scholarly journals SIMPLE MODELS FOR SCALING IN PHYLOGENETIC TREES

2010 ◽  
Vol 20 (03) ◽  
pp. 805-811 ◽  
Author(s):  
EMILIO HERNÁNDEZ-GARCÍA ◽  
MURAT TUĞRUL ◽  
E. ALEJANDRO HERRADA ◽  
VÍCTOR M. EGUÍLUZ ◽  
KONSTANTIN KLEMM
Keyword(s):  
Power Law ◽  
Phylogenetic Trees ◽  
Critical Parameter ◽  
Biological Species ◽  
Tree Size ◽  
Evolutionary Relationships ◽  
Asymptotic Regime ◽  
New Model ◽  
Large Tree ◽  
Number Of Leaves

Many processes and models — in biological, physical, social, and other contexts — produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological species, are examples of trees for which such scaling is not observed. With this goal, we analyze numerically two branching models leading to nonlogarithmic scaling of the depth with the number of leaves. For Ford's alpha model, although a power-law scaling of the depth with tree size was established analytically, our numerical results illustrate that the asymptotic regime is approached only at very large tree sizes. We introduce here a new model, the activity model, showing analytically and numerically that it also displays a power-law scaling of the depth with tree size at a critical parameter value.

scholarly journals On the emergent system mass function: the contest between accretion and fragmentation

2020 ◽  
Vol 500 (2) ◽  
pp. 1697-1707
Author(s):  
Paul C Clark ◽  
Anthony P Whitworth
Keyword(s):  
Star Formation ◽  
Standard Deviation ◽  
Mass Distribution ◽  
Power Law ◽  
Accretion Rate ◽  
Mass Function ◽  
High Mass ◽  
New Model ◽  
System Formation ◽  
Low Mass

ABSTRACT We propose a new model for the evolution of a star cluster’s system mass function (SMF). The model involves both turbulent fragmentation and competitive accretion. Turbulent fragmentation creates low-mass seed proto-systems (i.e. single and multiple protostars). Some of these low-mass seed proto-systems then grow by competitive accretion to produce the high-mass power-law tail of the SMF. Turbulent fragmentation is relatively inefficient, in the sense that the creation of low-mass seed proto-systems only consumes a fraction, ${\sim }23{{\ \rm per\ cent}}$ (at most ${\sim }50{{\ \rm per\ cent}}$), of the mass available for star formation. The remaining mass is consumed by competitive accretion. Provided the accretion rate on to a proto-system is approximately proportional to its mass (dm/dt ∝ m), the SMF develops a power-law tail at high masses with the Salpeter slope (∼−2.3). If the rate of supply of mass accelerates, the rate of proto-system formation also accelerates, as appears to be observed in many clusters. However, even if the rate of supply of mass decreases, or ceases and then resumes, the SMF evolves homologously, retaining the same overall shape, and the high-mass power-law tail simply extends to ever higher masses until the supply of gas runs out completely. The Chabrier SMF can be reproduced very accurately if the seed proto-systems have an approximately lognormal mass distribution with median mass ${\sim } 0.11 \, {\rm M}_{\odot }$ and logarithmic standard deviation $\sigma _{\log _{10}({M/M}_\odot)}\sim 0.47$).

scholarly journals Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

2000 ◽  
Vol 64 (1) ◽  
pp. 202-236 ◽  
Author(s):  
Carl R. Woese ◽  
Gary J. Olsen ◽  
Michael Ibba ◽  
Dieter Söll
Keyword(s):  
Genetic Code ◽  
Phylogenetic Trees ◽  
Genetic Material ◽  
Evolutionary Process ◽  
Group Iv ◽  
Evolutionary Relationships ◽  
Evolutionary Stage ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
The Individual

SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.

scholarly journals Whole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia

2021 ◽  
Vol 15 (8) ◽  
pp. e0009665
Author(s):  
Shuai Xu ◽  
Zhenpeng Li ◽  
Yuanming Huang ◽  
Lichao Han ◽  
Yanlin Che ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Gene Families ◽  
Single Copy ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Evolutionary Relationships ◽  
Taxonomic Structure ◽  
Pan Genome ◽  
Dipeptidyl Aminopeptidase

Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.

scholarly journals Evolutionary relationships of completely sequenced Clostridia species and close relatives

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4276-4283 ◽  
Author(s):  
Takashi Kunisawa
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Gene Arrangement ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Sequence Information ◽  
Bayesian Tree ◽  
Maximum Likelihood Methods ◽  
Genome Sequence Information ◽  
Close Relatives

The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.

