The Phylogenetic Method in Taxonomy. H. M. Hall , F. E. Clements

1926 ◽  
Vol 82 (1) ◽  
pp. 110-111 ◽  
Keyword(s):  
Phylogenetic Method

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

2019 ◽  
Author(s):  
Daniel Vitales ◽  
Sònia Garcia ◽  
Steven Dodsworth
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Similarity ◽  
Information Source ◽  
Repeat Sequence ◽  
Combined Application ◽  
Novel Approach ◽  
Genome Wide ◽  
History Of ◽  
Sequence Similarities ◽  
Phylogenetic Method

AbstractA recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.

scholarly journals Is Phylotranscriptomics as Reliable as Phylogenomics?

2020 ◽  
Vol 37 (12) ◽  
pp. 3672-3683 ◽  
Author(s):  
Seongmin Cheon ◽  
Jianzhi Zhang ◽  
Chungoo Park
Keyword(s):  
Genome Sequencing ◽  
Dna Sequences ◽  
Orthologous Gene ◽  
Gene Identification ◽  
Sequencing Data ◽  
Genome Sequences ◽  
Phylogenetic Information ◽  
Tissue Of Origin ◽  
Phylogenetic Method ◽  
Rigorous Method

Abstract Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here, we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.

Modern phylogenetics in paleontology: comments on Vermeij 1999

Paleobiology ◽  
2001 ◽  
Vol 27 (1) ◽  
pp. 174-176 ◽  
Author(s):  
Christopher A. Brochu ◽  
Harold N. Bryant ◽  
Jessica M. Theodor ◽  
Maureen A. O'Leary ◽  
Jonathan M. Adrain ◽  
...  
Keyword(s):  
Temporal Evolution ◽  
Fundamental Problem ◽  
Cladistic Analysis ◽  
Biological Processes ◽  
Phylogenetic Method

In a recent Matters of the Record, Vermeij (1999) identifies what he regards as a fundamental problem with cladistic analysis. “The phylogenetic method,” he states (p. 431), “derives phylogeny in one part of the tree by relying on character-taxon relationships in another part of the tree, in direct violation of the principle that clades, once they have diverged from each other, are independent of one another.” Vermeij fails to appreciate the distinction between pattern-based cladograms, which are hierarchies founded on homology hypotheses, and logically contingent, process-based trees, which are depictions of temporal evolution. As a result, he treats cladograms as literal and direct estimates of evolution and thus confuses the treatment of characters and taxa in parsimony analyses with biological processes and interactions.

scholarly journals Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY

2015 ◽  
Author(s):  
Abhishek Kumar
Keyword(s):  
Classification System ◽  
Tertiary Structure ◽  
Acid Sites ◽  
Phylogeny Analysis ◽  
Mechanism Of Inhibition ◽  
Mammalian Genomes ◽  
Large Clusters ◽  
Bayesian Phylogeny ◽  
Phylogenetic Method ◽  
Suicide Mechanism

The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins can be conveniently classified into six groups (V1-V6), based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system, using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have less than 10 serpins, which expanded into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 ) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, the phylogenetic history and genomic characteristics of vertebrate serpins were revisited.

scholarly journals Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY

2015 ◽  
Author(s):  
Abhishek Kumar
Keyword(s):  
Classification System ◽  
Tertiary Structure ◽  
Acid Sites ◽  
Phylogeny Analysis ◽  
Mechanism Of Inhibition ◽  
Mammalian Genomes ◽  
Large Clusters ◽  
Bayesian Phylogeny ◽  
Phylogenetic Method ◽  
Suicide Mechanism

The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins can be conveniently classified into six groups (V1-V6), based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system, using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have less than 10 serpins, which expanded into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 ) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, the phylogenetic history and genomic characteristics of vertebrate serpins were revisited.

scholarly journals Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method

2018 ◽  
Author(s):  
Xuhua Xia
Keyword(s):  
Parameter Estimation ◽  
Purifying Selection ◽  
Tree Topology ◽  
Likelihood Method ◽  
Estimation Bias ◽  
Likelihood Methods ◽  
Rate Heterogeneity ◽  
Star Tree ◽  
Constant Rate ◽  
Phylogenetic Method

