features that responded m ore quickly to selective pressures and therefore indicated only recent ancestry.

scholarly journals A likelihood ratio test for changes in homeolog expression bias

2017 ◽  
Author(s):  
Ronald D. Smith ◽  
Taliesin J. Kinser ◽  
Gregory D. Conradi Smith ◽  
Joshua R. Puzey
Keyword(s):  
Likelihood Ratio ◽  
Likelihood Ratio Test ◽  
Expression Patterns ◽  
Raw Material ◽  
Duplicate Genes ◽  
Ratio Test ◽  
Expression Bias ◽  
Ancestral Function ◽  
Life On Earth ◽  
Diversity Of Life

AbstractBackground: Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may retain their ancestral function, sub- or neofunctionalize, or be lost entirely. A primary way that duplicate genes may evolve new functions is by altering their expression patterns. Comparing the expression patterns of duplicate genes may give clues as to whether any of these evolutionary processes have occurred.Results: We develop a likelihood ratio test for the analysis of the expression ratios of duplicate genes across two conditions (e.g., tissues). We demonstrate an application of this test by comparing homeolog expression patterns of 1,448 homeologous gene pairs using RNA-seq data generated from the leaves and petals of an allotetraploid monkeyflower (Mimulus luteus). We assess the sensitivity of this test to different levels of homeolog expression bias and compare the method to several alternatives.Conclusions: The likelihood ratio test derived here is a direct, transparent, and easily implemented method for detecting changes in homeolog expression bias that outperforms three alternative approaches. While our method was derived with homeolog analysis in mind, this method can be used to analyze changes in the ratio of expression levels between any two genes in any two conditions.

scholarly journals A simplified correlation between vertebrate evolution and Paleozoic geomagnetism

2019 ◽  
Author(s):  
John P Staub
Keyword(s):  
Atmospheric Oxygen ◽  
Low Frequency ◽  
Strong Relationship ◽  
Evolutionary Patterns ◽  
Geologic Time Scale ◽  
Polarity Reversals ◽  
Low Levels ◽  
Geomagnetic Polarity ◽  
Taxonomic Groups ◽  
Biologic Factors

Background. Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth’s geomagnetic field. The transition time during the collapse of the Earth’s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects. Methods. Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein’s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals. Results. From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson’s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism. Discussion. The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?

scholarly journals Circulation Pathways of Trematodes of Freshwater Gastropod Mollusks in Forest Biocenoses of the Ukrainian Polissia

2019 ◽  
Vol 53 (1) ◽  
pp. 13-22 ◽  
Author(s):  
E. P. Zhytova ◽  
L. D. Romanchuk ◽  
S. V. Guralska ◽  
O. Yu. Andreieva ◽  
M. V. Shvets
Keyword(s):  
Life Cycle ◽  
Life Cycles ◽  
Trematode Species ◽  
Intermediate Hosts ◽  
Alaria Alata ◽  
Gastropod Mollusks ◽  
Second Intermediate Host ◽  
Host Life ◽  
Taxonomic Groups ◽  
Diversity Of Life

Abstract This is the first review of life cycles of trematodes with parthenitae and larvae in freshwater gastropods from forest biocoenoses of Ukrainian Polissia. Altogether 26 trematode species from 14 families were found circulating in 13 ways in molluscs from reservoirs connected with forest ecosystems of the region. Three-host life cycle is typical of 18 trematode species, two-host life cycle has found in 7 species, and four-host cycles has found in one species. Alaria alata Goeze, 1782, has three-host (Shults, 1972) and four-host cycles. Opisthioglyphe ranae (Froehlich, 1791) can change three-host life cycle to two-host cycle replacing the second intermediate host (Niewiadomska et al., 2006) with the definitive host. Species with primary two-host life cycle belong to Notocotylidae Lühe, 1909, Paramphistomidae Fischoeder, 1901 and Fasciolidae Railliet, 1758 families. Trematodes with three-host cycle have variable second intermediate hosts, including invertebrates and aquatic or amphibious vertebrates. Definitive hosts of trematodes are always vertebrates from different taxonomic groups. The greatest diversity of life cycles is typical for trematodes of birds. Trematodes in the forest biocoenoses of Ukrainian Polissia infect birds in six ways, mammals in three, amphibians in four, and reptiles in one way. The following species have epizootic significance: Liorchis scotiae (Willmott, 1950); Parafasciolopsis fasciolaemorpha Ejsmont, 1932; Notocotylus seineti Fuhrmann, 1919; Catatropis verrucosa (Frölich, 1789) Odhner, 1905; Cotylurus cornutus (Rudolphi, 1808); Echinostoma revolutum (Fröhlich, 1802) Dietz, 1909; Echinoparyphium aconiatum Dietz, 1909; Echinoparyphium recurvatum (Linstow, 1873); Hypoderaeum conoideum (Bloch, 1782) Dietz, 1909; Paracoenogonimus ovatus Kasturada, 1914; Alaria alata Goeze, 1782.

scholarly journals Assembling an illustrated family-level tree of life for exploration in mobile devices

2021 ◽  
Author(s):  
Andres A. Del Risco ◽  
Diego A. Chacon ◽  
Lucia Angel ◽  
David A. Garcia
Keyword(s):  
Dna Sequences ◽  
Morphological Diversity ◽  
Mobile App ◽  
Tree Of Life ◽  
Phylogenetic Studies ◽  
Large Trees ◽  
Family Level ◽  
Phylogenetic Hypotheses ◽  
Life On Earth ◽  
Diversity Of Life

Since the concept of the tree of life was introduced by Darwin about a century and a half ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive tree of life for its exploration has been a difficult task to achieve due to two main obstacles: i) information is scattered into a plethora of individual sources and ii) practical visualization tools for exceptionally large trees are lacking. To overcome both challenges, we aimed to synthetize a family-level tree of life by compiling over 1400 published phylogenetic studies, ensuring that the source trees represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the synthetic tree by employing over 550 secondary-calibration points, using publicly available sequences for more than 5000 taxa, and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app (Tree of Life) for smartphones in order to facilitate the visualization and interactive exploration of the resulting tree. Interactive features include an easy exploration by zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, a timescale to determine extinction and divergence dates, and quick links to Wikipedia. Small illustrations of organisms are displayed at the tips of the branches, to better visualize the morphological diversity of life on earth. Our assembled Tree of Life currently includes over 7000 taxonomic families (about half of the total family-level diversity) and its content will be gradually expanded through regular updates to cover all life on earth at family-level.

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