The Dynamics of Web Traffic

2018 ◽  
pp. 82-101
Author(s):  
Bruce Rogers
Keyword(s):  
Mathematical Models ◽  
Power Law ◽  
Equity Market ◽  
Biological Species ◽  
Web Traffic ◽  
New Models ◽  
Over Time ◽  
The Web

This chapter aims to build better models of web traffic. It shows how web traffic is roughly power law distributed, in which a highly concentrated “head” of the Web is coupled with a long, diffuse “tail” of tiny sites. These power law-like patterns have provoked vigorous debate about whether the Web is dominated by new or old elites. To address these issues, this chapter builds new models that scale seamlessly from the largest websites down to hundreds of smaller ones. It builds and tests these models with a rich dataset from Hitwise, a web measurement firm. As this chapter shows, digital audience growth follows predictable patterns. These patterns look much like the growth of cities over time, or the fluctuations of stocks on an equity market (more on that shortly), or even the growth and decline of biological species. This chapter borrows mathematical models and techniques from other disciplines to demonstrate these patterns, focus with a focus on understanding the principles and intuition behind the models.

scholarly journals Novel Molecular Synapomorphies Demarcate Different Main Groups/Subgroups of Plasmodium and Piroplasmida Species Clarifying Their Evolutionary Relationships

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 490 ◽  
Author(s):  
Sharma ◽  
Gupta
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Trees ◽  
Plasmodium Species ◽  
Protein Sequences ◽  
Evolutionary Relationships ◽  
Major Life ◽  
Comparative Analyses ◽  
Large Numbers ◽  
Conserved Signature Indels ◽  
Relationship Of

The class Hematozoa encompasses several clinically important genera, including Plasmodium, whose members cause the major life-threating disease malaria. Hence, a good understanding of the interrelationships of organisms from this class and reliable means for distinguishing them are of much importance. This study reports comprehensive phylogenetic and comparative analyses on protein sequences on the genomes of 28 hematozoa species to understand their interrelationships. In addition to phylogenetic trees based on two large datasets of protein sequences, detailed comparative analyses were carried out on the genomes of hematozoa species to identify novel molecular synapomorphies consisting of conserved signature indels (CSIs) in protein sequences. These studies have identified 79 CSIs that are exclusively present in specific groups of Hematozoa/Plasmodium species, also supported by phylogenetic analysis, providing reliable means for the identification of these species groups and understanding their interrelationships. Of these CSIs, six CSIs are specifically shared by all hematozoa species, two CSIs serve to distinguish members of the order Piroplasmida, five CSIs are uniquely found in all Piroplasmida species except B. microti and two CSIs are specific for the genus Theileria. Additionally, we also describe 23 CSIs that are exclusively present in all genome-sequenced Plasmodium species and two, nine, ten and eight CSIs which are specific for members of the Plasmodium subgenera Haemamoeba, Laverania, Vinckeia and Plasmodium (excluding P. ovale and P. malariae), respectively. Additionally, our work has identified several CSIs that support species relationships which are not evident from phylogenetic analysis. Of these CSIs, one CSI supports the ancestral nature of the avian-Plasmodium species in comparison to the mammalian-infecting groups of Plasmodium species, four CSIs strongly support a specific relationship of species between the subgenera Plasmodium and Vinckeia and three CSIs each that reliably group P. malariae with members of the subgenus Plasmodium and P. ovale within the subgenus Vinckeia, respectively. These results provide a reliable framework for understanding the evolutionary relationships among the Plasmodium/Piroplasmida species. Further, in view of the exclusivity of the described molecular markers for the indicated groups of hematozoa species, particularly large numbers of unique characteristics that are specific for all Plasmodium species, they provide important molecular tools for biochemical/genetic studies and for developing novel diagnostics and therapeutics for these organisms.

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.

Generic delimitation and phylogenetic uncertainty: an example from a group that has undergone an explosive radiation

2005 ◽  
Vol 18 (1) ◽  
pp. 41 ◽  
Author(s):  
L. A. Orthia ◽  
L. G. Cook ◽  
M. D. Crisp
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Relationships ◽  
Recent Proposal ◽  
Generic Delimitation ◽  
Dna Sequence Data ◽  
Single Genus ◽  
Phylogeny Estimation

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience.

scholarly journals Mapping phylogenetic trees to reveal distinct patterns of evolution

2015 ◽  
Author(s):  
Michelle Kendall ◽  
Caroline Colijn
Keyword(s):  
Phylogenetic Trees ◽  
Vaccine Development ◽  
Evolutionary Relationships ◽  
Complex Data ◽  
Phylogenetic Methods ◽  
Phylogenetic Signature

Evolutionary relationships are described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. Obtaining credible trees that capture the relationships present in complex data is one of the fundamental challenges in evolution today. We present a way to map trees which extracts distinct alternative evolutionary relationships embedded in data and resolves phylogenetic uncertainty. Our method reveals a remarkably distinct phylogenetic signature in the VP30 gene of Ebolavirus, indicating possible recombination with significant implications for vaccine development. Moving to higher organisms, we use our approach to detect alternative histories of the evolution of anole lizards. Our approach has the capacity to resolve key areas of uncertainty in the study of evolution, and to broaden the credibility and appeal of phylogenetic methods.

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