ABSTRACTI analyzed various site pattern combinations in a 4-OTU case to identify sources of starless bias and parameter-estimation bias in likelihood-based phylogenetic methods, and reported three significant contributions. First, the likelihood method is odd in that it may not generate a star tree with sequences that are equidistant from each other. This behaviour, dubbed starless bias, happens in a 4-OTU tree when there is an excess (i.e., more than expected from a star tree and a substitution model) of conflicting phylogenetic signals supporting the three resolved topologies equally. Special site pattern combinations leading to rejection of a star tree, when sequences are equidistant from each other, were identified. Second, fitting gamma distribution to model rate heterogeneity over sites is strongly confounded with tree topology, especially in conjunction with the starless bias. I present examples to show dramatic differences in the estimated shape parameter α between a star tree and a resolved tree. There may be no rate heterogeneity over sites (with the estimated α > 10000) when a star tree is imposed, but α < 1 (suggesting strong rate heterogeneity over sites) when an (incorrect) resolved tree is imposed. Thus, the dependence of “rate heterogeneity” on tree topology implies that “rate heterogeneity” is not a sequence-specific feature, cautioning against interpreting a small α to mean that some sites are under strong purifying selection and others not. Thirdly, because there is no existing (and working) likelihood method for evaluating a star tree with continuous gamma-distributed rate, I have implemented the method for JC69 in a self-contained R script for a four-OTU tree (star or resolved), in addition to another R script assuming a constant rate over sites. These R scripts should be useful for teaching and exploring likelihood methods in phylogenetics.

Postscript

2021 ◽  
pp. 354-358
Author(s):  
Andrew V. Z. Brower ◽  
Randall T. Schuh
Keyword(s):  
Empirical Evidence ◽  
Biological Diversity ◽  
Statistical Tools ◽  
Common Cause ◽  
Explanatory Framework ◽  
Scientific Inference ◽  
The World ◽  
Principle Of Parsimony ◽  
Phylogenetic Method

This postscript reflects on the role of parsimony in the future of systematics. Under the view of systematics advocated in this book, the exuberantly messy data of biological diversity are organized into a clear and coherent explanatory framework through the application of the principle of parsimony. The principle of common cause, the principle of cause and effect, and the principle of uniformitarianism are all applications of the principle of parsimony to the explanation of events unfolding in time. Thus, parsimony is not merely an old-fashioned phylogenetic method that has been superceded by purportedly more powerful and sophisticated statistical tools: it is the epistemological key to evaluating empirical evidence and discovering orderly patterns in the world to the extent that our perceptions allow. Ultimately, the success of every scientific inference and prediction relating to empirical phenomena in the world hinges upon parsimony.

The critical thermal maximum: history and critique

1997 ◽  
Vol 75 (10) ◽  
pp. 1561-1574 ◽  
Author(s):  
William I. Lutterschmidt ◽  
Victor H. Hutchison
Keyword(s):  
Thermal Tolerance ◽  
Critical Thermal Maximum ◽  
Comparative Physiology ◽  
Lethal Temperature ◽  
Heating Rates ◽  
Righting Response ◽  
Thermal Maximum ◽  
History Of ◽  
Using Data ◽  
Phylogenetic Method

We reviewed 725 papers published since Cowles and Bogert's paper on thermal tolerance (R.B. Cowles and C.M. Bogert. 1944. Bull. Am. Mus. Nat. Hist. 83: 261–296) to create a data base of studies that used critical thermal maximum or lethal-temperature methods. We found data from 388 of these papers to provide a historical and taxonomic review of various methodologies used in measuring tolerance of high temperature. We conducted this literature review of previous studies to (i) describe the history of the study of thermal tolerance and show the chronological trends in the use of lethal temperature and critical thermal maximum methods, (ii) illustrate the diversity of taxa used in thermal-tolerance studies, (iii) summarize the diversity of protocols (i.e., end points, heating rates, acclimations, etc.) used for determining thermal tolerance, (iv) provide physiological reasons why the onset of spasms is more meaningful biologically than the loss of righting response, and (v) discuss the difficulties in using data from studies in which widely divergent methods were used and the importance of obtaining comparative thermal-tolerance data for comparative physiology. The adoption of the onset of spasms as a standard end point would allow for valid comparisons of data from different studies and among taxa, an important consideration for current investigations of comparative physiology that use the comparative phylogenetic method.

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